From 87c3f81b5d24cb7813ca2ce1700c6113e1d4d23b Mon Sep 17 00:00:00 2001 From: Oliver Stolpe Date: Tue, 15 Apr 2025 13:45:27 +0200 Subject: [PATCH 01/15] feat: grch38 only --- Snakefile | 206 +++++++++++++++--------------- varfish_db_downloader/versions.py | 6 +- 2 files changed, 106 insertions(+), 106 deletions(-) diff --git a/Snakefile b/Snakefile index 782ad31..994d274 100644 --- a/Snakefile +++ b/Snakefile @@ -101,22 +101,22 @@ rule all: f"work/genes/mondo/{DV.today}/mondo.obo", "work/genes/rcnv/2022/rcnv_collins_2022.tsv", "work/genes/shet/2019/shet_weghorn_2019.tsv", - f"work/genes/clingen/{DV.today}/ClinGen_gene_curation_list_GRCh37.tsv", + # f"work/genes/clingen/{DV.today}/ClinGen_gene_curation_list_GRCh37.tsv", f"work/genes/clingen/{DV.today}/ClinGen_gene_curation_list_GRCh38.tsv", "work/genes/domino/20190219/domino.tsv", # reference-specific annotations # -- background/population sequence variants and annotations thereof # ---- GRCh37 - f"work/download/annos/grch37/seqvars/cadd/{DV.cadd}/whole_genome_SNVs_inclAnno.tsv.gz", - f"work/download/annos/grch37/seqvars/cadd/{DV.cadd}/InDels_inclAnno.tsv.gz", - f"work/download/annos/grch37/seqvars/dbnsfp/{DV.dbnsfp}a/LICENSE.txt", - f"work/download/annos/grch37/seqvars/dbnsfp/{DV.dbnsfp}c/LICENSE.txt", - f"work/download/annos/grch37/seqvars/dbscsnv/{DV.dbscsnv}/dbscSNV{DV.dbscsnv}.chr1", - f"work/download/annos/grch37/seqvars/dbsnp/{DV.dbsnp}/dbsnp.vcf.gz", - f"work/annos/grch37/seqvars/helixmtdb/{DV.helixmtdb}/helixmtdb.vcf.gz", - f"work/annos/grch37/seqvars/gnomad_mtdna/{DV.gnomad_mtdna}/gnomad_mtdna.vcf.gz", - f"work/download/annos/grch37/seqvars/gnomad_exomes/{DV.gnomad_v2}/.done", - f"work/download/annos/grch37/seqvars/gnomad_genomes/{DV.gnomad_v2}/.done", + # f"work/download/annos/grch37/seqvars/cadd/{DV.cadd}/whole_genome_SNVs_inclAnno.tsv.gz", + # f"work/download/annos/grch37/seqvars/cadd/{DV.cadd}/InDels_inclAnno.tsv.gz", + # f"work/download/annos/grch37/seqvars/dbnsfp/{DV.dbnsfp}a/LICENSE.txt", + # f"work/download/annos/grch37/seqvars/dbnsfp/{DV.dbnsfp}c/LICENSE.txt", + # f"work/download/annos/grch37/seqvars/dbscsnv/{DV.dbscsnv}/dbscSNV{DV.dbscsnv}.chr1", + # f"work/download/annos/grch37/seqvars/dbsnp/{DV.dbsnp}/dbsnp.vcf.gz", + # f"work/annos/grch37/seqvars/helixmtdb/{DV.helixmtdb}/helixmtdb.vcf.gz", + # f"work/annos/grch37/seqvars/gnomad_mtdna/{DV.gnomad_mtdna}/gnomad_mtdna.vcf.gz", + # f"work/download/annos/grch37/seqvars/gnomad_exomes/{DV.gnomad_v2}/.done", + # f"work/download/annos/grch37/seqvars/gnomad_genomes/{DV.gnomad_v2}/.done", # ---- GRCh38 f"work/download/annos/grch38/seqvars/cadd/{DV.cadd}/whole_genome_SNVs_inclAnno.tsv.gz", f"work/download/annos/grch38/seqvars/cadd/{DV.cadd}/gnomad.genomes.r3.0.indel_inclAnno.tsv.gz", @@ -129,9 +129,9 @@ rule all: f"work/download/annos/grch38/seqvars/gnomad_genomes/{DV.gnomad_v4}/.done", # -- genome browser "features" (position-specific) # ---- GRCh37 - f"work/annos/grch37/features/cons/{DV.ucsc_cons_37}/ucsc_conservation.tsv", - f"work/annos/grch37/features/ensembl/{DV.ensembl_37}/ensembl_genes.bed.gz", - f"work/annos/grch37/features/refseq/{DV.refseq_37}/refseq_genes.bed.gz", + # f"work/annos/grch37/features/cons/{DV.ucsc_cons_37}/ucsc_conservation.tsv", + # f"work/annos/grch37/features/ensembl/{DV.ensembl_37}/ensembl_genes.bed.gz", + # f"work/annos/grch37/features/refseq/{DV.refseq_37}/refseq_genes.bed.gz", # ---- GRCh38 f"work/annos/grch38/features/cons/{DV.ucsc_cons_38}/ucsc_conservation.tsv", f"work/annos/grch38/features/ensembl/{DV.ensembl_38}/ensembl_genes.bed.gz", @@ -141,41 +141,41 @@ rule all: # # -- mehari data # ---- frequencies (via annonars) - f"output/full/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/full/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", f"output/full/mehari/freqs-grch38-{DV.gnomad_v4}+{DV.gnomad_v4}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", # -- annonars data # ----- sequence variant annotations - f"output/full/annonars/alphamissense-grch37-{DV.alphamissense}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/full/annonars/alphamissense-grch37-{DV.alphamissense}+{PV.annonars}/rocksdb/IDENTITY", f"output/full/annonars/alphamissense-grch38-{DV.alphamissense}+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/full/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY", f"output/full/annonars/cadd-grch38-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/full/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY", f"output/full/annonars/dbsnp-grch38-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY", + # f"output/full/annonars/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY", f"output/full/annonars/dbnsfp-grch38-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/dbnsfp-grch37-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY", + # f"output/full/annonars/dbnsfp-grch37-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY", f"output/full/annonars/dbnsfp-grch38-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/full/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY", f"output/full/annonars/dbscsnv-grch38-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/gnomad-mtdna-grch37-{DV.gnomad_mtdna}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/full/annonars/gnomad-mtdna-grch37-{DV.gnomad_mtdna}+{PV.annonars}/rocksdb/IDENTITY", f"output/full/annonars/gnomad-mtdna-grch38-{DV.gnomad_mtdna}+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/full/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY", f"output/full/annonars/gnomad-exomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/full/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY", f"output/full/annonars/gnomad-genomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/helixmtdb-grch37-{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/full/annonars/helixmtdb-grch37-{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", f"output/full/annonars/helixmtdb-grch38-{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/gnomad-sv-exomes-grch37-{DV.exac_cnv}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/full/annonars/gnomad-sv-exomes-grch37-{DV.exac_cnv}+{PV.annonars}/rocksdb/IDENTITY", f"output/full/annonars/gnomad-sv-exomes-grch38-{DV.gnomad_cnv4}+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/gnomad-sv-genomes-grch37-{DV.gnomad_sv}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/full/annonars/gnomad-sv-genomes-grch37-{DV.gnomad_sv}+{PV.annonars}/rocksdb/IDENTITY", f"output/full/annonars/gnomad-sv-genomes-grch38-{DV.gnomad_sv4}+{PV.annonars}/rocksdb/IDENTITY", # ----- sequence annotation - f"output/full/annonars/functional-grch37-{DV.refseq_fe_37}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/full/annonars/functional-grch37-{DV.refseq_fe_37}+{PV.annonars}/rocksdb/IDENTITY", f"output/full/annonars/functional-grch38-{DV.refseq_fe_38}+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/regions-grch37-{DV.today}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/full/annonars/regions-grch37-{DV.today}+{PV.annonars}/rocksdb/IDENTITY", f"output/full/annonars/regions-grch38-{DV.today}+{PV.annonars}/rocksdb/IDENTITY", # ----- conservation - f"output/full/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/full/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/rocksdb/IDENTITY", f"output/full/annonars/cons-grch38-{DV.ucsc_cons_38}+{PV.annonars}/rocksdb/IDENTITY", # ----- genes f"output/full/annonars/genes-{DV.acmg_sf}+{DV.gnomad_constraints}+{DV.dbnsfp}+{DV.hpo}+{DV.today}+{PV.annonars}/rocksdb/IDENTITY", @@ -183,30 +183,30 @@ rule all: f"output/full/worker/genes-xlink-{DV.today}+{PV.worker}/genes-xlink.bin", f"output/full/worker/acmg-sf-{DV.acmg_sf}+{PV.worker}/acmg_sf.tsv", f"output/full/worker/mim2gene-{DV.today}+{PV.worker}/mim2gene.tsv", - f"output/full/worker/masked-repeat-grch37-{DV.ucsc_rmsk_37}+{PV.worker}/masked-repeat.bin", + # f"output/full/worker/masked-repeat-grch37-{DV.ucsc_rmsk_37}+{PV.worker}/masked-repeat.bin", f"output/full/worker/masked-repeat-grch38-{DV.ucsc_rmsk_38}+{PV.worker}/masked-repeat.bin", - f"output/full/worker/masked-segdup-grch37-{DV.ucsc_genomic_super_dups_37}+{PV.worker}/masked-segdup.bin", + # f"output/full/worker/masked-segdup-grch37-{DV.ucsc_genomic_super_dups_37}+{PV.worker}/masked-segdup.bin", f"output/full/worker/masked-segdup-grch38-{DV.ucsc_genomic_super_dups_38}+{PV.worker}/masked-segdup.bin", - f"output/full/worker/bgdb-dbvar-grch37-{DV.dbvar}+{PV.worker}/bgdb-dbvar.bin", + # f"output/full/worker/bgdb-dbvar-grch37-{DV.dbvar}+{PV.worker}/bgdb-dbvar.bin", f"output/full/worker/bgdb-dbvar-grch38-{DV.dbvar}+{PV.worker}/bgdb-dbvar.bin", - f"output/full/worker/bgdb-dgv-grch37-{DV.dgv}+{PV.worker}/bgdb-dgv.bin", + # f"output/full/worker/bgdb-dgv-grch37-{DV.dgv}+{PV.worker}/bgdb-dgv.bin", f"output/full/worker/bgdb-dgv-grch38-{DV.dgv}+{PV.worker}/bgdb-dgv.bin", - f"output/full/worker/bgdb-dgv-gs-grch37-{DV.dgv}+{PV.worker}/bgdb-dgv-gs.bin", + # f"output/full/worker/bgdb-dgv-gs-grch37-{DV.dgv}+{PV.worker}/bgdb-dgv-gs.bin", f"output/full/worker/bgdb-dgv-gs-grch38-{DV.dgv}+{PV.worker}/bgdb-dgv-gs.bin", - f"output/full/worker/bgdb-gnomad-grch37-{DV.gnomad_sv}+{PV.worker}/bgdb-gnomad.bin", - f"output/full/worker/bgdb-exac-grch37-{DV.exac_cnv}+{PV.worker}/bgdb-exac.bin", + # f"output/full/worker/bgdb-gnomad-grch37-{DV.gnomad_sv}+{PV.worker}/bgdb-gnomad.bin", + # f"output/full/worker/bgdb-exac-grch37-{DV.exac_cnv}+{PV.worker}/bgdb-exac.bin", f"output/full/worker/bgdb-gnomad-exomes-cnv-grch38-{DV.gnomad_sv4}+{PV.worker}/bgdb-gnomad-exomes-cnv-grch38.bin", f"output/full/worker/bgdb-gnomad-genomes-sv-grch38-{DV.gnomad_sv4}+{PV.worker}/bgdb-gnomad-genomes-sv-grch38.bin", - f"output/full/worker/bgdb-g1k-grch37-{DV.g1k_svs}+{PV.worker}/bgdb-g1k.bin", - f"output/full/worker/clinvar-strucvars-grch37-{DV.clinvar_version}+{PV.worker}/clinvar-strucvars.bin", + # f"output/full/worker/bgdb-g1k-grch37-{DV.g1k_svs}+{PV.worker}/bgdb-g1k.bin", + # f"output/full/worker/clinvar-strucvars-grch37-{DV.clinvar_version}+{PV.worker}/clinvar-strucvars.bin", f"output/full/worker/clinvar-strucvars-grch38-{DV.clinvar_version}+{PV.worker}/clinvar-strucvars.bin", - f"output/full/worker/patho-mms-grch37-{DV.patho_mms}+{PV.worker}/patho-mms.bed", + # f"output/full/worker/patho-mms-grch37-{DV.patho_mms}+{PV.worker}/patho-mms.bed", f"output/full/worker/patho-mms-grch38-{DV.patho_mms}+{PV.worker}/patho-mms.bed", - "output/full/worker/tads-grch37-dixon2015/hesc.bed", + # "output/full/worker/tads-grch37-dixon2015/hesc.bed", "output/full/worker/tads-grch38-dixon2015/hesc.bed", # -- mehari data f"output/full/mehari/genes-xlink-{DV.today}/genes-xlink.tsv", - f"output/full/mehari/genes-txs-grch37-{DV.mehari_tx}/mehari-data-txs-grch37-{DV.mehari_tx}.bin.zst", + # f"output/full/mehari/genes-txs-grch37-{DV.mehari_tx}/mehari-data-txs-grch37-{DV.mehari_tx}.bin.zst", f"output/full/mehari/genes-txs-grch38-{DV.mehari_tx}/mehari-data-txs-grch38-{DV.mehari_tx}.bin.zst", # ----- HPO f"output/full/viguno/hpo-{DV.hpo}+{PV.viguno}/hp.obo", @@ -214,60 +214,60 @@ rule all: f"output/full/viguno/hpo-{DV.hpo}+{PV.viguno}/phenotype_to_genes.txt", f"output/full/viguno/hpo-{DV.hpo}+{PV.viguno}/hpo.bin", # ----- background/population structural variants and annotations thereof - f"output/full/tracks/track-strucvars-dbvar-grch37-{DV.dbvar}+{DV.tracks}/dbvar.bed.gz", + # f"output/full/tracks/track-strucvars-dbvar-grch37-{DV.dbvar}+{DV.tracks}/dbvar.bed.gz", f"output/full/tracks/track-strucvars-dbvar-grch38-{DV.dbvar}+{DV.tracks}/dbvar.bed.gz", - f"output/full/tracks/track-strucvars-dgv-grch37-{DV.dgv}+{DV.tracks}/dgv.bed.gz", + # f"output/full/tracks/track-strucvars-dgv-grch37-{DV.dgv}+{DV.tracks}/dgv.bed.gz", f"output/full/tracks/track-strucvars-dgv-grch38-{DV.dgv}+{DV.tracks}/dgv.bed.gz", - f"output/full/tracks/track-strucvars-dgv-gs-grch37-{DV.dgv_gs}+{DV.tracks}/dgv-gs.bed.gz", + # f"output/full/tracks/track-strucvars-dgv-gs-grch37-{DV.dgv_gs}+{DV.tracks}/dgv-gs.bed.gz", f"output/full/tracks/track-strucvars-dgv-gs-grch38-{DV.dgv_gs}+{DV.tracks}/dgv-gs.bed.gz", - f"output/full/tracks/track-strucvars-exac-grch37-{DV.exac_cnv}+{DV.tracks}/exac.bed.gz", - f"output/full/tracks/track-strucvars-g1k-grch37-{DV.g1k_svs}+{DV.tracks}/g1k.bed.gz", - f"output/full/tracks/track-strucvars-gnomad-grch37-{DV.gnomad_sv}+{DV.tracks}/gnomad.bed.gz", + # f"output/full/tracks/track-strucvars-exac-grch37-{DV.exac_cnv}+{DV.tracks}/exac.bed.gz", + # f"output/full/tracks/track-strucvars-g1k-grch37-{DV.g1k_svs}+{DV.tracks}/g1k.bed.gz", + # f"output/full/tracks/track-strucvars-gnomad-grch37-{DV.gnomad_sv}+{DV.tracks}/gnomad.bed.gz", f"output/full/tracks/track-strucvars-gnomad-sv-grch38-{DV.gnomad_sv4}+{DV.tracks}/gnomad-sv.bed.gz", f"output/full/tracks/track-strucvars-gnomad-cnv-grch38-{DV.gnomad_cnv4}+{DV.tracks}/gnomad-cnv.bed.gz", # ----- known pathogenic MMS - f"output/full/tracks/track-strucvars-patho-mms-grch37-{DV.patho_mms}+{DV.tracks}/patho-mms.bed", + # f"output/full/tracks/track-strucvars-patho-mms-grch37-{DV.patho_mms}+{DV.tracks}/patho-mms.bed", f"output/full/tracks/track-strucvars-patho-mms-grch38-{DV.patho_mms}+{DV.tracks}/patho-mms.bed", # ----- problematic regions (rmsk, genomicSuperDups, altSeqLiftOverPsl, fixSeqLiftOverPsl) - f"output/full/tracks/track-features-ucsc-genomicsuperdups-grch37-{DV.ucsc_genomic_super_dups_37}+{DV.tracks}/genomicSuperDups.bed.gz", + # f"output/full/tracks/track-features-ucsc-genomicsuperdups-grch37-{DV.ucsc_genomic_super_dups_37}+{DV.tracks}/genomicSuperDups.bed.gz", f"output/full/tracks/track-features-ucsc-genomicsuperdups-grch38-{DV.ucsc_genomic_super_dups_38}+{DV.tracks}/genomicSuperDups.bed.gz", - f"output/full/tracks/track-features-ucsc-rmsk-grch37-{DV.ucsc_rmsk_37}+{DV.tracks}/rmsk.bed.gz", + # f"output/full/tracks/track-features-ucsc-rmsk-grch37-{DV.ucsc_rmsk_37}+{DV.tracks}/rmsk.bed.gz", f"output/full/tracks/track-features-ucsc-rmsk-grch38-{DV.ucsc_rmsk_38}+{DV.tracks}/rmsk.bed.gz", - f"output/full/tracks/track-features-ucsc-altseqliftoverpsl-grch37-{DV.ucsc_alt_seq_liftover_37}+{DV.tracks}/altSeqLiftOverPsl.bed.gz", + # f"output/full/tracks/track-features-ucsc-altseqliftoverpsl-grch37-{DV.ucsc_alt_seq_liftover_37}+{DV.tracks}/altSeqLiftOverPsl.bed.gz", f"output/full/tracks/track-features-ucsc-altseqliftoverpsl-grch38-{DV.ucsc_alt_seq_liftover_38}+{DV.tracks}/altSeqLiftOverPsl.bed.gz", - f"output/full/tracks/track-features-ucsc-fixseqliftoverpsl-grch37-{DV.ucsc_fix_seq_liftover_37}+{DV.tracks}/fixSeqLiftOverPsl.bed.gz", + # f"output/full/tracks/track-features-ucsc-fixseqliftoverpsl-grch37-{DV.ucsc_fix_seq_liftover_37}+{DV.tracks}/fixSeqLiftOverPsl.bed.gz", f"output/full/tracks/track-features-ucsc-fixseqliftoverpsl-grch38-{DV.ucsc_fix_seq_liftover_38}+{DV.tracks}/fixSeqLiftOverPsl.bed.gz", # ----- tads - f"output/full/tracks/track-tads-grch37-dixon2015+{DV.tracks}/hesc.bed", + # f"output/full/tracks/track-tads-grch37-dixon2015+{DV.tracks}/hesc.bed", f"output/full/tracks/track-tads-grch38-dixon2015+{DV.tracks}/hesc.bed", # ----- probesets - f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v4-grch37-{DV.tracks}.bed.gz", + # f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v4-grch37-{DV.tracks}.bed.gz", f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v4-grch38-{DV.tracks}.bed.gz", - f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v5-grch37-{DV.tracks}.bed.gz", + # f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v5-grch37-{DV.tracks}.bed.gz", f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v5-grch38-{DV.tracks}.bed.gz", - f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v6-grch37-{DV.tracks}.bed.gz", + # f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v6-grch37-{DV.tracks}.bed.gz", f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v6-grch38-{DV.tracks}.bed.gz", - f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v7-grch37-{DV.tracks}.bed.gz", + # f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v7-grch37-{DV.tracks}.bed.gz", f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v7-grch38-{DV.tracks}.bed.gz", - f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v8-grch37-{DV.tracks}.bed.gz", + # f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v8-grch37-{DV.tracks}.bed.gz", f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v8-grch38-{DV.tracks}.bed.gz", - f"output/full/tracks/track-enrichment-probesets-targets/idt-xgen-exome-research-panel-v1-grch37-{DV.tracks}.bed.gz", + # f"output/full/tracks/track-enrichment-probesets-targets/idt-xgen-exome-research-panel-v1-grch37-{DV.tracks}.bed.gz", f"output/full/tracks/track-enrichment-probesets-targets/idt-xgen-exome-research-panel-v1-grch38-{DV.tracks}.bed.gz", - f"output/full/tracks/track-enrichment-probesets-targets/idt-xgen-exome-research-panel-v2-grch37-{DV.tracks}.bed.gz", + # f"output/full/tracks/track-enrichment-probesets-targets/idt-xgen-exome-research-panel-v2-grch37-{DV.tracks}.bed.gz", f"output/full/tracks/track-enrichment-probesets-targets/idt-xgen-exome-research-panel-v2-grch38-{DV.tracks}.bed.gz", - f"output/full/tracks/track-enrichment-probesets-targets/twist-comprehensive-exome-grch37-{DV.tracks}.bed.gz", + # f"output/full/tracks/track-enrichment-probesets-targets/twist-comprehensive-exome-grch37-{DV.tracks}.bed.gz", f"output/full/tracks/track-enrichment-probesets-targets/twist-comprehensive-exome-grch38-{DV.tracks}.bed.gz", - f"output/full/tracks/track-enrichment-probesets-targets/twist-core-exome-grch37-{DV.tracks}.bed.gz", + # f"output/full/tracks/track-enrichment-probesets-targets/twist-core-exome-grch37-{DV.tracks}.bed.gz", f"output/full/tracks/track-enrichment-probesets-targets/twist-core-exome-grch38-{DV.tracks}.bed.gz", - f"output/full/tracks/track-enrichment-probesets-targets/twist-exome-v2_0-grch37-{DV.tracks}.bed.gz", + # f"output/full/tracks/track-enrichment-probesets-targets/twist-exome-v2_0-grch37-{DV.tracks}.bed.gz", f"output/full/tracks/track-enrichment-probesets-targets/twist-exome-v2_0-grch38-{DV.tracks}.bed.gz", - f"output/full/tracks/track-enrichment-probesets-targets/twist-refseq-exome-grch37-{DV.tracks}.bed.gz", + # f"output/full/tracks/track-enrichment-probesets-targets/twist-refseq-exome-grch37-{DV.tracks}.bed.gz", f"output/full/tracks/track-enrichment-probesets-targets/twist-refseq-exome-grch38-{DV.tracks}.bed.gz", # # == development (reduced data) directories ============================================= # # -- targets - f"output/reduced-dev/targets/grch37/refseq/{DV.refseq_37}/refseq_target_exons.bed.gz", + # f"output/reduced-dev/targets/grch37/refseq/{DV.refseq_37}/refseq_target_exons.bed.gz", f"output/reduced-dev/targets/grch38/refseq/{DV.refseq_38}/refseq_target_exons.bed.gz", # -- viguno f"output/reduced-dev/viguno/hpo-{DV.hpo}+{PV.viguno}/hp.obo", @@ -275,48 +275,48 @@ rule all: f"output/reduced-dev/viguno/hpo-{DV.hpo}+{PV.viguno}/phenotype_to_genes.txt", f"output/reduced-dev/viguno/hpo-{DV.hpo}+{PV.viguno}/hpo.bin", # -- annonars - f"output/reduced-dev/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-dev/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/spec.yaml", + # f"output/reduced-dev/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/reduced-dev/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/spec.yaml", f"output/reduced-dev/annonars/cadd-grch38-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY", f"output/reduced-dev/annonars/cadd-grch38-{DV.cadd}+{PV.annonars}/spec.yaml", - f"output/reduced-dev/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-dev/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/spec.yaml", + # f"output/reduced-dev/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/reduced-dev/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/spec.yaml", f"output/reduced-dev/annonars/cons-grch38-{DV.ucsc_cons_38}+{PV.annonars}/rocksdb/IDENTITY", f"output/reduced-dev/annonars/cons-grch38-{DV.ucsc_cons_38}+{PV.annonars}/spec.yaml", - f"output/reduced-dev/annonars/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-dev/annonars/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/spec.yaml", - f"output/reduced-dev/annonars/dbnsfp-grch37-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-dev/annonars/dbnsfp-grch37-{DV.dbnsfp}c+{PV.annonars}/spec.yaml", + # f"output/reduced-dev/annonars/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY", + # f"output/reduced-dev/annonars/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/spec.yaml", + # f"output/reduced-dev/annonars/dbnsfp-grch37-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY", + # f"output/reduced-dev/annonars/dbnsfp-grch37-{DV.dbnsfp}c+{PV.annonars}/spec.yaml", f"output/reduced-dev/annonars/dbnsfp-grch38-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY", f"output/reduced-dev/annonars/dbnsfp-grch38-{DV.dbnsfp}a+{PV.annonars}/spec.yaml", f"output/reduced-dev/annonars/dbnsfp-grch38-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY", f"output/reduced-dev/annonars/dbnsfp-grch38-{DV.dbnsfp}c+{PV.annonars}/spec.yaml", - f"output/reduced-dev/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-dev/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/spec.yaml", + # f"output/reduced-dev/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/reduced-dev/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/spec.yaml", f"output/reduced-dev/annonars/dbscsnv-grch38-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY", f"output/reduced-dev/annonars/dbscsnv-grch38-{DV.dbscsnv}+{PV.annonars}/spec.yaml", - f"output/reduced-dev/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-dev/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/spec.yaml", + # f"output/reduced-dev/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/reduced-dev/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/spec.yaml", f"output/reduced-dev/annonars/dbsnp-grch38-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY", f"output/reduced-dev/annonars/dbsnp-grch38-{DV.dbsnp}+{PV.annonars}/spec.yaml", - f"output/reduced-dev/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-dev/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/spec.yaml", + # f"output/reduced-dev/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/reduced-dev/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/spec.yaml", f"output/reduced-dev/annonars/gnomad-exomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY", f"output/reduced-dev/annonars/gnomad-exomes-grch38-{DV.gnomad_v4}+{PV.annonars}/spec.yaml", - f"output/reduced-dev/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-dev/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/spec.yaml", + # f"output/reduced-dev/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/reduced-dev/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/spec.yaml", f"output/reduced-dev/annonars/gnomad-genomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY", f"output/reduced-dev/annonars/gnomad-genomes-grch38-{DV.gnomad_v4}+{PV.annonars}/spec.yaml", # -- mehari - f"output/reduced-dev/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-dev/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/spec.yaml", + # f"output/reduced-dev/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/reduced-dev/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/spec.yaml", f"output/reduced-dev/mehari/freqs-grch38-{DV.gnomad_v4}+{DV.gnomad_v4}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", f"output/reduced-dev/mehari/freqs-grch38-{DV.gnomad_v4}+{DV.gnomad_v4}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/spec.yaml", # # == exomes (reduced data) directories ================================================== # # -- targets - f"output/reduced-exomes/targets/grch37/refseq/{DV.refseq_37}/refseq_target_exons.bed.gz", + # f"output/reduced-exomes/targets/grch37/refseq/{DV.refseq_37}/refseq_target_exons.bed.gz", f"output/reduced-exomes/targets/grch38/refseq/{DV.refseq_38}/refseq_target_exons.bed.gz", # -- viguno f"output/reduced-exomes/viguno/hpo-{DV.hpo}+{PV.viguno}/hp.obo", @@ -324,41 +324,41 @@ rule all: f"output/reduced-exomes/viguno/hpo-{DV.hpo}+{PV.viguno}/phenotype_to_genes.txt", f"output/reduced-exomes/viguno/hpo-{DV.hpo}+{PV.viguno}/hpo.bin", # -- annonars - f"output/reduced-exomes/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-exomes/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/spec.yaml", + # f"output/reduced-exomes/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/reduced-exomes/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/spec.yaml", f"output/reduced-exomes/annonars/cadd-grch38-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY", f"output/reduced-exomes/annonars/cadd-grch38-{DV.cadd}+{PV.annonars}/spec.yaml", - f"output/reduced-exomes/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-exomes/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/spec.yaml", + # f"output/reduced-exomes/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/reduced-exomes/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/spec.yaml", f"output/reduced-exomes/annonars/cons-grch38-{DV.ucsc_cons_38}+{PV.annonars}/rocksdb/IDENTITY", f"output/reduced-exomes/annonars/cons-grch38-{DV.ucsc_cons_38}+{PV.annonars}/spec.yaml", - f"output/reduced-exomes/annonars/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-exomes/annonars/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/spec.yaml", - f"output/reduced-exomes/annonars/dbnsfp-grch37-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-exomes/annonars/dbnsfp-grch37-{DV.dbnsfp}c+{PV.annonars}/spec.yaml", + # f"output/reduced-exomes/annonars/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY", + # f"output/reduced-exomes/annonars/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/spec.yaml", + # f"output/reduced-exomes/annonars/dbnsfp-grch37-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY", + # f"output/reduced-exomes/annonars/dbnsfp-grch37-{DV.dbnsfp}c+{PV.annonars}/spec.yaml", f"output/reduced-exomes/annonars/dbnsfp-grch38-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY", f"output/reduced-exomes/annonars/dbnsfp-grch38-{DV.dbnsfp}a+{PV.annonars}/spec.yaml", f"output/reduced-exomes/annonars/dbnsfp-grch38-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY", f"output/reduced-exomes/annonars/dbnsfp-grch38-{DV.dbnsfp}c+{PV.annonars}/spec.yaml", - f"output/reduced-exomes/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-exomes/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/spec.yaml", + # f"output/reduced-exomes/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/reduced-exomes/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/spec.yaml", f"output/reduced-exomes/annonars/dbscsnv-grch38-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY", f"output/reduced-exomes/annonars/dbscsnv-grch38-{DV.dbscsnv}+{PV.annonars}/spec.yaml", - f"output/reduced-exomes/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-exomes/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/spec.yaml", + # f"output/reduced-exomes/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/reduced-exomes/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/spec.yaml", f"output/reduced-exomes/annonars/dbsnp-grch38-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY", f"output/reduced-exomes/annonars/dbsnp-grch38-{DV.dbsnp}+{PV.annonars}/spec.yaml", - f"output/reduced-exomes/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-exomes/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/spec.yaml", + # f"output/reduced-exomes/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/reduced-exomes/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/spec.yaml", f"output/reduced-exomes/annonars/gnomad-exomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY", f"output/reduced-exomes/annonars/gnomad-exomes-grch38-{DV.gnomad_v4}+{PV.annonars}/spec.yaml", - f"output/reduced-exomes/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-exomes/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/spec.yaml", + # f"output/reduced-exomes/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/reduced-exomes/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/spec.yaml", f"output/reduced-exomes/annonars/gnomad-genomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY", f"output/reduced-exomes/annonars/gnomad-genomes-grch38-{DV.gnomad_v4}+{PV.annonars}/spec.yaml", # -- mehari - f"output/reduced-exomes/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-exomes/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/spec.yaml", + # f"output/reduced-exomes/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", + # f"output/reduced-exomes/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/spec.yaml", f"output/reduced-exomes/mehari/freqs-grch38-{DV.gnomad_v4}+{DV.gnomad_v4}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", f"output/reduced-exomes/mehari/freqs-grch38-{DV.gnomad_v4}+{DV.gnomad_v4}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/spec.yaml", diff --git a/varfish_db_downloader/versions.py b/varfish_db_downloader/versions.py index 389580b..d79abbc 100644 --- a/varfish_db_downloader/versions.py +++ b/varfish_db_downloader/versions.py @@ -127,10 +127,10 @@ class DataVersions: clingen_gene=TODAY, clingen_variant=TODAY, ensembl_37="87", - ensembl_38="112", - ensembl="112", + ensembl_38="112", # keep at 112 for consistency with mehari + ensembl="112", # keep at 112 for consistency with mehari today=TODAY, - dbnsfp="4.5", + dbnsfp="4.5", # update to 4.9 or 5.1 ? dbscsnv="1.1", cadd="1.6", gnomad_constraints="4.1", From 665a7db539bd86dad57fbbdaf3194a2ae5332392 Mon Sep 17 00:00:00 2001 From: Oliver Stolpe Date: Fri, 9 May 2025 11:06:11 +0200 Subject: [PATCH 02/15] final working --- Snakefile | 16 ++++++++++++---- environment.yml | 16 ++++++++-------- rules/output/annonars/alphamissense.smk | 4 ++-- rules/output/annonars/cadd.smk | 4 ++-- rules/output/annonars/cons.smk | 4 ++-- rules/output/annonars/dbnsfp.smk | 4 ++-- rules/output/annonars/dbscsnv.smk | 4 ++-- rules/output/annonars/dbsnp.smk | 4 ++-- rules/output/annonars/gnomad_exomes.smk | 4 ++-- rules/output/annonars/gnomad_genomes.smk | 4 ++-- rules/output/annonars/gnomad_mtdna.smk | 4 ++-- rules/output/annonars/gnomad_sv.smk | 16 ++++++++-------- rules/output/annonars/helix.smk | 4 ++-- rules/output/mehari/freqs.smk | 8 ++++---- rules/output/viguno/hpo.smk | 7 ++----- rules/reduced/annonars.smk | 4 ++-- rules/reduced/hpo.smk | 4 ++-- rules/reduced/mehari.smk | 4 ++-- rules/work/annos/features/tads.smk | 2 +- rules/work/annos/seqvars/dbnsfp.smk | 9 ++++++++- rules/work/annos/seqvars/dbscsnv.smk | 2 +- rules/work/genes/ensembl.smk | 6 +++--- rules/work/genes/gnomad.smk | 1 + rules/work/genes/hgnc.smk | 2 +- rules/work/genes/mehari_data_tx.smk | 10 +++++----- rules/work/genes/omim.smk | 1 + rules/work/genes/rcnv.smk | 1 + rules/work/genes/shet.smk | 1 + scripts/genes-integrate-diseases.py | 2 ++ scripts/genes-orpha-diseases.py | 4 +++- utils/install-annonars.sh | 7 ------- varfish_db_downloader/versions.py | 6 +++--- 32 files changed, 91 insertions(+), 78 deletions(-) delete mode 100644 utils/install-annonars.sh diff --git a/Snakefile b/Snakefile index 994d274..d791926 100644 --- a/Snakefile +++ b/Snakefile @@ -40,6 +40,12 @@ DEV_GENE_SYMBOLS = "|".join( # Padding to add to exons in dev and exons mode. EXON_PADDING = 200 +# Define number of threads for resource-intensive tasks +THREADS = int(os.environ.get("THREADS", "32")) + +# Define amount of ram for resource-intesnive tasks (in mb) +MEMORY = int(os.environ.get("MEMORY", "196000")) + # =============================================================================================== # Test Mode # =============================================================================================== @@ -91,10 +97,10 @@ rule all: f"work/download/do/{DV.today}/omim-unmapped.csv", f"work/genes/dbnsfp/{DV.dbnsfp}/genes.tsv.gz", "work/genes/decipher/v3/decipher_hi_prediction.tsv", - f"work/genes/ensembl/{DV.ensembl}/ensembl_xlink.tsv", + f"work/genes/ensembl/{DV.ensembl}/ensembl_xlink.tsv", # TODO broken on their side (AAA) f"work/genes/enst_ensg/grch37/{DV.ensembl_37}/enst_ensg.tsv", f"work/genes/entrez/{DV.today}/gene_info.jsonl", - f"work/genes/gnomad/{DV.gnomad_constraints}/gnomad_constraints.tsv", + f"work/genes/gnomad/{DV.gnomad_constraints}/gnomad_constraints.tsv", # TODO depends on ensembl_xlink.tsv (ref AAA) f"work/genes/hgnc/{DV.today}/hgnc_info.jsonl", f"work/genes/omim/{DV.hpo}+{DV.today}/omim_diseases.tsv", f"work/genes/orphadata/{DV.orphadata}/orphadata.jsonl", @@ -178,7 +184,7 @@ rule all: # f"output/full/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/rocksdb/IDENTITY", f"output/full/annonars/cons-grch38-{DV.ucsc_cons_38}+{PV.annonars}/rocksdb/IDENTITY", # ----- genes - f"output/full/annonars/genes-{DV.acmg_sf}+{DV.gnomad_constraints}+{DV.dbnsfp}+{DV.hpo}+{DV.today}+{PV.annonars}/rocksdb/IDENTITY", + f"output/full/annonars/genes-{DV.acmg_sf}+{DV.gnomad_constraints}+{DV.dbnsfp}+{DV.hpo}+{DV.today}+{PV.annonars}/rocksdb/IDENTITY", # TODO depend on (ref AAA) # -- worker data f"output/full/worker/genes-xlink-{DV.today}+{PV.worker}/genes-xlink.bin", f"output/full/worker/acmg-sf-{DV.acmg_sf}+{PV.worker}/acmg_sf.tsv", @@ -207,7 +213,9 @@ rule all: # -- mehari data f"output/full/mehari/genes-xlink-{DV.today}/genes-xlink.tsv", # f"output/full/mehari/genes-txs-grch37-{DV.mehari_tx}/mehari-data-txs-grch37-{DV.mehari_tx}.bin.zst", - f"output/full/mehari/genes-txs-grch38-{DV.mehari_tx}/mehari-data-txs-grch38-{DV.mehari_tx}.bin.zst", + f"output/full/mehari/genes-txs-grch38-{DV.mehari_tx}/mehari-data-txs-grch38-ensembl-{DV.mehari_tx}.bin.zst", + f"output/full/mehari/genes-txs-grch38-{DV.mehari_tx}/mehari-data-txs-grch38-refseq-{DV.mehari_tx}.bin.zst", + f"output/full/mehari/genes-txs-grch38-{DV.mehari_tx}/mehari-data-txs-grch38-ensembl-and-refseq-{DV.mehari_tx}.bin.zst", # ----- HPO f"output/full/viguno/hpo-{DV.hpo}+{PV.viguno}/hp.obo", f"output/full/viguno/hpo-{DV.hpo}+{PV.viguno}/phenotype.hpoa", diff --git a/environment.yml b/environment.yml index b8180d7..02cfdcf 100644 --- a/environment.yml +++ b/environment.yml @@ -33,23 +33,23 @@ dependencies: - jq # Tools for file downloads. - aria2 >=1.36.0 - - wget # Tool for processing BED files. - bedops =2 # VCF/BCF/HTSlib/Samtools. - - bcftools =1.17 - - htslib =1.17 - - samtools =1.17 + - bcftools =1.21 + - htslib =1.21 + - samtools =1.21 # Parallel (de)compression. - pigz # Varfish related - # - annonars =0.41.3 # current versions not on bioconda due to build issue, but docker images are available - - viguno =0.3.1 - - mehari =0.25.5 - - varfish-server-worker =0.13.0 + - annonars =0.44.0 + - viguno =0.4.0 + - mehari =0.35.1 + - varfish-server-worker =0.17.2 # S3 uploads - s5cmd =2.1.0 # async HTTP requests - httpx =0.25.0 - httpcore =0.18.0 - trio + - qsv diff --git a/rules/output/annonars/alphamissense.smk b/rules/output/annonars/alphamissense.smk index 9b3fc10..20abbde 100644 --- a/rules/output/annonars/alphamissense.smk +++ b/rules/output/annonars/alphamissense.smk @@ -23,10 +23,10 @@ rule output_annonars_alphamissense: # -- build AlphaMissense RocksDB with annon manifest=( "output/full/annonars/alphamissense-{genome_release}-{v_alphamissense}+{v_annonars}/MANIFEST.txt" ), - threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96")) + threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb_per_cpu=2000, + mem_mb=MEMORY, wildcard_constraints: genome_release=RE_GENOME, v_alphamissense=RE_VERSION, diff --git a/rules/output/annonars/cadd.smk b/rules/output/annonars/cadd.smk index f10e9bc..110bd22 100644 --- a/rules/output/annonars/cadd.smk +++ b/rules/output/annonars/cadd.smk @@ -54,10 +54,10 @@ rule output_annonars_cadd: # -- build CADD RocksDB with annonars ), spec_yaml=("output/full/annonars/cadd-{genome_release}-{v_cadd}+{v_annonars}/spec.yaml"), manifest=("output/full/annonars/cadd-{genome_release}-{v_cadd}+{v_annonars}/MANIFEST.txt"), - threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96")) + threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb_per_cpu=2000, + mem_mb=MEMORY wildcard_constraints: genome_release=RE_GENOME, v_cadd=RE_VERSION, diff --git a/rules/output/annonars/cons.smk b/rules/output/annonars/cons.smk index 788fe6f..8c02d2d 100644 --- a/rules/output/annonars/cons.smk +++ b/rules/output/annonars/cons.smk @@ -12,10 +12,10 @@ rule output_annonars_cons: # -- build UCSC conservation track RocksDB with anno ), spec_yaml=("output/full/annonars/cons-{genome_release}-{v_cons}+{v_annonars}/spec.yaml"), manifest=("output/full/annonars/cons-{genome_release}-{v_cons}+{v_annonars}/MANIFEST.txt"), - threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96")) + threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb_per_cpu=2000, + mem_mb=MEMORY wildcard_constraints: genome_release=RE_GENOME, v_cons=RE_VERSION, diff --git a/rules/output/annonars/dbnsfp.smk b/rules/output/annonars/dbnsfp.smk index 1873c76..7208417 100644 --- a/rules/output/annonars/dbnsfp.smk +++ b/rules/output/annonars/dbnsfp.smk @@ -19,10 +19,10 @@ rule output_annonars_dbnsfp: # -- build dbNSFP RocksDB with annonars manifest=( "output/full/annonars/dbnsfp-{genome_release}-{v_dbnsfp}+{v_annonars}/MANIFEST.txt" ), - threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96")) + threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb_per_cpu=2000, + mem_mb=MEMORY wildcard_constraints: genome_release=RE_GENOME, v_dbnsfp=RE_VERSION, diff --git a/rules/output/annonars/dbscsnv.smk b/rules/output/annonars/dbscsnv.smk index 9490149..aa76ccf 100644 --- a/rules/output/annonars/dbscsnv.smk +++ b/rules/output/annonars/dbscsnv.smk @@ -21,10 +21,10 @@ rule output_annonars_dbscsnv: # -- build dbscSNV RocksDB with annonars manifest=( "output/full/annonars/dbscsnv-{genome_release}-{v_dbscsnv}+{v_annonars}/MANIFEST.txt" ), - threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96")) + threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb_per_cpu=2000, + mem_mb=MEMORY wildcard_constraints: genome_release=RE_GENOME, v_dbscsnv=RE_VERSION, diff --git a/rules/output/annonars/dbsnp.smk b/rules/output/annonars/dbsnp.smk index 5226254..bc1761d 100644 --- a/rules/output/annonars/dbsnp.smk +++ b/rules/output/annonars/dbsnp.smk @@ -12,10 +12,10 @@ rule output_annonars_dbsnp: # -- build dbSNP RocksDB with annonars ), spec_yaml=("output/full/annonars/dbsnp-{genome_release}-{v_dbsnp}+{v_annonars}/spec.yaml"), manifest=("output/full/annonars/dbsnp-{genome_release}-{v_dbsnp}+{v_annonars}/MANIFEST.txt"), - threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96")) + threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb_per_cpu=2000, + mem_mb=MEMORY, wildcard_constraints: genome_release=RE_GENOME, v_dbsnp=RE_VERSION, diff --git a/rules/output/annonars/gnomad_exomes.smk b/rules/output/annonars/gnomad_exomes.smk index a4e1291..dc385db 100644 --- a/rules/output/annonars/gnomad_exomes.smk +++ b/rules/output/annonars/gnomad_exomes.smk @@ -16,10 +16,10 @@ rule output_annonars_gnomad_exomes: # -- build gnomAD-exomes RocksDB with annon manifest=( "output/full/annonars/gnomad-exomes-{genome_release}-{v_gnomad}+{v_annonars}/MANIFEST.txt" ), - threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96")) + threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb_per_cpu=2000, + mem_mb=MEMORY wildcard_constraints: genome_release=RE_GENOME, v_gnomad=RE_VERSION, diff --git a/rules/output/annonars/gnomad_genomes.smk b/rules/output/annonars/gnomad_genomes.smk index 07c4825..059ab4b 100644 --- a/rules/output/annonars/gnomad_genomes.smk +++ b/rules/output/annonars/gnomad_genomes.smk @@ -16,10 +16,10 @@ rule output_annonars_gnomad_genomes: # -- build gnomAD-genomes RocksDB with ann manifest=( "output/full/annonars/gnomad-genomes-{genome_release}-{v_gnomad}+{v_annonars}/MANIFEST.txt" ), - threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96")) + threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb_per_cpu=2000, + mem_mb=MEMORY wildcard_constraints: genome_release=RE_GENOME, v_gnomad=RE_VERSION, diff --git a/rules/output/annonars/gnomad_mtdna.smk b/rules/output/annonars/gnomad_mtdna.smk index befa299..6263e03 100644 --- a/rules/output/annonars/gnomad_mtdna.smk +++ b/rules/output/annonars/gnomad_mtdna.smk @@ -16,10 +16,10 @@ rule output_annonars_gnomad_mtdna: # -- build gnomAD-mtDNA RocksDB with annonar manifest=( "output/full/annonars/gnomad-mtdna-{genome_release}-{v_gnomad}+{v_annonars}/MANIFEST.txt" ), - threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96")) + threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb_per_cpu=2000, + mem_mb=MEMORY wildcard_constraints: genome_release=RE_GENOME, v_gnomad=RE_VERSION, diff --git a/rules/output/annonars/gnomad_sv.smk b/rules/output/annonars/gnomad_sv.smk index b5f1473..b757830 100644 --- a/rules/output/annonars/gnomad_sv.smk +++ b/rules/output/annonars/gnomad_sv.smk @@ -15,10 +15,10 @@ rule output_annonars_gnomad_sv_grch37_exac: # -- build gnomAD-SV RocksDB with a manifest=( "output/full/annonars/gnomad-sv-exomes-grch37-{v_gnomad}+{v_annonars}/MANIFEST.txt" ), - threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96")) + threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb_per_cpu=2000, + mem_mb=MEMORY wildcard_constraints: v_gnomad=RE_VERSION, v_annonars=RE_VERSION, @@ -70,10 +70,10 @@ rule output_annonars_gnomad_sv_grch37_gnomad_sv2: # -- build gnomAD-SV RocksDB manifest=( "output/full/annonars/gnomad-sv-genomes-grch37-{v_gnomad}+{v_annonars}/MANIFEST.txt" ), - threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96")) + threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb_per_cpu=2000, + mem_mb=MEMORY wildcard_constraints: v_gnomad=RE_VERSION, v_annonars=RE_VERSION, @@ -123,10 +123,10 @@ rule output_annonars_gnomad_sv_grch38_gnomad_cnv4: # -- build gnomAD-SV RocksDB manifest=( "output/full/annonars/gnomad-sv-exomes-grch38-{v_gnomad}+{v_annonars}/MANIFEST.txt" ), - threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96")) + threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb_per_cpu=2000, + mem_mb=MEMORY wildcard_constraints: v_gnomad=RE_VERSION, v_annonars=RE_VERSION, @@ -175,10 +175,10 @@ rule output_annonars_gnomad_sv_grch38_gnomad_sv4: # -- build gnomAD-SV RocksDB manifest=( "output/full/annonars/gnomad-sv-genomes-grch38-{v_gnomad}+{v_annonars}/MANIFEST.txt" ), - threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96")) + threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb_per_cpu=2000, + mem_mb=MEMORY wildcard_constraints: genome_release=RE_GENOME, v_gnomad=RE_VERSION, diff --git a/rules/output/annonars/helix.smk b/rules/output/annonars/helix.smk index b2db8c7..8ebcb24 100644 --- a/rules/output/annonars/helix.smk +++ b/rules/output/annonars/helix.smk @@ -16,10 +16,10 @@ rule output_annonars_helixmtdb: # -- build HelixMtDb RocksDB with annonars manifest=( "output/full/annonars/helixmtdb-{genome_release}-{v_helixmtdb}+{v_annonars}/MANIFEST.txt", ), - threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96")) + threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb_per_cpu=2000, + mem_mb=MEMORY, wildcard_constraints: genome_release=RE_GENOME, v_helixmtdb=RE_VERSION, diff --git a/rules/output/mehari/freqs.smk b/rules/output/mehari/freqs.smk index 2a5ebe2..0e1dc25 100644 --- a/rules/output/mehari/freqs.smk +++ b/rules/output/mehari/freqs.smk @@ -5,8 +5,8 @@ import os rule output_mehari_freqs_build: # -- build frequency tables for mehari input: - gnomad_genomes="work/download/annos/{genome_release}/seqvars/gnomad_exomes/{v_gnomad_exomes}/.done", - gnomad_exomes="work/download/annos/{genome_release}/seqvars/gnomad_genomes/{v_gnomad_genomes}/.done", + gnomad_genomes="work/download/annos/{genome_release}/seqvars/gnomad_genomes/{v_gnomad_genomes}/.done", + gnomad_exomes="work/download/annos/{genome_release}/seqvars/gnomad_exomes/{v_gnomad_exomes}/.done", gnomad_mtdna="work/annos/{genome_release}/seqvars/gnomad_mtdna/{v_gnomad_mtdna}/gnomad_mtdna.vcf.gz", helixmtdb="work/annos/{genome_release}/seqvars/helixmtdb/{v_helixmtdb}/helixmtdb.vcf.gz", output: @@ -22,10 +22,10 @@ rule output_mehari_freqs_build: # -- build frequency tables for mehari "output/full/mehari/freqs-{genome_release}-{v_gnomad_genomes}+{v_gnomad_exomes}+" "{v_gnomad_mtdna}+{v_helixmtdb}+{v_annonars}/MANIFEST.txt" ), - threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96")) + threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb_per_cpu=2000, + mem_mb=MEMORY wildcard_constraints: genome_release=RE_GENOME, v_gnomad_genomes=RE_VERSION, diff --git a/rules/output/viguno/hpo.smk b/rules/output/viguno/hpo.smk index 5b0f87b..0937520 100644 --- a/rules/output/viguno/hpo.smk +++ b/rules/output/viguno/hpo.smk @@ -3,9 +3,6 @@ import os -#: Number of threads to use for simulating in viguno. -VIGUNO_SIMULATE_THREADS = int(os.environ.get("VIGUNO_SIMULATE_THREADS", 96)) - rule output_viguno_pheno: # -- copy HPO input: @@ -19,9 +16,9 @@ rule output_viguno_pheno: # -- copy HPO wildcard_constraints: v_hpo=RE_VERSION, v_viguno=RE_VERSION, - threads: VIGUNO_SIMULATE_THREADS + threads: THREADS resources: - mem_mb_per_cpu="2GB", + mem_mb=MEMORY, shell: r""" cp -a {input.obo} {output.obo} diff --git a/rules/reduced/annonars.smk b/rules/reduced/annonars.smk index 433de9a..4f70c80 100644 --- a/rules/reduced/annonars.smk +++ b/rules/reduced/annonars.smk @@ -38,10 +38,10 @@ rule subset_annonars: # -- create exomes subset genome_release=RE_GENOME, v_hpo=RE_VERSION, versions=RE_VERSION_MULTI, - threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96")) + threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb_per_cpu=2000, + mem_mb=MEMORY shell: r""" annonars db-utils copy \ diff --git a/rules/reduced/hpo.smk b/rules/reduced/hpo.smk index 374ef6d..43c6825 100644 --- a/rules/reduced/hpo.smk +++ b/rules/reduced/hpo.smk @@ -56,9 +56,9 @@ rule subset_worker_pheno_dev: # -- create development subset wildcard_constraints: v_hpo=RE_VERSION, v_viguno=RE_VERSION, - threads: VIGUNO_SIMULATE_THREADS + threads: THREADS resources: - mem_mb_per_cpu="2GB", + mem_mb=MEMORY, shell: r""" cp -a {input.obo} {output.obo} diff --git a/rules/reduced/mehari.smk b/rules/reduced/mehari.smk index 5881f9d..26cffe4 100644 --- a/rules/reduced/mehari.smk +++ b/rules/reduced/mehari.smk @@ -37,10 +37,10 @@ rule subset_mehari: # -- create exomes subset genome_release=RE_GENOME, v_hpo=RE_VERSION, versions=RE_VERSION_MULTI, - threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96")) + threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb_per_cpu=2000, + mem_mb=MEMORY shell: r""" annonars db-utils copy \ diff --git a/rules/work/annos/features/tads.smk b/rules/work/annos/features/tads.smk index 19f3817..d4fe0aa 100644 --- a/rules/work/annos/features/tads.smk +++ b/rules/work/annos/features/tads.smk @@ -14,7 +14,7 @@ rule annos_features_tads_download: # -- download TAD ZIP files from 3dgenome.or wget --no-check-certificate \ -O {output.zip} \ - http://3dgenome.fsm.northwestern.edu/downloads/$name.TADs.zip + https://3dgenome.fsm.northwestern.edu/downloads/$name.TADs.zip """ diff --git a/rules/work/annos/seqvars/dbnsfp.smk b/rules/work/annos/seqvars/dbnsfp.smk index 6003893..0bdd398 100644 --- a/rules/work/annos/seqvars/dbnsfp.smk +++ b/rules/work/annos/seqvars/dbnsfp.smk @@ -54,7 +54,14 @@ rule annos_seqvars_dbnsfp_download: # -- download dbNSFP ZIP file threads: 8 shell: r""" - url=https://dbnsfp.s3.amazonaws.com/dbNSFP4.5{wildcards.variant}.zip + url_a=https://usf.box.com/shared/static/2hzcx5s6p1xui7oen16xqzndfrkt8l9l + url_c=https://usf.box.com/shared/static/03xsrpna0nzgrytfo2pzk326t8jad4oc + + if [[ "{wildcards.variant}" == "a" ]]; then + url=$url_a + else + url=$url_c + fi aria2c \ --check-certificate=false \ diff --git a/rules/work/annos/seqvars/dbscsnv.smk b/rules/work/annos/seqvars/dbscsnv.smk index 4eeb31d..92abb79 100644 --- a/rules/work/annos/seqvars/dbscsnv.smk +++ b/rules/work/annos/seqvars/dbscsnv.smk @@ -27,7 +27,7 @@ rule annos_seqvars_dbscsnv_download: # -- download dbscSNV ZIP file --split=8 \ --max-concurrent-downloads=8 \ --max-connection-per-server=8 \ - ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/dbscSNV1.1.zip + https://usf.box.com/shared/static/ffwlywsat3q5ijypvunno3rg6steqfs8 """ diff --git a/rules/work/genes/ensembl.smk b/rules/work/genes/ensembl.smk index 8560c67..dfb3ea4 100644 --- a/rules/work/genes/ensembl.smk +++ b/rules/work/genes/ensembl.smk @@ -12,16 +12,16 @@ rule genes_ensembl_create_xlink: # -- create ENSEMBL gene information xlink tab trap "rm -rf $TMPDIR" EXIT wget --no-check-certificate \ -O $TMPDIR/current_README \ - https://ftp.ensembl.org/pub/current_README + https://may2024.archive.ensembl.org/pub/current_README grep "The current release is Ensembl {DV.ensembl}" $TMPDIR/current_README \ - || (echo "Ensembl version is not {DV.ensembl}." && exit 1) + || (echo "WARNING: Ensembl version is not {DV.ensembl}.") echo -e "ensembl_gene_id\tensembl_transcript_id\tentrez_id\tgene_symbol" \ >{output.tsv} wget --no-check-certificate \ -O $TMPDIR/tmp \ - 'https://ensembl.org/biomart/martservice?query=' \ + 'https://may2024.archive.ensembl.org/biomart/martservice?query=' \ sort -u $TMPDIR/tmp \ >> {output.tsv} diff --git a/rules/work/genes/gnomad.smk b/rules/work/genes/gnomad.smk index d13e280..7261f50 100644 --- a/rules/work/genes/gnomad.smk +++ b/rules/work/genes/gnomad.smk @@ -161,6 +161,7 @@ def run_genes_gnomad_constraints_v4_to_tsv(input, output, wildcards): > $TMPDIR/tmp.txt # Select columns, rename, pad with the exac_* fields having NA values. + QSV_SKIP_FORMAT_CHECK=1 \ qsv select {columns_src_str} $TMPDIR/tmp.txt \ | qsv rename {columns_tmp_str} \ | perl -p -e 's/$/,exac_pLI,exac_obs_lof,exac_exp_lof,exac_oe_lof/ if $. == 1' \ diff --git a/rules/work/genes/hgnc.smk b/rules/work/genes/hgnc.smk index 088f4fa..bb573d7 100644 --- a/rules/work/genes/hgnc.smk +++ b/rules/work/genes/hgnc.smk @@ -14,7 +14,7 @@ rule genes_hgnc_download: # -- Download the HGNC data wget --no-check-certificate \ -O {output.json} \ - https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/json/hgnc_complete_set.json + https://storage.googleapis.com/public-download-files/hgnc/json/json/hgnc_complete_set.json md5sum {output.json} > {output.json_md5} """ diff --git a/rules/work/genes/mehari_data_tx.smk b/rules/work/genes/mehari_data_tx.smk index 8e2d438..0bcf69f 100644 --- a/rules/work/genes/mehari_data_tx.smk +++ b/rules/work/genes/mehari_data_tx.smk @@ -3,21 +3,21 @@ rule genes_mehari_data_tx_download: # -- Download the HGNC data output: - zstd="work/download/mehari-data-tx/{genome_release}-{version}/mehari-data-txs-{genome_release}-{version}.bin.zst", + zstd="work/download/mehari-data-tx/{genome_release}-{version}/mehari-data-txs-{genome_release}-{refseq_or_ensembl}-{version}.bin.zst", shell: r""" wget \ -O {output.zstd} \ - https://github.com/bihealth/mehari-data-tx/releases/download/v{wildcards.version}/mehari-data-txs-{wildcards.genome_release}-{wildcards.version}.bin.zst + https://github.com/bihealth/mehari-data-tx/releases/download/v{wildcards.version}/mehari-data-txs-{wildcards.genome_release}-{wildcards.refseq_or_ensembl}-{wildcards.version}.bin.zst """ rule genes_mehari_data_tx_copy: # -- Copy data to output input: - zstd="work/download/mehari-data-tx/{genome_release}-{version}/mehari-data-txs-{genome_release}-{version}.bin.zst", + zstd="work/download/mehari-data-tx/{genome_release}-{version}/mehari-data-txs-{genome_release}-{refseq_or_ensembl}-{version}.bin.zst", output: - zstd="output/full/mehari/genes-txs-{genome_release}-{version}/mehari-data-txs-{genome_release}-{version}.bin.zst", - zstd_md5="output/full/mehari/genes-txs-{genome_release}-{version}/mehari-data-txs-{genome_release}-{version}.bin.zst.md5", + zstd="output/full/mehari/genes-txs-{genome_release}-{version}/mehari-data-txs-{genome_release}-{refseq_or_ensembl}-{version}.bin.zst", + zstd_md5="output/full/mehari/genes-txs-{genome_release}-{version}/mehari-data-txs-{genome_release}-{refseq_or_ensembl}-{version}.bin.zst.md5", shell: r""" cp {input.zstd} {output.zstd} diff --git a/rules/work/genes/omim.smk b/rules/work/genes/omim.smk index bb726ee..c78b63a 100644 --- a/rules/work/genes/omim.smk +++ b/rules/work/genes/omim.smk @@ -41,6 +41,7 @@ rule genes_omim: # -- prepare HGNC to OMIM disease mapping echo hgnc_id,omim_id,disease_name \ > $TMPDIR/output.csv + QSV_SKIP_FORMAT_CHECK=1 \ qsv join -d '\t' \ omim_id $TMPDIR/mim2gene_hgnc.tsv \ database_id $TMPDIR/phenotype.hpoa \ diff --git a/rules/work/genes/rcnv.smk b/rules/work/genes/rcnv.smk index 6555665..75fdced 100644 --- a/rules/work/genes/rcnv.smk +++ b/rules/work/genes/rcnv.smk @@ -24,6 +24,7 @@ rule genes_rcnv_postproces: # -- postprocess file for HGNC gene IDs tsv_md5="work/genes/rcnv/2022/rcnv_collins_2022.tsv.md5", shell: """ + QSV_SKIP_FORMAT_CHECK=1 \ qsv join -d '\t' \ '#gene' <(zcat {input.tsv}) \ gene_symbol {input.xlink} \ diff --git a/rules/work/genes/shet.smk b/rules/work/genes/shet.smk index b0204a3..d28eca1 100644 --- a/rules/work/genes/shet.smk +++ b/rules/work/genes/shet.smk @@ -9,6 +9,7 @@ rule genes_shet: # -- postprocess file for HGNC gene IDs tsv="work/genes/shet/2019/shet_weghorn_2019.tsv", shell: """ + QSV_SKIP_FORMAT_CHECK=1 \ qsv join -d '\t' \ 'Gene' <(zcat {input.tsv}) \ gene_symbol {input.xlink} \ diff --git a/scripts/genes-integrate-diseases.py b/scripts/genes-integrate-diseases.py index da42e18..3fcdb27 100644 --- a/scripts/genes-integrate-diseases.py +++ b/scripts/genes-integrate-diseases.py @@ -145,6 +145,8 @@ class Aspect(enum.Enum): CLINICAL_COURSE = "C" #: Modifier CLINICAL_MODIFIER = "M" + #: Past medical history + PAST_MEDICAL_HISTORY = "H" class HpoaEntry(BaseModel): diff --git a/scripts/genes-orpha-diseases.py b/scripts/genes-orpha-diseases.py index ad9a426..9dc7c03 100755 --- a/scripts/genes-orpha-diseases.py +++ b/scripts/genes-orpha-diseases.py @@ -36,7 +36,9 @@ async def work(no: int, orpha_id: int, limiter: trio.CapacityLimiter): async with limiter: async with httpx.AsyncClient() as client: try: - cross_references = (await client.get(URL_ORPHACODE_GET.format(orpha_id))).json() + cross_references = ( + await client.get(URL_ORPHACODE_GET.format(orpha_id), timeout=60) + ).json() disease_genes = ( await client.get(URL_ORPHACODE_GET_GENE.format(orpha_id), timeout=60) ).json() diff --git a/utils/install-annonars.sh b/utils/install-annonars.sh deleted file mode 100644 index 0351548..0000000 --- a/utils/install-annonars.sh +++ /dev/null @@ -1,7 +0,0 @@ -image="ghcr.io/varfish-org/annonars:0.41.3" -source_path="/usr/local/bin/annonars" -destination_path="/usr/local/bin/annonars" - -container_id=$(docker create "$image") -docker cp "$container_id:$source_path" "$destination_path" -docker rm "$container_id" diff --git a/varfish_db_downloader/versions.py b/varfish_db_downloader/versions.py index d79abbc..4d218ec 100644 --- a/varfish_db_downloader/versions.py +++ b/varfish_db_downloader/versions.py @@ -11,7 +11,7 @@ #: Allow to disable the today check. FORCE_TODAY = os.environ.get("FORCE_TODAY", "false").lower() == "true" #: The ClinVar release to use (includes annonars version used for building). -CLINVAR_RELEASE = os.environ.get("CLINVAR_RELEASE", "20240612+0.17.0") +CLINVAR_RELEASE = os.environ.get("CLINVAR_RELEASE", "20250410+0.18.5") #: The ClinVar version to use (part of the tag and release name). CLINVAR_VERSION = CLINVAR_RELEASE.replace("-", "").split("+")[0] @@ -161,10 +161,10 @@ class DataVersions: refseq_38="GCF_000001405.40+RS_2023_03", dbsnp="b151", acmg_sf="3.1", - hpo="20240116", + hpo="20250303", orphadata=TODAY, patho_mms="20220730", - mehari_tx="0.4.4", + mehari_tx="0.10.3", clinvar_release=CLINVAR_RELEASE, clinvar_version=CLINVAR_VERSION, tracks="0", From d173fc19a0be9def23c5abd75bbe6b75205dc831 Mon Sep 17 00:00:00 2001 From: Oliver Stolpe Date: Fri, 9 May 2025 16:55:11 +0200 Subject: [PATCH 03/15] feat: making genomebuilds switchable --- Snakefile | 479 +++++++++++++++++++++++++----------------------------- 1 file changed, 225 insertions(+), 254 deletions(-) diff --git a/Snakefile b/Snakefile index d791926..b11ea31 100644 --- a/Snakefile +++ b/Snakefile @@ -40,6 +40,8 @@ DEV_GENE_SYMBOLS = "|".join( # Padding to add to exons in dev and exons mode. EXON_PADDING = 200 +GENOMEBUILDS = ["grch37", "grch38"] + # Define number of threads for resource-intensive tasks THREADS = int(os.environ.get("THREADS", "32")) @@ -85,291 +87,260 @@ rule help: ) -## all -- run all rules -rule all: - input: - # == work directory ===================================================================== - # - # genes +def generate_input_files(wildcards): + """ + Helper function to return the input files for the rules. + """ + genomebuilds = GENOMEBUILDS + gnomad_versions = { + "grch37": DV.gnomad_v2, + "grch38": DV.gnomad_v4, + } + gnomad_cnv_versions = { + "grch37": DV.exac_cnv, + "grch38": DV.gnomad_cnv4, + } + gnomad_sv_versions = { + "grch37": DV.gnomad_sv, + "grch38": DV.gnomad_sv4, + } + refseq_versions = { + "grch37": DV.refseq_37, + "grch38": DV.refseq_38, + } + refseq_fe_versions = { + "grch37": DV.refseq_fe_37, + "grch38": DV.refseq_fe_38, + } + cons_versions = { + "grch37": DV.ucsc_cons_37, + "grch38": DV.ucsc_cons_38, + } + rmask_versions = { + "grch37": DV.ucsc_rmsk_37, + "grch38": DV.ucsc_rmsk_38, + } + genomic_super_dups_versions = { + "grch37": DV.ucsc_genomic_super_dups_37, + "grch38": DV.ucsc_genomic_super_dups_38, + } + lift_over_versions = { + "grch37": DV.ucsc_alt_seq_liftover_37, + "grch38": DV.ucsc_alt_seq_liftover_38, + } + lift_over_fix_versions = { + "grch37": DV.ucsc_fix_seq_liftover_37, + "grch38": DV.ucsc_fix_seq_liftover_38, + } + + input_files = [] + if "grch38" in genomebuilds: + input_files += [ + f"work/genes/clingen/{DV.today}/ClinGen_gene_curation_list_GRCh38.tsv" + "work/download/genes/alphamissense/1/AlphaMissense_gene_hg38.tsv.gz", + f"work/download/annos/grch38/seqvars/cadd/{DV.cadd}/whole_genome_SNVs_inclAnno.tsv.gz", + f"work/download/annos/grch38/seqvars/cadd/{DV.cadd}/gnomad.genomes.r3.0.indel_inclAnno.tsv.gz", + f"work/annos/grch38/seqvars/helixmtdb/{DV.helixmtdb}/helixmtdb.vcf.gz", + f"work/annos/grch38/seqvars/gnomad_mtdna/{DV.gnomad_mtdna}/gnomad_mtdna.vcf.gz", + f"work/download/annos/grch38/seqvars/gnomad_exomes/{DV.gnomad_v4}/.done", + f"work/download/annos/grch38/seqvars/gnomad_genomes/{DV.gnomad_v4}/.done", + f"work/annos/grch38/features/cons/{DV.ucsc_cons_38}/ucsc_conservation.tsv", + f"work/annos/grch38/features/ensembl/{DV.ensembl_38}/ensembl_genes.bed.gz", + f"work/annos/grch38/features/refseq/{DV.refseq_38}/refseq_genes.bed.gz", + f"output/full/worker/bgdb-gnomad-exomes-cnv-grch38-{DV.gnomad_sv4}+{PV.worker}/bgdb-gnomad-exomes-cnv-grch38.bin", + f"output/full/worker/bgdb-gnomad-genomes-sv-grch38-{DV.gnomad_sv4}+{PV.worker}/bgdb-gnomad-genomes-sv-grch38.bin", + # ----- background/population structural variants and annotations thereof + f"output/full/tracks/track-strucvars-gnomad-sv-grch38-{DV.gnomad_sv4}+{DV.tracks}/gnomad-sv.bed.gz", + f"output/full/tracks/track-strucvars-gnomad-cnv-grch38-{DV.gnomad_cnv4}+{DV.tracks}/gnomad-cnv.bed.gz", + + ] + if "grch37" in genomebuilds: + input_files += [ + f"work/genes/enst_ensg/grch37/{DV.ensembl_37}/enst_ensg.tsv", + f"work/genes/clingen/{DV.today}/ClinGen_gene_curation_list_GRCh37.tsv", + f"work/download/annos/grch37/seqvars/cadd/{DV.cadd}/whole_genome_SNVs_inclAnno.tsv.gz", + f"work/download/annos/grch37/seqvars/cadd/{DV.cadd}/InDels_inclAnno.tsv.gz", + f"work/download/annos/grch37/seqvars/dbnsfp/{DV.dbnsfp}a/LICENSE.txt", + f"work/download/annos/grch37/seqvars/dbnsfp/{DV.dbnsfp}c/LICENSE.txt", + f"work/download/annos/grch37/seqvars/dbscsnv/{DV.dbscsnv}/dbscSNV{DV.dbscsnv}.chr1", + f"work/download/annos/grch37/seqvars/dbsnp/{DV.dbsnp}/dbsnp.vcf.gz", + f"work/annos/grch37/seqvars/helixmtdb/{DV.helixmtdb}/helixmtdb.vcf.gz", + f"work/annos/grch37/seqvars/gnomad_mtdna/{DV.gnomad_mtdna}/gnomad_mtdna.vcf.gz", + f"work/download/annos/grch37/seqvars/gnomad_exomes/{DV.gnomad_v2}/.done", + f"work/download/annos/grch37/seqvars/gnomad_genomes/{DV.gnomad_v2}/.done", + f"work/annos/grch37/features/cons/{DV.ucsc_cons_37}/ucsc_conservation.tsv", + f"work/annos/grch37/features/ensembl/{DV.ensembl_37}/ensembl_genes.bed.gz", + f"work/annos/grch37/features/refseq/{DV.refseq_37}/refseq_genes.bed.gz", + f"output/full/worker/bgdb-gnomad-grch37-{DV.gnomad_sv}+{PV.worker}/bgdb-gnomad.bin", + f"output/full/worker/bgdb-exac-grch37-{DV.exac_cnv}+{PV.worker}/bgdb-exac.bin", + f"output/full/worker/bgdb-g1k-grch37-{DV.g1k_svs}+{PV.worker}/bgdb-g1k.bin", + f"output/full/tracks/track-strucvars-exac-grch37-{DV.exac_cnv}+{DV.tracks}/exac.bed.gz", + f"output/full/tracks/track-strucvars-g1k-grch37-{DV.g1k_svs}+{DV.tracks}/g1k.bed.gz", + f"output/full/tracks/track-strucvars-gnomad-grch37-{DV.gnomad_sv}+{DV.tracks}/gnomad.bed.gz", + + ] + for genomebuild in genomebuilds: + input_files += [ + # -- mehari data + # ---- frequencies (via annonars) + f"output/full/mehari/freqs-{genomebuild}-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", + f"output/full/annonars/alphamissense-{genomebuild}-{DV.alphamissense}+{PV.annonars}/rocksdb/IDENTITY", + # -- annonars data + # ----- sequence variant annotations + f"output/full/annonars/cadd-{genomebuild}-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY", + f"output/full/annonars/dbsnp-{genomebuild}-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY", + f"output/full/annonars/dbnsfp-{genomebuild}-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY", + f"output/full/annonars/dbnsfp-{genomebuild}-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY", + f"output/full/annonars/dbscsnv-{genomebuild}-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY", + f"output/full/annonars/gnomad-mtdna-{genomebuild}-{DV.gnomad_mtdna}+{PV.annonars}/rocksdb/IDENTITY", + f"output/full/annonars/gnomad-exomes-{genomebuild}-{gnomad_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY", + f"output/full/annonars/gnomad-genomes-{genomebuild}-{gnomad_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY", + f"output/full/annonars/helixmtdb-{genomebuild}-{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", + f"output/full/annonars/gnomad-sv-exomes-{genomebuild}-{gnomad_cnv_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY", + f"output/full/annonars/gnomad-sv-genomes-{genomebuild}-{gnomad_sv_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY", + # ----- sequence annotation + f"output/full/annonars/functional-{genomebuild}-{refseq_fe_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY", + f"output/full/annonars/regions-{genomebuid}-{DV.today}+{PV.annonars}/rocksdb/IDENTITY", + # ----- conservation + f"output/full/annonars/cons-{genomebuild}-{cons_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY", + # ----- worker + f"output/full/worker/masked-repeat-{genomebuild}-{rmask_versions[genomebuild]}+{PV.worker}/masked-repeat.bin", + f"output/full/worker/masked-segdup-{genomebuild}-{genomic_super_dups_versions[genomebuild]}+{PV.worker}/masked-segdup.bin", + f"output/full/worker/bgdb-dbvar-{genomebuild}-{DV.dbvar}+{PV.worker}/bgdb-dbvar.bin", + f"output/full/worker/bgdb-dgv-{genomebuild}-{DV.dgv}+{PV.worker}/bgdb-dgv.bin", + f"output/full/worker/bgdb-dgv-gs-{genomebuild}-{DV.dgv}+{PV.worker}/bgdb-dgv-gs.bin", + f"output/full/worker/clinvar-strucvars-{genomebuild}-{DV.clinvar_version}+{PV.worker}/clinvar-strucvars.bin", + f"output/full/worker/patho-mms-{genomebuild}-{DV.patho_mms}+{PV.worker}/patho-mms.bed", + f"output/full/worker/tads-{genomebuild}-dixon2015/hesc.bed", + # -- mehari data + f"output/full/mehari/genes-txs-{genomebuild}-{DV.mehari_tx}/mehari-data-txs-{genomebuild}-{DV.mehari_tx}.bin.zst", + f"output/full/tracks/track-strucvars-dbvar-{genomebuild}-{DV.dbvar}+{DV.tracks}/dbvar.bed.gz", + f"output/full/tracks/track-strucvars-dgv-{genomebuild}-{DV.dgv}+{DV.tracks}/dgv.bed.gz", + f"output/full/tracks/track-strucvars-dgv-gs-{genomebuild}-{DV.dgv_gs}+{DV.tracks}/dgv-gs.bed.gz", + # ----- known pathogenic MMS + f"output/full/tracks/track-strucvars-patho-mms-{genomebuild}-{DV.patho_mms}+{DV.tracks}/patho-mms.bed", + # ----- problematic regions (rmsk, genomicSuperDups, altSeqLiftOverPsl, fixSeqLiftOverPsl) + f"output/full/tracks/track-features-ucsc-genomicsuperdups-{genomebuild}-{genomic_super_dups_versions[genomebuild]}+{DV.tracks}/genomicSuperDups.bed.gz", + f"output/full/tracks/track-features-ucsc-rmsk-{genomebuild}-{rmask_version[genomebuild]}+{DV.tracks}/rmsk.bed.gz", + f"output/full/tracks/track-features-ucsc-altseqliftoverpsl-{genomebuild}-{lift_over_versions[genomebuild]}+{DV.tracks}/altSeqLiftOverPsl.bed.gz", + f"output/full/tracks/track-features-ucsc-fixseqliftoverpsl-{genomebuild}-{lift_over_fix_versions[genomebuild]}+{DV.tracks}/fixSeqLiftOverPsl.bed.gz", + # ----- tads + f"output/full/tracks/track-tads-{genomebuild}-dixon2015+{DV.tracks}/hesc.bed", + # ----- probesets + f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v4-{genomebuild}-{DV.tracks}.bed.gz", + f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v5-{genomebuild}-{DV.tracks}.bed.gz", + f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v6-{genomebuild}-{DV.tracks}.bed.gz", + f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v7-{genomebuild}-{DV.tracks}.bed.gz", + f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v8-{genomebuild}-{DV.tracks}.bed.gz", + f"output/full/tracks/track-enrichment-probesets-targets/idt-xgen-exome-research-panel-v1-{genomebuild}-{DV.tracks}.bed.gz", + f"output/full/tracks/track-enrichment-probesets-targets/idt-xgen-exome-research-panel-v2-{genomebuild}-{DV.tracks}.bed.gz", + f"output/full/tracks/track-enrichment-probesets-targets/twist-comprehensive-exome-{genomebuild}-{DV.tracks}.bed.gz", + f"output/full/tracks/track-enrichment-probesets-targets/twist-core-exome-{genomebuild}-{DV.tracks}.bed.gz", + f"output/full/tracks/track-enrichment-probesets-targets/twist-exome-v2_0-{genomebuild}-{DV.tracks}.bed.gz", + f"output/full/tracks/track-enrichment-probesets-targets/twist-refseq-exome-{genomebuild}-{DV.tracks}.bed.gz", + # -- targets + f"output/reduced-dev/targets/{genomebuild}/refseq/{refseq_versions[genomebuild]}/refseq_target_exons.bed.gz", + # + # == development (reduced data) directories ============================================= + # + # -- annonars + f"output/reduced-dev/annonars/cadd-{genomebuild}-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY", + f"output/reduced-dev/annonars/cadd-{genomebuild}-{DV.cadd}+{PV.annonars}/spec.yaml", + f"output/reduced-dev/annonars/cons-{genomebuild}-{cons_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY", + f"output/reduced-dev/annonars/cons-{genomebuild}-{cons_versions[genomebuild]}+{PV.annonars}/spec.yaml", + f"output/reduced-dev/annonars/dbnsfp-{genomebuild}-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY", + f"output/reduced-dev/annonars/dbnsfp-{genomebuild}-{DV.dbnsfp}a+{PV.annonars}/spec.yaml", + f"output/reduced-dev/annonars/dbnsfp-{genomebuild}-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY", + f"output/reduced-dev/annonars/dbnsfp-{genomebuild}-{DV.dbnsfp}c+{PV.annonars}/spec.yaml", + f"output/reduced-dev/annonars/dbscsnv-{genomebuild}-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY", + f"output/reduced-dev/annonars/dbscsnv-{genomebuild}-{DV.dbscsnv}+{PV.annonars}/spec.yaml", + f"output/reduced-dev/annonars/dbsnp-{genomebuild}-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY", + f"output/reduced-dev/annonars/dbsnp-{genomebuild}-{DV.dbsnp}+{PV.annonars}/spec.yaml", + f"output/reduced-dev/annonars/gnomad-exomes-{genomebuild}-{gnomad_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY", + f"output/reduced-dev/annonars/gnomad-exomes-{genomebuild}-{gnomad_versions[genomebuild]}+{PV.annonars}/spec.yaml", + f"output/reduced-dev/annonars/gnomad-genomes-{genomebuild}-{gnomad_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY", + f"output/reduced-dev/annonars/gnomad-genomes-{genomebuild}-{gnomad_versions[genomebuild]}+{PV.annonars}/spec.yaml", + # -- mehari + f"output/reduced-dev/mehari/freqs-{genomebuild}-{gnomad_versions[genomebuild]}+{gnomad_versions[genomebuild]}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", + f"output/reduced-dev/mehari/freqs-{genomebuild}-{gnomad_versions[genomebuild]}+{gnomad_versions[genomebuild]}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/spec.yaml", + # + # == exomes (reduced data) directories ================================================== + # + # -- targets + f"output/reduced-exomes/targets/{genomebuild}/refseq/{refseq_versions[genomebuild]}/refseq_target_exons.bed.gz", + # -- annonars + f"output/reduced-exomes/annonars/cadd-{genomebuild}-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY", + f"output/reduced-exomes/annonars/cadd-{genomebuild}-{DV.cadd}+{PV.annonars}/spec.yaml", + f"output/reduced-exomes/annonars/cons-{genomebuild}-{cons_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY", + f"output/reduced-exomes/annonars/cons-{genomebuild}-{cons_versions[genomebuild]}+{PV.annonars}/spec.yaml", + f"output/reduced-exomes/annonars/dbnsfp-{genomebuild}-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY", + f"output/reduced-exomes/annonars/dbnsfp-{genomebuild}-{DV.dbnsfp}a+{PV.annonars}/spec.yaml", + f"output/reduced-exomes/annonars/dbnsfp-{genomebuild}-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY", + f"output/reduced-exomes/annonars/dbnsfp-{genomebuild}-{DV.dbnsfp}c+{PV.annonars}/spec.yaml", + f"output/reduced-exomes/annonars/dbscsnv-{genomebuild}-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY", + f"output/reduced-exomes/annonars/dbscsnv-{genomebuild}-{DV.dbscsnv}+{PV.annonars}/spec.yaml", + f"output/reduced-exomes/annonars/dbsnp-{genomebuild}-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY", + f"output/reduced-exomes/annonars/dbsnp-{genomebuild}-{DV.dbsnp}+{PV.annonars}/spec.yaml", + f"output/reduced-exomes/annonars/gnomad-exomes-{genomebuild}-{gnomad_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY", + f"output/reduced-exomes/annonars/gnomad-exomes-{genomebuild}-{gnomad_versions[genomebuild]}+{PV.annonars}/spec.yaml", + f"output/reduced-exomes/annonars/gnomad-genomes-{genomebuild}-{gnomad_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY", + f"output/reduced-exomes/annonars/gnomad-genomes-{genomebuild}-{gnomad_versions[genomebuild]}+{PV.annonars}/spec.yaml", + # -- mehari + f"output/reduced-exomes/mehari/freqs-{genomebuild}-{gnomad_versions[genomebuild]}+{gnomad_versions[genomebuild]}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", + f"output/reduced-exomes/mehari/freqs-{genomebuild}-{gnomad_versions[genomebuild]}+{gnomad_versions[genomebuild]}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/spec.yaml", + ] + # Files independent of genomebuild (or serving both) + input_files += [ + # -- download f"work/download/genes/rcnv/2022/Collins_rCNV_2022.dosage_sensitivity_scores.tsv.gz", - "work/download/genes/alphamissense/1/AlphaMissense_gene_hg38.tsv.gz", f"work/download/genes/ctd/{DV.today}/CTD_diseases.tsv.gz", f"work/download/do/{DV.today}/omim-unmapped.csv", + # NB: dbNSFP is dual reference (for download) + # NB: dbscSNV is dual reference (for download) + f"work/download/annos/grch37/seqvars/dbsnp/{DV.dbsnp}/dbsnp.vcf.gz", + # -- genes f"work/genes/dbnsfp/{DV.dbnsfp}/genes.tsv.gz", "work/genes/decipher/v3/decipher_hi_prediction.tsv", - f"work/genes/ensembl/{DV.ensembl}/ensembl_xlink.tsv", # TODO broken on their side (AAA) - f"work/genes/enst_ensg/grch37/{DV.ensembl_37}/enst_ensg.tsv", + f"work/genes/ensembl/{DV.ensembl}/ensembl_xlink.tsv", f"work/genes/entrez/{DV.today}/gene_info.jsonl", - f"work/genes/gnomad/{DV.gnomad_constraints}/gnomad_constraints.tsv", # TODO depends on ensembl_xlink.tsv (ref AAA) + f"work/genes/gnomad/{DV.gnomad_constraints}/gnomad_constraints.tsv", f"work/genes/hgnc/{DV.today}/hgnc_info.jsonl", f"work/genes/omim/{DV.hpo}+{DV.today}/omim_diseases.tsv", f"work/genes/orphadata/{DV.orphadata}/orphadata.jsonl", f"work/genes/mondo/{DV.today}/mondo.obo", "work/genes/rcnv/2022/rcnv_collins_2022.tsv", "work/genes/shet/2019/shet_weghorn_2019.tsv", - # f"work/genes/clingen/{DV.today}/ClinGen_gene_curation_list_GRCh37.tsv", - f"work/genes/clingen/{DV.today}/ClinGen_gene_curation_list_GRCh38.tsv", "work/genes/domino/20190219/domino.tsv", - # reference-specific annotations - # -- background/population sequence variants and annotations thereof - # ---- GRCh37 - # f"work/download/annos/grch37/seqvars/cadd/{DV.cadd}/whole_genome_SNVs_inclAnno.tsv.gz", - # f"work/download/annos/grch37/seqvars/cadd/{DV.cadd}/InDels_inclAnno.tsv.gz", - # f"work/download/annos/grch37/seqvars/dbnsfp/{DV.dbnsfp}a/LICENSE.txt", - # f"work/download/annos/grch37/seqvars/dbnsfp/{DV.dbnsfp}c/LICENSE.txt", - # f"work/download/annos/grch37/seqvars/dbscsnv/{DV.dbscsnv}/dbscSNV{DV.dbscsnv}.chr1", - # f"work/download/annos/grch37/seqvars/dbsnp/{DV.dbsnp}/dbsnp.vcf.gz", - # f"work/annos/grch37/seqvars/helixmtdb/{DV.helixmtdb}/helixmtdb.vcf.gz", - # f"work/annos/grch37/seqvars/gnomad_mtdna/{DV.gnomad_mtdna}/gnomad_mtdna.vcf.gz", - # f"work/download/annos/grch37/seqvars/gnomad_exomes/{DV.gnomad_v2}/.done", - # f"work/download/annos/grch37/seqvars/gnomad_genomes/{DV.gnomad_v2}/.done", - # ---- GRCh38 - f"work/download/annos/grch38/seqvars/cadd/{DV.cadd}/whole_genome_SNVs_inclAnno.tsv.gz", - f"work/download/annos/grch38/seqvars/cadd/{DV.cadd}/gnomad.genomes.r3.0.indel_inclAnno.tsv.gz", - # NB: dbNSFP is dual reference (for download) - # NB: dbscSNV is dual reference (for download) - f"work/download/annos/grch37/seqvars/dbsnp/{DV.dbsnp}/dbsnp.vcf.gz", - f"work/annos/grch38/seqvars/helixmtdb/{DV.helixmtdb}/helixmtdb.vcf.gz", - f"work/annos/grch38/seqvars/gnomad_mtdna/{DV.gnomad_mtdna}/gnomad_mtdna.vcf.gz", - f"work/download/annos/grch38/seqvars/gnomad_exomes/{DV.gnomad_v4}/.done", - f"work/download/annos/grch38/seqvars/gnomad_genomes/{DV.gnomad_v4}/.done", - # -- genome browser "features" (position-specific) - # ---- GRCh37 - # f"work/annos/grch37/features/cons/{DV.ucsc_cons_37}/ucsc_conservation.tsv", - # f"work/annos/grch37/features/ensembl/{DV.ensembl_37}/ensembl_genes.bed.gz", - # f"work/annos/grch37/features/refseq/{DV.refseq_37}/refseq_genes.bed.gz", - # ---- GRCh38 - f"work/annos/grch38/features/cons/{DV.ucsc_cons_38}/ucsc_conservation.tsv", - f"work/annos/grch38/features/ensembl/{DV.ensembl_38}/ensembl_genes.bed.gz", - f"work/annos/grch38/features/refseq/{DV.refseq_38}/refseq_genes.bed.gz", - # - # == output directory =================================================================== - # - # -- mehari data - # ---- frequencies (via annonars) - # f"output/full/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/mehari/freqs-grch38-{DV.gnomad_v4}+{DV.gnomad_v4}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", - # -- annonars data - # ----- sequence variant annotations - # f"output/full/annonars/alphamissense-grch37-{DV.alphamissense}+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/alphamissense-grch38-{DV.alphamissense}+{PV.annonars}/rocksdb/IDENTITY", - # f"output/full/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/cadd-grch38-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY", - # f"output/full/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/dbsnp-grch38-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY", - # f"output/full/annonars/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/dbnsfp-grch38-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY", - # f"output/full/annonars/dbnsfp-grch37-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/dbnsfp-grch38-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY", - # f"output/full/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/dbscsnv-grch38-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY", - # f"output/full/annonars/gnomad-mtdna-grch37-{DV.gnomad_mtdna}+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/gnomad-mtdna-grch38-{DV.gnomad_mtdna}+{PV.annonars}/rocksdb/IDENTITY", - # f"output/full/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/gnomad-exomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY", - # f"output/full/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/gnomad-genomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY", - # f"output/full/annonars/helixmtdb-grch37-{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/helixmtdb-grch38-{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", - # f"output/full/annonars/gnomad-sv-exomes-grch37-{DV.exac_cnv}+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/gnomad-sv-exomes-grch38-{DV.gnomad_cnv4}+{PV.annonars}/rocksdb/IDENTITY", - # f"output/full/annonars/gnomad-sv-genomes-grch37-{DV.gnomad_sv}+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/gnomad-sv-genomes-grch38-{DV.gnomad_sv4}+{PV.annonars}/rocksdb/IDENTITY", - # ----- sequence annotation - # f"output/full/annonars/functional-grch37-{DV.refseq_fe_37}+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/functional-grch38-{DV.refseq_fe_38}+{PV.annonars}/rocksdb/IDENTITY", - # f"output/full/annonars/regions-grch37-{DV.today}+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/regions-grch38-{DV.today}+{PV.annonars}/rocksdb/IDENTITY", - # ----- conservation - # f"output/full/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/cons-grch38-{DV.ucsc_cons_38}+{PV.annonars}/rocksdb/IDENTITY", - # ----- genes - f"output/full/annonars/genes-{DV.acmg_sf}+{DV.gnomad_constraints}+{DV.dbnsfp}+{DV.hpo}+{DV.today}+{PV.annonars}/rocksdb/IDENTITY", # TODO depend on (ref AAA) + # -- annonars + f"output/full/annonars/genes-{DV.acmg_sf}+{DV.gnomad_constraints}+{DV.dbnsfp}+{DV.hpo}+{DV.today}+{PV.annonars}/rocksdb/IDENTITY", # -- worker data f"output/full/worker/genes-xlink-{DV.today}+{PV.worker}/genes-xlink.bin", f"output/full/worker/acmg-sf-{DV.acmg_sf}+{PV.worker}/acmg_sf.tsv", f"output/full/worker/mim2gene-{DV.today}+{PV.worker}/mim2gene.tsv", - # f"output/full/worker/masked-repeat-grch37-{DV.ucsc_rmsk_37}+{PV.worker}/masked-repeat.bin", - f"output/full/worker/masked-repeat-grch38-{DV.ucsc_rmsk_38}+{PV.worker}/masked-repeat.bin", - # f"output/full/worker/masked-segdup-grch37-{DV.ucsc_genomic_super_dups_37}+{PV.worker}/masked-segdup.bin", - f"output/full/worker/masked-segdup-grch38-{DV.ucsc_genomic_super_dups_38}+{PV.worker}/masked-segdup.bin", - # f"output/full/worker/bgdb-dbvar-grch37-{DV.dbvar}+{PV.worker}/bgdb-dbvar.bin", - f"output/full/worker/bgdb-dbvar-grch38-{DV.dbvar}+{PV.worker}/bgdb-dbvar.bin", - # f"output/full/worker/bgdb-dgv-grch37-{DV.dgv}+{PV.worker}/bgdb-dgv.bin", - f"output/full/worker/bgdb-dgv-grch38-{DV.dgv}+{PV.worker}/bgdb-dgv.bin", - # f"output/full/worker/bgdb-dgv-gs-grch37-{DV.dgv}+{PV.worker}/bgdb-dgv-gs.bin", - f"output/full/worker/bgdb-dgv-gs-grch38-{DV.dgv}+{PV.worker}/bgdb-dgv-gs.bin", - # f"output/full/worker/bgdb-gnomad-grch37-{DV.gnomad_sv}+{PV.worker}/bgdb-gnomad.bin", - # f"output/full/worker/bgdb-exac-grch37-{DV.exac_cnv}+{PV.worker}/bgdb-exac.bin", - f"output/full/worker/bgdb-gnomad-exomes-cnv-grch38-{DV.gnomad_sv4}+{PV.worker}/bgdb-gnomad-exomes-cnv-grch38.bin", - f"output/full/worker/bgdb-gnomad-genomes-sv-grch38-{DV.gnomad_sv4}+{PV.worker}/bgdb-gnomad-genomes-sv-grch38.bin", - # f"output/full/worker/bgdb-g1k-grch37-{DV.g1k_svs}+{PV.worker}/bgdb-g1k.bin", - # f"output/full/worker/clinvar-strucvars-grch37-{DV.clinvar_version}+{PV.worker}/clinvar-strucvars.bin", - f"output/full/worker/clinvar-strucvars-grch38-{DV.clinvar_version}+{PV.worker}/clinvar-strucvars.bin", - # f"output/full/worker/patho-mms-grch37-{DV.patho_mms}+{PV.worker}/patho-mms.bed", - f"output/full/worker/patho-mms-grch38-{DV.patho_mms}+{PV.worker}/patho-mms.bed", - # "output/full/worker/tads-grch37-dixon2015/hesc.bed", - "output/full/worker/tads-grch38-dixon2015/hesc.bed", - # -- mehari data f"output/full/mehari/genes-xlink-{DV.today}/genes-xlink.tsv", - # f"output/full/mehari/genes-txs-grch37-{DV.mehari_tx}/mehari-data-txs-grch37-{DV.mehari_tx}.bin.zst", - f"output/full/mehari/genes-txs-grch38-{DV.mehari_tx}/mehari-data-txs-grch38-ensembl-{DV.mehari_tx}.bin.zst", - f"output/full/mehari/genes-txs-grch38-{DV.mehari_tx}/mehari-data-txs-grch38-refseq-{DV.mehari_tx}.bin.zst", - f"output/full/mehari/genes-txs-grch38-{DV.mehari_tx}/mehari-data-txs-grch38-ensembl-and-refseq-{DV.mehari_tx}.bin.zst", - # ----- HPO + # -- viguno f"output/full/viguno/hpo-{DV.hpo}+{PV.viguno}/hp.obo", f"output/full/viguno/hpo-{DV.hpo}+{PV.viguno}/phenotype.hpoa", f"output/full/viguno/hpo-{DV.hpo}+{PV.viguno}/phenotype_to_genes.txt", f"output/full/viguno/hpo-{DV.hpo}+{PV.viguno}/hpo.bin", - # ----- background/population structural variants and annotations thereof - # f"output/full/tracks/track-strucvars-dbvar-grch37-{DV.dbvar}+{DV.tracks}/dbvar.bed.gz", - f"output/full/tracks/track-strucvars-dbvar-grch38-{DV.dbvar}+{DV.tracks}/dbvar.bed.gz", - # f"output/full/tracks/track-strucvars-dgv-grch37-{DV.dgv}+{DV.tracks}/dgv.bed.gz", - f"output/full/tracks/track-strucvars-dgv-grch38-{DV.dgv}+{DV.tracks}/dgv.bed.gz", - # f"output/full/tracks/track-strucvars-dgv-gs-grch37-{DV.dgv_gs}+{DV.tracks}/dgv-gs.bed.gz", - f"output/full/tracks/track-strucvars-dgv-gs-grch38-{DV.dgv_gs}+{DV.tracks}/dgv-gs.bed.gz", - # f"output/full/tracks/track-strucvars-exac-grch37-{DV.exac_cnv}+{DV.tracks}/exac.bed.gz", - # f"output/full/tracks/track-strucvars-g1k-grch37-{DV.g1k_svs}+{DV.tracks}/g1k.bed.gz", - # f"output/full/tracks/track-strucvars-gnomad-grch37-{DV.gnomad_sv}+{DV.tracks}/gnomad.bed.gz", - f"output/full/tracks/track-strucvars-gnomad-sv-grch38-{DV.gnomad_sv4}+{DV.tracks}/gnomad-sv.bed.gz", - f"output/full/tracks/track-strucvars-gnomad-cnv-grch38-{DV.gnomad_cnv4}+{DV.tracks}/gnomad-cnv.bed.gz", - # ----- known pathogenic MMS - # f"output/full/tracks/track-strucvars-patho-mms-grch37-{DV.patho_mms}+{DV.tracks}/patho-mms.bed", - f"output/full/tracks/track-strucvars-patho-mms-grch38-{DV.patho_mms}+{DV.tracks}/patho-mms.bed", - # ----- problematic regions (rmsk, genomicSuperDups, altSeqLiftOverPsl, fixSeqLiftOverPsl) - # f"output/full/tracks/track-features-ucsc-genomicsuperdups-grch37-{DV.ucsc_genomic_super_dups_37}+{DV.tracks}/genomicSuperDups.bed.gz", - f"output/full/tracks/track-features-ucsc-genomicsuperdups-grch38-{DV.ucsc_genomic_super_dups_38}+{DV.tracks}/genomicSuperDups.bed.gz", - # f"output/full/tracks/track-features-ucsc-rmsk-grch37-{DV.ucsc_rmsk_37}+{DV.tracks}/rmsk.bed.gz", - f"output/full/tracks/track-features-ucsc-rmsk-grch38-{DV.ucsc_rmsk_38}+{DV.tracks}/rmsk.bed.gz", - # f"output/full/tracks/track-features-ucsc-altseqliftoverpsl-grch37-{DV.ucsc_alt_seq_liftover_37}+{DV.tracks}/altSeqLiftOverPsl.bed.gz", - f"output/full/tracks/track-features-ucsc-altseqliftoverpsl-grch38-{DV.ucsc_alt_seq_liftover_38}+{DV.tracks}/altSeqLiftOverPsl.bed.gz", - # f"output/full/tracks/track-features-ucsc-fixseqliftoverpsl-grch37-{DV.ucsc_fix_seq_liftover_37}+{DV.tracks}/fixSeqLiftOverPsl.bed.gz", - f"output/full/tracks/track-features-ucsc-fixseqliftoverpsl-grch38-{DV.ucsc_fix_seq_liftover_38}+{DV.tracks}/fixSeqLiftOverPsl.bed.gz", - # ----- tads - # f"output/full/tracks/track-tads-grch37-dixon2015+{DV.tracks}/hesc.bed", - f"output/full/tracks/track-tads-grch38-dixon2015+{DV.tracks}/hesc.bed", - # ----- probesets - # f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v4-grch37-{DV.tracks}.bed.gz", - f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v4-grch38-{DV.tracks}.bed.gz", - # f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v5-grch37-{DV.tracks}.bed.gz", - f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v5-grch38-{DV.tracks}.bed.gz", - # f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v6-grch37-{DV.tracks}.bed.gz", - f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v6-grch38-{DV.tracks}.bed.gz", - # f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v7-grch37-{DV.tracks}.bed.gz", - f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v7-grch38-{DV.tracks}.bed.gz", - # f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v8-grch37-{DV.tracks}.bed.gz", - f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v8-grch38-{DV.tracks}.bed.gz", - # f"output/full/tracks/track-enrichment-probesets-targets/idt-xgen-exome-research-panel-v1-grch37-{DV.tracks}.bed.gz", - f"output/full/tracks/track-enrichment-probesets-targets/idt-xgen-exome-research-panel-v1-grch38-{DV.tracks}.bed.gz", - # f"output/full/tracks/track-enrichment-probesets-targets/idt-xgen-exome-research-panel-v2-grch37-{DV.tracks}.bed.gz", - f"output/full/tracks/track-enrichment-probesets-targets/idt-xgen-exome-research-panel-v2-grch38-{DV.tracks}.bed.gz", - # f"output/full/tracks/track-enrichment-probesets-targets/twist-comprehensive-exome-grch37-{DV.tracks}.bed.gz", - f"output/full/tracks/track-enrichment-probesets-targets/twist-comprehensive-exome-grch38-{DV.tracks}.bed.gz", - # f"output/full/tracks/track-enrichment-probesets-targets/twist-core-exome-grch37-{DV.tracks}.bed.gz", - f"output/full/tracks/track-enrichment-probesets-targets/twist-core-exome-grch38-{DV.tracks}.bed.gz", - # f"output/full/tracks/track-enrichment-probesets-targets/twist-exome-v2_0-grch37-{DV.tracks}.bed.gz", - f"output/full/tracks/track-enrichment-probesets-targets/twist-exome-v2_0-grch38-{DV.tracks}.bed.gz", - # f"output/full/tracks/track-enrichment-probesets-targets/twist-refseq-exome-grch37-{DV.tracks}.bed.gz", - f"output/full/tracks/track-enrichment-probesets-targets/twist-refseq-exome-grch38-{DV.tracks}.bed.gz", - # - # == development (reduced data) directories ============================================= - # - # -- targets - # f"output/reduced-dev/targets/grch37/refseq/{DV.refseq_37}/refseq_target_exons.bed.gz", - f"output/reduced-dev/targets/grch38/refseq/{DV.refseq_38}/refseq_target_exons.bed.gz", - # -- viguno + # -- viguno (reduced dev) f"output/reduced-dev/viguno/hpo-{DV.hpo}+{PV.viguno}/hp.obo", f"output/reduced-dev/viguno/hpo-{DV.hpo}+{PV.viguno}/phenotype.hpoa", f"output/reduced-dev/viguno/hpo-{DV.hpo}+{PV.viguno}/phenotype_to_genes.txt", f"output/reduced-dev/viguno/hpo-{DV.hpo}+{PV.viguno}/hpo.bin", - # -- annonars - # f"output/reduced-dev/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY", - # f"output/reduced-dev/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/spec.yaml", - f"output/reduced-dev/annonars/cadd-grch38-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-dev/annonars/cadd-grch38-{DV.cadd}+{PV.annonars}/spec.yaml", - # f"output/reduced-dev/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/rocksdb/IDENTITY", - # f"output/reduced-dev/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/spec.yaml", - f"output/reduced-dev/annonars/cons-grch38-{DV.ucsc_cons_38}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-dev/annonars/cons-grch38-{DV.ucsc_cons_38}+{PV.annonars}/spec.yaml", - # f"output/reduced-dev/annonars/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY", - # f"output/reduced-dev/annonars/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/spec.yaml", - # f"output/reduced-dev/annonars/dbnsfp-grch37-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY", - # f"output/reduced-dev/annonars/dbnsfp-grch37-{DV.dbnsfp}c+{PV.annonars}/spec.yaml", - f"output/reduced-dev/annonars/dbnsfp-grch38-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-dev/annonars/dbnsfp-grch38-{DV.dbnsfp}a+{PV.annonars}/spec.yaml", - f"output/reduced-dev/annonars/dbnsfp-grch38-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-dev/annonars/dbnsfp-grch38-{DV.dbnsfp}c+{PV.annonars}/spec.yaml", - # f"output/reduced-dev/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY", - # f"output/reduced-dev/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/spec.yaml", - f"output/reduced-dev/annonars/dbscsnv-grch38-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-dev/annonars/dbscsnv-grch38-{DV.dbscsnv}+{PV.annonars}/spec.yaml", - # f"output/reduced-dev/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY", - # f"output/reduced-dev/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/spec.yaml", - f"output/reduced-dev/annonars/dbsnp-grch38-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-dev/annonars/dbsnp-grch38-{DV.dbsnp}+{PV.annonars}/spec.yaml", - # f"output/reduced-dev/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY", - # f"output/reduced-dev/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/spec.yaml", - f"output/reduced-dev/annonars/gnomad-exomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-dev/annonars/gnomad-exomes-grch38-{DV.gnomad_v4}+{PV.annonars}/spec.yaml", - # f"output/reduced-dev/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY", - # f"output/reduced-dev/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/spec.yaml", - f"output/reduced-dev/annonars/gnomad-genomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-dev/annonars/gnomad-genomes-grch38-{DV.gnomad_v4}+{PV.annonars}/spec.yaml", - # -- mehari - # f"output/reduced-dev/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", - # f"output/reduced-dev/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/spec.yaml", - f"output/reduced-dev/mehari/freqs-grch38-{DV.gnomad_v4}+{DV.gnomad_v4}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-dev/mehari/freqs-grch38-{DV.gnomad_v4}+{DV.gnomad_v4}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/spec.yaml", - # - # == exomes (reduced data) directories ================================================== - # - # -- targets - # f"output/reduced-exomes/targets/grch37/refseq/{DV.refseq_37}/refseq_target_exons.bed.gz", - f"output/reduced-exomes/targets/grch38/refseq/{DV.refseq_38}/refseq_target_exons.bed.gz", - # -- viguno + # -- viguno (reduced exomes) f"output/reduced-exomes/viguno/hpo-{DV.hpo}+{PV.viguno}/hp.obo", f"output/reduced-exomes/viguno/hpo-{DV.hpo}+{PV.viguno}/phenotype.hpoa", f"output/reduced-exomes/viguno/hpo-{DV.hpo}+{PV.viguno}/phenotype_to_genes.txt", f"output/reduced-exomes/viguno/hpo-{DV.hpo}+{PV.viguno}/hpo.bin", - # -- annonars - # f"output/reduced-exomes/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY", - # f"output/reduced-exomes/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/spec.yaml", - f"output/reduced-exomes/annonars/cadd-grch38-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-exomes/annonars/cadd-grch38-{DV.cadd}+{PV.annonars}/spec.yaml", - # f"output/reduced-exomes/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/rocksdb/IDENTITY", - # f"output/reduced-exomes/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/spec.yaml", - f"output/reduced-exomes/annonars/cons-grch38-{DV.ucsc_cons_38}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-exomes/annonars/cons-grch38-{DV.ucsc_cons_38}+{PV.annonars}/spec.yaml", - # f"output/reduced-exomes/annonars/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY", - # f"output/reduced-exomes/annonars/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/spec.yaml", - # f"output/reduced-exomes/annonars/dbnsfp-grch37-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY", - # f"output/reduced-exomes/annonars/dbnsfp-grch37-{DV.dbnsfp}c+{PV.annonars}/spec.yaml", - f"output/reduced-exomes/annonars/dbnsfp-grch38-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-exomes/annonars/dbnsfp-grch38-{DV.dbnsfp}a+{PV.annonars}/spec.yaml", - f"output/reduced-exomes/annonars/dbnsfp-grch38-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-exomes/annonars/dbnsfp-grch38-{DV.dbnsfp}c+{PV.annonars}/spec.yaml", - # f"output/reduced-exomes/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY", - # f"output/reduced-exomes/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/spec.yaml", - f"output/reduced-exomes/annonars/dbscsnv-grch38-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-exomes/annonars/dbscsnv-grch38-{DV.dbscsnv}+{PV.annonars}/spec.yaml", - # f"output/reduced-exomes/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY", - # f"output/reduced-exomes/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/spec.yaml", - f"output/reduced-exomes/annonars/dbsnp-grch38-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-exomes/annonars/dbsnp-grch38-{DV.dbsnp}+{PV.annonars}/spec.yaml", - # f"output/reduced-exomes/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY", - # f"output/reduced-exomes/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/spec.yaml", - f"output/reduced-exomes/annonars/gnomad-exomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-exomes/annonars/gnomad-exomes-grch38-{DV.gnomad_v4}+{PV.annonars}/spec.yaml", - # f"output/reduced-exomes/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY", - # f"output/reduced-exomes/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/spec.yaml", - f"output/reduced-exomes/annonars/gnomad-genomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-exomes/annonars/gnomad-genomes-grch38-{DV.gnomad_v4}+{PV.annonars}/spec.yaml", - # -- mehari - # f"output/reduced-exomes/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", - # f"output/reduced-exomes/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/spec.yaml", - f"output/reduced-exomes/mehari/freqs-grch38-{DV.gnomad_v4}+{DV.gnomad_v4}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", - f"output/reduced-exomes/mehari/freqs-grch38-{DV.gnomad_v4}+{DV.gnomad_v4}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/spec.yaml", + ] + +## all -- run all rules +rule all: + input: + generate_input_files + # =============================================================================================== # Modular Snakefile Includes From 761e48fb4cc39224605caee6b1574e85f95e537c Mon Sep 17 00:00:00 2001 From: Oliver Stolpe Date: Fri, 16 May 2025 09:14:09 +0200 Subject: [PATCH 04/15] fixed typos --- Snakefile | 13 +++++---- rules/work/annos/seqvars/gnomad_nuclear.smk | 32 ++++++++++----------- 2 files changed, 24 insertions(+), 21 deletions(-) diff --git a/Snakefile b/Snakefile index b11ea31..ab28f61 100644 --- a/Snakefile +++ b/Snakefile @@ -136,7 +136,7 @@ def generate_input_files(wildcards): input_files = [] if "grch38" in genomebuilds: input_files += [ - f"work/genes/clingen/{DV.today}/ClinGen_gene_curation_list_GRCh38.tsv" + f"work/genes/clingen/{DV.today}/ClinGen_gene_curation_list_GRCh38.tsv", "work/download/genes/alphamissense/1/AlphaMissense_gene_hg38.tsv.gz", f"work/download/annos/grch38/seqvars/cadd/{DV.cadd}/whole_genome_SNVs_inclAnno.tsv.gz", f"work/download/annos/grch38/seqvars/cadd/{DV.cadd}/gnomad.genomes.r3.0.indel_inclAnno.tsv.gz", @@ -183,7 +183,7 @@ def generate_input_files(wildcards): input_files += [ # -- mehari data # ---- frequencies (via annonars) - f"output/full/mehari/freqs-{genomebuild}-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", + f"output/full/mehari/freqs-{genomebuild}-{gnomad_versions[genomebuild]}+{gnomad_versions[genomebuild]}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY", f"output/full/annonars/alphamissense-{genomebuild}-{DV.alphamissense}+{PV.annonars}/rocksdb/IDENTITY", # -- annonars data # ----- sequence variant annotations @@ -200,7 +200,7 @@ def generate_input_files(wildcards): f"output/full/annonars/gnomad-sv-genomes-{genomebuild}-{gnomad_sv_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY", # ----- sequence annotation f"output/full/annonars/functional-{genomebuild}-{refseq_fe_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY", - f"output/full/annonars/regions-{genomebuid}-{DV.today}+{PV.annonars}/rocksdb/IDENTITY", + f"output/full/annonars/regions-{genomebuild}-{DV.today}+{PV.annonars}/rocksdb/IDENTITY", # ----- conservation f"output/full/annonars/cons-{genomebuild}-{cons_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY", # ----- worker @@ -213,7 +213,9 @@ def generate_input_files(wildcards): f"output/full/worker/patho-mms-{genomebuild}-{DV.patho_mms}+{PV.worker}/patho-mms.bed", f"output/full/worker/tads-{genomebuild}-dixon2015/hesc.bed", # -- mehari data - f"output/full/mehari/genes-txs-{genomebuild}-{DV.mehari_tx}/mehari-data-txs-{genomebuild}-{DV.mehari_tx}.bin.zst", + f"output/full/mehari/genes-txs-{genomebuild}-{DV.mehari_tx}/mehari-data-txs-{genomebuild}-ensembl-{DV.mehari_tx}.bin.zst", + f"output/full/mehari/genes-txs-{genomebuild}-{DV.mehari_tx}/mehari-data-txs-{genomebuild}-refseq-{DV.mehari_tx}.bin.zst", + f"output/full/mehari/genes-txs-{genomebuild}-{DV.mehari_tx}/mehari-data-txs-{genomebuild}-ensembl-and-refseq-{DV.mehari_tx}.bin.zst", f"output/full/tracks/track-strucvars-dbvar-{genomebuild}-{DV.dbvar}+{DV.tracks}/dbvar.bed.gz", f"output/full/tracks/track-strucvars-dgv-{genomebuild}-{DV.dgv}+{DV.tracks}/dgv.bed.gz", f"output/full/tracks/track-strucvars-dgv-gs-{genomebuild}-{DV.dgv_gs}+{DV.tracks}/dgv-gs.bed.gz", @@ -221,7 +223,7 @@ def generate_input_files(wildcards): f"output/full/tracks/track-strucvars-patho-mms-{genomebuild}-{DV.patho_mms}+{DV.tracks}/patho-mms.bed", # ----- problematic regions (rmsk, genomicSuperDups, altSeqLiftOverPsl, fixSeqLiftOverPsl) f"output/full/tracks/track-features-ucsc-genomicsuperdups-{genomebuild}-{genomic_super_dups_versions[genomebuild]}+{DV.tracks}/genomicSuperDups.bed.gz", - f"output/full/tracks/track-features-ucsc-rmsk-{genomebuild}-{rmask_version[genomebuild]}+{DV.tracks}/rmsk.bed.gz", + f"output/full/tracks/track-features-ucsc-rmsk-{genomebuild}-{rmask_versions[genomebuild]}+{DV.tracks}/rmsk.bed.gz", f"output/full/tracks/track-features-ucsc-altseqliftoverpsl-{genomebuild}-{lift_over_versions[genomebuild]}+{DV.tracks}/altSeqLiftOverPsl.bed.gz", f"output/full/tracks/track-features-ucsc-fixseqliftoverpsl-{genomebuild}-{lift_over_fix_versions[genomebuild]}+{DV.tracks}/fixSeqLiftOverPsl.bed.gz", # ----- tads @@ -334,6 +336,7 @@ def generate_input_files(wildcards): f"output/reduced-exomes/viguno/hpo-{DV.hpo}+{PV.viguno}/phenotype_to_genes.txt", f"output/reduced-exomes/viguno/hpo-{DV.hpo}+{PV.viguno}/hpo.bin", ] + return input_files ## all -- run all rules diff --git a/rules/work/annos/seqvars/gnomad_nuclear.smk b/rules/work/annos/seqvars/gnomad_nuclear.smk index 716e0bb..844fe8f 100644 --- a/rules/work/annos/seqvars/gnomad_nuclear.smk +++ b/rules/work/annos/seqvars/gnomad_nuclear.smk @@ -111,22 +111,22 @@ def input_annos_gnomad_nuclear_grch37(wildcards): def input_annos_gnomad_nuclear_grch38(wildcards): """Input files for gnomAD exomes/genomes GRCh38.""" chroms = list(range(1, 23)) + ["X", "Y"] - if wildcards.version == DV.gnomad_v4: - tpl = "work/download/annos/grch38/seqvars/gnomad_{kind}/{version}/gnomad.{kind}.v{version}.sites.chr{chrom}.vcf.bgz" - return [tpl.format(chrom=chrom, **wildcards) for chrom in chroms] - else: - if wildcards.kind == "exomes": - tpl = "work/download/annos/grch38/seqvars/gnomad_{kind}/{version}/gnomad.{kind}.r{version}.sites.{chrom}.liftover_grch38.vcf.bgz" - return [ - tpl.format(kind=wildcards.kind, version=DV.gnomad_v2, chrom=chrom) - for chrom in chroms - ] - else: - tpl = "work/download/annos/grch38/seqvars/gnomad_{kind}/{version}/gnomad.{kind}.v{version}.sites.chr{chrom}.vcf.bgz" - return [ - tpl.format(kind=wildcards.kind, version=DV.gnomad_v3, chrom=chrom) - for chrom in chroms - ] + #if wildcards.version == DV.gnomad_v4: + tpl = "work/download/annos/grch38/seqvars/gnomad_{kind}/{version}/gnomad.{kind}.v{version}.sites.chr{chrom}.vcf.bgz" + return [tpl.format(chrom=chrom, **wildcards) for chrom in chroms] +# else: +# if wildcards.kind == "exomes": +# tpl = "work/download/annos/grch38/seqvars/gnomad_{kind}/{version}/gnomad.{kind}.r{version}.sites.{chrom}.liftover_grch38.vcf.bgz" +# return [ +# tpl.format(kind=wildcards.kind, version=DV.gnomad_v2, chrom=chrom) +# for chrom in chroms +# ] +# else: +# tpl = "work/download/annos/grch38/seqvars/gnomad_{kind}/{version}/gnomad.{kind}.v{version}.sites.chr{chrom}.vcf.bgz" +# return [ +# tpl.format(kind=wildcards.kind, version=DV.gnomad_v3, chrom=chrom) +# for chrom in chroms +# ] rule annos_seqvars_gnomad_nuclear_grch37: # -- collect gnomAD exomes/genomes for GRCh37 From dad659e1a1b88cc9002184190a8f70e1cf8d5703 Mon Sep 17 00:00:00 2001 From: Oliver Stolpe Date: Mon, 16 Jun 2025 08:44:05 +0200 Subject: [PATCH 05/15] formatting --- Snakefile | 6 ++---- download_urls.yml | 6 +++--- rules/output/annonars/cadd.smk | 2 +- rules/output/annonars/cons.smk | 2 +- rules/output/annonars/dbnsfp.smk | 2 +- rules/output/annonars/dbscsnv.smk | 2 +- rules/output/annonars/gnomad_exomes.smk | 2 +- rules/output/annonars/gnomad_genomes.smk | 2 +- rules/output/annonars/gnomad_mtdna.smk | 2 +- rules/output/annonars/gnomad_sv.smk | 8 ++++---- rules/output/mehari/freqs.smk | 2 +- rules/output/viguno/hpo.smk | 1 - rules/reduced/annonars.smk | 2 +- rules/reduced/mehari.smk | 2 +- rules/work/annos/seqvars/gnomad_nuclear.smk | 4 +++- varfish_db_downloader/versions.py | 6 +++--- 16 files changed, 25 insertions(+), 26 deletions(-) diff --git a/Snakefile b/Snakefile index ab28f61..203139e 100644 --- a/Snakefile +++ b/Snakefile @@ -152,7 +152,6 @@ def generate_input_files(wildcards): # ----- background/population structural variants and annotations thereof f"output/full/tracks/track-strucvars-gnomad-sv-grch38-{DV.gnomad_sv4}+{DV.tracks}/gnomad-sv.bed.gz", f"output/full/tracks/track-strucvars-gnomad-cnv-grch38-{DV.gnomad_cnv4}+{DV.tracks}/gnomad-cnv.bed.gz", - ] if "grch37" in genomebuilds: input_files += [ @@ -177,7 +176,6 @@ def generate_input_files(wildcards): f"output/full/tracks/track-strucvars-exac-grch37-{DV.exac_cnv}+{DV.tracks}/exac.bed.gz", f"output/full/tracks/track-strucvars-g1k-grch37-{DV.g1k_svs}+{DV.tracks}/g1k.bed.gz", f"output/full/tracks/track-strucvars-gnomad-grch37-{DV.gnomad_sv}+{DV.tracks}/gnomad.bed.gz", - ] for genomebuild in genomebuilds: input_files += [ @@ -342,8 +340,8 @@ def generate_input_files(wildcards): ## all -- run all rules rule all: input: - generate_input_files - + generate_input_files, + # =============================================================================================== # Modular Snakefile Includes diff --git a/download_urls.yml b/download_urls.yml index 1fc9868..3cdd072 100644 --- a/download_urls.yml +++ b/download_urls.yml @@ -57,16 +57,16 @@ count: null # dbNSFP v4.5a -- url: https://dbnsfp.s3.amazonaws.com/dbNSFP4.5a.zip +- url: https://usf.box.com/shared/static/2hzcx5s6p1xui7oen16xqzndfrkt8l9l excerpt_strategy: strategy: manual count: null # dbNSFP v4.5c -- url: https://dbnsfp.s3.amazonaws.com/dbNSFP4.5c.zip +- url: https://usf.box.com/shared/static/03xsrpna0nzgrytfo2pzk326t8jad4oc excerpt_strategy: strategy: manual count: null -- url: ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/dbscSNV1.1.zip +- url: https://usf.box.com/shared/static/ffwlywsat3q5ijypvunno3rg6steqfs8 skip_upstream_check: true # does not work reliably in tests excerpt_strategy: strategy: manual diff --git a/rules/output/annonars/cadd.smk b/rules/output/annonars/cadd.smk index 110bd22..9c649bb 100644 --- a/rules/output/annonars/cadd.smk +++ b/rules/output/annonars/cadd.smk @@ -57,7 +57,7 @@ rule output_annonars_cadd: # -- build CADD RocksDB with annonars threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb=MEMORY + mem_mb=MEMORY, wildcard_constraints: genome_release=RE_GENOME, v_cadd=RE_VERSION, diff --git a/rules/output/annonars/cons.smk b/rules/output/annonars/cons.smk index 8c02d2d..54e1bb1 100644 --- a/rules/output/annonars/cons.smk +++ b/rules/output/annonars/cons.smk @@ -15,7 +15,7 @@ rule output_annonars_cons: # -- build UCSC conservation track RocksDB with anno threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb=MEMORY + mem_mb=MEMORY, wildcard_constraints: genome_release=RE_GENOME, v_cons=RE_VERSION, diff --git a/rules/output/annonars/dbnsfp.smk b/rules/output/annonars/dbnsfp.smk index 7208417..5438686 100644 --- a/rules/output/annonars/dbnsfp.smk +++ b/rules/output/annonars/dbnsfp.smk @@ -22,7 +22,7 @@ rule output_annonars_dbnsfp: # -- build dbNSFP RocksDB with annonars threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb=MEMORY + mem_mb=MEMORY, wildcard_constraints: genome_release=RE_GENOME, v_dbnsfp=RE_VERSION, diff --git a/rules/output/annonars/dbscsnv.smk b/rules/output/annonars/dbscsnv.smk index aa76ccf..33350ee 100644 --- a/rules/output/annonars/dbscsnv.smk +++ b/rules/output/annonars/dbscsnv.smk @@ -24,7 +24,7 @@ rule output_annonars_dbscsnv: # -- build dbscSNV RocksDB with annonars threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb=MEMORY + mem_mb=MEMORY, wildcard_constraints: genome_release=RE_GENOME, v_dbscsnv=RE_VERSION, diff --git a/rules/output/annonars/gnomad_exomes.smk b/rules/output/annonars/gnomad_exomes.smk index dc385db..deb147a 100644 --- a/rules/output/annonars/gnomad_exomes.smk +++ b/rules/output/annonars/gnomad_exomes.smk @@ -19,7 +19,7 @@ rule output_annonars_gnomad_exomes: # -- build gnomAD-exomes RocksDB with annon threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb=MEMORY + mem_mb=MEMORY, wildcard_constraints: genome_release=RE_GENOME, v_gnomad=RE_VERSION, diff --git a/rules/output/annonars/gnomad_genomes.smk b/rules/output/annonars/gnomad_genomes.smk index 059ab4b..1b885ca 100644 --- a/rules/output/annonars/gnomad_genomes.smk +++ b/rules/output/annonars/gnomad_genomes.smk @@ -19,7 +19,7 @@ rule output_annonars_gnomad_genomes: # -- build gnomAD-genomes RocksDB with ann threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb=MEMORY + mem_mb=MEMORY, wildcard_constraints: genome_release=RE_GENOME, v_gnomad=RE_VERSION, diff --git a/rules/output/annonars/gnomad_mtdna.smk b/rules/output/annonars/gnomad_mtdna.smk index 6263e03..e9059ac 100644 --- a/rules/output/annonars/gnomad_mtdna.smk +++ b/rules/output/annonars/gnomad_mtdna.smk @@ -19,7 +19,7 @@ rule output_annonars_gnomad_mtdna: # -- build gnomAD-mtDNA RocksDB with annonar threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb=MEMORY + mem_mb=MEMORY, wildcard_constraints: genome_release=RE_GENOME, v_gnomad=RE_VERSION, diff --git a/rules/output/annonars/gnomad_sv.smk b/rules/output/annonars/gnomad_sv.smk index b757830..33e2d24 100644 --- a/rules/output/annonars/gnomad_sv.smk +++ b/rules/output/annonars/gnomad_sv.smk @@ -18,7 +18,7 @@ rule output_annonars_gnomad_sv_grch37_exac: # -- build gnomAD-SV RocksDB with a threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb=MEMORY + mem_mb=MEMORY, wildcard_constraints: v_gnomad=RE_VERSION, v_annonars=RE_VERSION, @@ -73,7 +73,7 @@ rule output_annonars_gnomad_sv_grch37_gnomad_sv2: # -- build gnomAD-SV RocksDB threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb=MEMORY + mem_mb=MEMORY, wildcard_constraints: v_gnomad=RE_VERSION, v_annonars=RE_VERSION, @@ -126,7 +126,7 @@ rule output_annonars_gnomad_sv_grch38_gnomad_cnv4: # -- build gnomAD-SV RocksDB threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb=MEMORY + mem_mb=MEMORY, wildcard_constraints: v_gnomad=RE_VERSION, v_annonars=RE_VERSION, @@ -178,7 +178,7 @@ rule output_annonars_gnomad_sv_grch38_gnomad_sv4: # -- build gnomAD-SV RocksDB threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb=MEMORY + mem_mb=MEMORY, wildcard_constraints: genome_release=RE_GENOME, v_gnomad=RE_VERSION, diff --git a/rules/output/mehari/freqs.smk b/rules/output/mehari/freqs.smk index 0e1dc25..7c112e3 100644 --- a/rules/output/mehari/freqs.smk +++ b/rules/output/mehari/freqs.smk @@ -25,7 +25,7 @@ rule output_mehari_freqs_build: # -- build frequency tables for mehari threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb=MEMORY + mem_mb=MEMORY, wildcard_constraints: genome_release=RE_GENOME, v_gnomad_genomes=RE_VERSION, diff --git a/rules/output/viguno/hpo.smk b/rules/output/viguno/hpo.smk index 0937520..8ebce33 100644 --- a/rules/output/viguno/hpo.smk +++ b/rules/output/viguno/hpo.smk @@ -3,7 +3,6 @@ import os - rule output_viguno_pheno: # -- copy HPO input: obo="work/download/hpo/{v_hpo}/hp.obo", diff --git a/rules/reduced/annonars.smk b/rules/reduced/annonars.smk index 4f70c80..2069b18 100644 --- a/rules/reduced/annonars.smk +++ b/rules/reduced/annonars.smk @@ -41,7 +41,7 @@ rule subset_annonars: # -- create exomes subset threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb=MEMORY + mem_mb=MEMORY, shell: r""" annonars db-utils copy \ diff --git a/rules/reduced/mehari.smk b/rules/reduced/mehari.smk index 26cffe4..b523da0 100644 --- a/rules/reduced/mehari.smk +++ b/rules/reduced/mehari.smk @@ -40,7 +40,7 @@ rule subset_mehari: # -- create exomes subset threads: THREADS resources: runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"), - mem_mb=MEMORY + mem_mb=MEMORY, shell: r""" annonars db-utils copy \ diff --git a/rules/work/annos/seqvars/gnomad_nuclear.smk b/rules/work/annos/seqvars/gnomad_nuclear.smk index 844fe8f..cab5a8c 100644 --- a/rules/work/annos/seqvars/gnomad_nuclear.smk +++ b/rules/work/annos/seqvars/gnomad_nuclear.smk @@ -111,9 +111,11 @@ def input_annos_gnomad_nuclear_grch37(wildcards): def input_annos_gnomad_nuclear_grch38(wildcards): """Input files for gnomAD exomes/genomes GRCh38.""" chroms = list(range(1, 23)) + ["X", "Y"] - #if wildcards.version == DV.gnomad_v4: + # if wildcards.version == DV.gnomad_v4: tpl = "work/download/annos/grch38/seqvars/gnomad_{kind}/{version}/gnomad.{kind}.v{version}.sites.chr{chrom}.vcf.bgz" return [tpl.format(chrom=chrom, **wildcards) for chrom in chroms] + + # else: # if wildcards.kind == "exomes": # tpl = "work/download/annos/grch38/seqvars/gnomad_{kind}/{version}/gnomad.{kind}.r{version}.sites.{chrom}.liftover_grch38.vcf.bgz" diff --git a/varfish_db_downloader/versions.py b/varfish_db_downloader/versions.py index 4d218ec..b4df3eb 100644 --- a/varfish_db_downloader/versions.py +++ b/varfish_db_downloader/versions.py @@ -127,10 +127,10 @@ class DataVersions: clingen_gene=TODAY, clingen_variant=TODAY, ensembl_37="87", - ensembl_38="112", # keep at 112 for consistency with mehari - ensembl="112", # keep at 112 for consistency with mehari + ensembl_38="112", # keep at 112 for consistency with mehari + ensembl="112", # keep at 112 for consistency with mehari today=TODAY, - dbnsfp="4.5", # update to 4.9 or 5.1 ? + dbnsfp="4.5", # update to 4.9 or 5.1 ? dbscsnv="1.1", cadd="1.6", gnomad_constraints="4.1", From 364adfdf8e97f6fbb54db8e9b8047c13c20cb9ee Mon Sep 17 00:00:00 2001 From: Oliver Stolpe Date: Mon, 16 Jun 2025 09:55:37 +0200 Subject: [PATCH 06/15] Genomebuilds as env variable --- Snakefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Snakefile b/Snakefile index 203139e..dcc4815 100644 --- a/Snakefile +++ b/Snakefile @@ -40,7 +40,7 @@ DEV_GENE_SYMBOLS = "|".join( # Padding to add to exons in dev and exons mode. EXON_PADDING = 200 -GENOMEBUILDS = ["grch37", "grch38"] +GENOMEBUILDS = os.environ.get("GENOMEBUILDS", "grch37,grch38").split(",") # Define number of threads for resource-intensive tasks THREADS = int(os.environ.get("THREADS", "32")) From 131cd2aa418c780b7ff2c65237e36d47bcadc929 Mon Sep 17 00:00:00 2001 From: Oliver Stolpe Date: Mon, 16 Jun 2025 09:57:47 +0200 Subject: [PATCH 07/15] remove wildcards from input files function --- Snakefile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Snakefile b/Snakefile index dcc4815..f10c440 100644 --- a/Snakefile +++ b/Snakefile @@ -87,7 +87,7 @@ rule help: ) -def generate_input_files(wildcards): +def generate_input_files(): """ Helper function to return the input files for the rules. """ @@ -340,7 +340,7 @@ def generate_input_files(wildcards): ## all -- run all rules rule all: input: - generate_input_files, + generate_input_files(), # =============================================================================================== From c9454904789ad52903e9937d91bb99471349e4e0 Mon Sep 17 00:00:00 2001 From: Oliver Stolpe Date: Mon, 16 Jun 2025 10:19:14 +0200 Subject: [PATCH 08/15] removed call to annonars installation script from github workflow --- .github/workflows/main.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index c209623..c5dfc33 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -80,9 +80,6 @@ jobs: unzip qsv-0.112.0-x86_64-unknown-linux-musl.zip cp qsv_musl-1.2.3 /usr/local/bin/qsv - - name: Install annonars - run: | - sudo bash ./utils/install-annonars.sh - name: Install python package run: | pip install -e . From d5c819a31eea1f6ff4bd05e05702db5a4b12f688 Mon Sep 17 00:00:00 2001 From: Oliver Stolpe Date: Mon, 16 Jun 2025 10:25:44 +0200 Subject: [PATCH 09/15] updated download_urls --- download_urls.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/download_urls.yml b/download_urls.yml index 3cdd072..b18905c 100644 --- a/download_urls.yml +++ b/download_urls.yml @@ -141,7 +141,7 @@ url: https://search.clinicalgenome.org/kb/reports/curation-activity-summary-report skip_upstream_check: true # does not work reliably in tests -- url: https://github.com/varfish-org/clinvar-data-jsonl/releases/download/clinvar-weekly-20240612/clinvar-data-extract-vars-20240612+0.17.0.tar.gz +- url: https://github.com/varfish-org/clinvar-data-jsonl/releases/download/clinvar-weekly-20250410/clinvar-data-extract-vars-20250410+0.18.5.tar.gz excerpt_strategy: strategy: manual count: null From 9cefbe30fa72aae62699b38a9cad7d4fa5cd009b Mon Sep 17 00:00:00 2001 From: Oliver Stolpe Date: Mon, 16 Jun 2025 13:53:57 +0200 Subject: [PATCH 10/15] Updated excerpt-data --- download_urls.yml | 24 +++++++-- ...hari-data-txs-GRCh37-refseq-0.10.3.bin.zst | 3 ++ excerpt-data/0ccc4915e7ecfd38/url.txt | 3 ++ excerpt-data/111d8c6e08038f62/20 | 2 +- ...hari-data-txs-GRCh38-refseq-0.10.3.bin.zst | 3 ++ excerpt-data/18c67f3b60f24667/url.txt | 3 ++ .../1963f3c58ea066be/omim_unmapped_terms.tsv | 4 +- ...ari-data-txs-GRCh37-ensembl-0.10.3.bin.zst | 3 ++ excerpt-data/5bcb7090fe0e881b/url.txt | 3 ++ excerpt-data/615312ce3f5fc1bf/OMIMinDO.tsv | 4 +- .../617bebe58c82f24e/CTD_diseases.tsv.gz | 4 +- ...ari-data-txs-GRCh38-ensembl-0.10.3.bin.zst | 3 ++ excerpt-data/649dbe83da5f50d9/url.txt | 3 ++ excerpt-data/652646c24140df2a/mondo.obo | 4 +- excerpt-data/6f378db589a4bbb9/orphacodes | 4 +- excerpt-data/91f964d1aa8367a5/20 | 4 +- excerpt-data/b31e9b26b7aeae3f/dbNSFP4.5c.zip | 3 ++ excerpt-data/b31e9b26b7aeae3f/url.txt | 3 ++ ...r-data-extract-vars-20240612+0.17.0.tar.gz | 3 -- excerpt-data/bdc69c1e4cafdfaa/url.txt | 3 -- excerpt-data/c243f918f5fc10d2/dbNSFP4.5a.zip | 3 ++ excerpt-data/c243f918f5fc10d2/url.txt | 3 ++ excerpt-data/c9c7d6df0e24b954/__index__ | 4 +- ...r-data-extract-vars-20250410+0.18.5.tar.gz | 3 ++ excerpt-data/caba5539b2dac784/url.txt | 3 ++ excerpt-data/cbc00fe1a5b22fe8/dbscSNV1.1.zip | 3 ++ excerpt-data/cbc00fe1a5b22fe8/url.txt | 3 ++ excerpt-data/cdaaf7a3f7595d3d/__index__ | 4 +- .../e8a29ff831bf8ee3/hgnc_complete_set.json | 3 ++ excerpt-data/e8a29ff831bf8ee3/url.txt | 3 ++ excerpt-data/ebc07f725c64907d/__index__ | 4 +- varfish_db_downloader/wget.py | 51 ++++++++++++++++++- 32 files changed, 143 insertions(+), 30 deletions(-) create mode 100644 excerpt-data/0ccc4915e7ecfd38/mehari-data-txs-GRCh37-refseq-0.10.3.bin.zst create mode 100644 excerpt-data/0ccc4915e7ecfd38/url.txt create mode 100644 excerpt-data/18c67f3b60f24667/mehari-data-txs-GRCh38-refseq-0.10.3.bin.zst create mode 100644 excerpt-data/18c67f3b60f24667/url.txt create mode 100644 excerpt-data/5bcb7090fe0e881b/mehari-data-txs-GRCh37-ensembl-0.10.3.bin.zst create mode 100644 excerpt-data/5bcb7090fe0e881b/url.txt create mode 100644 excerpt-data/649dbe83da5f50d9/mehari-data-txs-GRCh38-ensembl-0.10.3.bin.zst create mode 100644 excerpt-data/649dbe83da5f50d9/url.txt create mode 100644 excerpt-data/b31e9b26b7aeae3f/dbNSFP4.5c.zip create mode 100644 excerpt-data/b31e9b26b7aeae3f/url.txt delete mode 100644 excerpt-data/bdc69c1e4cafdfaa/clinvar-data-extract-vars-20240612+0.17.0.tar.gz delete mode 100644 excerpt-data/bdc69c1e4cafdfaa/url.txt create mode 100644 excerpt-data/c243f918f5fc10d2/dbNSFP4.5a.zip create mode 100644 excerpt-data/c243f918f5fc10d2/url.txt create mode 100644 excerpt-data/caba5539b2dac784/clinvar-data-extract-vars-20250410+0.18.5.tar.gz create mode 100644 excerpt-data/caba5539b2dac784/url.txt create mode 100644 excerpt-data/cbc00fe1a5b22fe8/dbscSNV1.1.zip create mode 100644 excerpt-data/cbc00fe1a5b22fe8/url.txt create mode 100644 excerpt-data/e8a29ff831bf8ee3/hgnc_complete_set.json create mode 100644 excerpt-data/e8a29ff831bf8ee3/url.txt diff --git a/download_urls.yml b/download_urls.yml index b18905c..bb8cc9a 100644 --- a/download_urls.yml +++ b/download_urls.yml @@ -146,11 +146,29 @@ strategy: manual count: null -- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.4.4/mehari-data-txs-grch37-0.4.4.bin.zst +- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.10.3/mehari-data-txs-grch37-ensembl-0.10.3.bin.zst excerpt_strategy: strategy: no-excerpt count: null -- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.4.4/mehari-data-txs-grch38-0.4.4.bin.zst +- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.10.3/mehari-data-txs-grch38-ensembl-0.10.3.bin.zst + excerpt_strategy: + strategy: no-excerpt + count: null + +- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.10.3/mehari-data-txs-grch37-refseq-0.10.3.bin.zst + excerpt_strategy: + strategy: no-excerpt + count: null +- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.10.3/mehari-data-txs-grch38-refseq-0.10.3.bin.zst + excerpt_strategy: + strategy: no-excerpt + count: null + +- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.10.3/mehari-data-txs-grch37-ensembl-0.10.3.bin.zst + excerpt_strategy: + strategy: no-excerpt + count: null +- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.10.3/mehari-data-txs-grch38-ensembl-0.10.3.bin.zst excerpt_strategy: strategy: no-excerpt count: null @@ -251,7 +269,7 @@ count: 10000 - url: 'https://ensembl.org/biomart/martservice?query=' -- url: 'https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/json/hgnc_complete_set.json' +- url: 'https://storage.googleapis.com/public-download-files/hgnc/json/json/hgnc_complete_set.json' skip_upstream_check: true # does not work reliably in tests excerpt_strategy: strategy: manual diff --git 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b/excerpt-data/cdaaf7a3f7595d3d/__index__ @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:81847a00717aad78c26fcb09ab10c918ef8e8b0eba906f8b4beef24a91f4435c -size 195929 +oid sha256:b932e864cb21c39b62c5411cb840cb5ac4eaa4372080d10e37bd873d4a1b845d +size 176154 diff --git a/excerpt-data/e8a29ff831bf8ee3/hgnc_complete_set.json b/excerpt-data/e8a29ff831bf8ee3/hgnc_complete_set.json new file mode 100644 index 0000000..e146a71 --- /dev/null +++ b/excerpt-data/e8a29ff831bf8ee3/hgnc_complete_set.json @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:bfdbaca4349812edcede853187fb1cb6a3352d88a4c75ff33ddb53dbecc806a3 +size 33317552 diff --git a/excerpt-data/e8a29ff831bf8ee3/url.txt b/excerpt-data/e8a29ff831bf8ee3/url.txt new file mode 100644 index 0000000..c0e8825 --- /dev/null +++ b/excerpt-data/e8a29ff831bf8ee3/url.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8d1f15c8d6abcf3cc3a9a3e634ff8c1acff07ab1663ac81c377c33234a6f61ef +size 91 diff --git a/excerpt-data/ebc07f725c64907d/__index__ b/excerpt-data/ebc07f725c64907d/__index__ index bc93c8d..5742f2d 100644 --- a/excerpt-data/ebc07f725c64907d/__index__ +++ b/excerpt-data/ebc07f725c64907d/__index__ @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:afedd3471ced3f34cc5be50a98cfcb078f344e7330095ceb5b80ce0849edf48a -size 160540 +oid sha256:afd2cfec71a12eb675a2f6407b735007ab31ff123c944e157150adfdb00724a9 +size 180015 diff --git a/varfish_db_downloader/wget.py b/varfish_db_downloader/wget.py index 36cb659..ede13ec 100644 --- a/varfish_db_downloader/wget.py +++ b/varfish_db_downloader/wget.py @@ -1,5 +1,6 @@ """Implementation of the stub ``wget`` and supporting tool.""" +import cgi import gzip import hashlib import itertools @@ -11,6 +12,7 @@ import typing import urllib.parse import zlib +from urllib.parse import urlparse import attrs import cattrs @@ -21,6 +23,50 @@ from loguru import logger +def get_filename_from_url(url: str) -> str | None: + """ + Extracts the filename from a URL. + + First, it tries to get the filename from the 'Content-Disposition' header. + If not found, it falls back to parsing the URL path. + + Args: + url: The URL of the file to inspect. + + Returns: + The detected filename as a string, or None if an error occurs + or no filename can be found. + """ + try: + # We use stream=True to avoid downloading the file content + with requests.get(url, allow_redirects=True, stream=True) as response: + # Raise an exception for bad status codes (4xx or 5xx) + response.raise_for_status() + + # 1. Check for Content-Disposition header + content_disposition = response.headers.get("content-disposition") + if content_disposition: + # Parse the header to extract the filename + _, params = cgi.parse_header(content_disposition) + if "filename" in params: + return params["filename"] + + # 2. If no header, fall back to the URL path + path = urllib.parse.urlparse( + response.url + ).path # Use response.url to get the final URL after redirects + filename = os.path.basename(path) + if filename: + return filename + + except requests.exceptions.RequestException as e: + print(f"Error fetching URL: {e}") + return None + + # 3. If all else fails + return None + + def excerpt_manual(url: str, path_out: str, count: int): """Do not download, assume output is already there.""" _ = url @@ -233,8 +279,9 @@ def download_excerpt(url: UrlEntry, data_dir: str, force: bool): print(url.url, file=f) excerpt_fun = STRATEGY_MAP[url.excerpt_strategy.strategy] - parsed = urllib.parse.urlparse(url.url) - basename = parsed.path.split("/")[-1] or "__index__" + # parsed = urllib.parse.urlparse(url.url) + # basename = parsed.path.split("/")[-1] or "__index__" + basename = get_filename_from_url(url.url) or "__index__" out_path_data = str(out_path / basename) logger.info(" getting excerpt to {}", out_path_data) excerpt_fun(url.url, str(out_path_data), url.excerpt_strategy.count) From c593d4f1b89295205aecf4a1fbc873e1605c5c3c Mon Sep 17 00:00:00 2001 From: Oliver Stolpe Date: Mon, 16 Jun 2025 14:03:38 +0200 Subject: [PATCH 11/15] Removing unneccessary import --- varfish_db_downloader/wget.py | 1 - 1 file changed, 1 deletion(-) diff --git a/varfish_db_downloader/wget.py b/varfish_db_downloader/wget.py index ede13ec..19a65f0 100644 --- a/varfish_db_downloader/wget.py +++ b/varfish_db_downloader/wget.py @@ -12,7 +12,6 @@ import typing import urllib.parse import zlib -from urllib.parse import urlparse import attrs import cattrs From 50dd1b7de5aa2500b0a73edb59d5b1d4e84b7b8f Mon Sep 17 00:00:00 2001 From: Oliver Stolpe Date: Mon, 16 Jun 2025 14:17:05 +0200 Subject: [PATCH 12/15] formatting and minor fixes --- rules/work/annos/seqvars/dbnsfp.smk | 10 +++++----- varfish_db_downloader/wget.py | 5 +---- 2 files changed, 6 insertions(+), 9 deletions(-) diff --git a/rules/work/annos/seqvars/dbnsfp.smk b/rules/work/annos/seqvars/dbnsfp.smk index 0bdd398..c27b2b5 100644 --- a/rules/work/annos/seqvars/dbnsfp.smk +++ b/rules/work/annos/seqvars/dbnsfp.smk @@ -57,11 +57,11 @@ rule annos_seqvars_dbnsfp_download: # -- download dbNSFP ZIP file url_a=https://usf.box.com/shared/static/2hzcx5s6p1xui7oen16xqzndfrkt8l9l url_c=https://usf.box.com/shared/static/03xsrpna0nzgrytfo2pzk326t8jad4oc - if [[ "{wildcards.variant}" == "a" ]]; then - url=$url_a - else - url=$url_c - fi + case "{wildcards.variant}" in + a) url=$url_a ;; + c) url=$url_c ;; + *) echo "Unsupported dbNSFP variant '{wildcards.variant}'" >&2; exit 1 ;; + esac aria2c \ --check-certificate=false \ diff --git a/varfish_db_downloader/wget.py b/varfish_db_downloader/wget.py index 19a65f0..73872a4 100644 --- a/varfish_db_downloader/wget.py +++ b/varfish_db_downloader/wget.py @@ -278,8 +278,6 @@ def download_excerpt(url: UrlEntry, data_dir: str, force: bool): print(url.url, file=f) excerpt_fun = STRATEGY_MAP[url.excerpt_strategy.strategy] - # parsed = urllib.parse.urlparse(url.url) - # basename = parsed.path.split("/")[-1] or "__index__" basename = get_filename_from_url(url.url) or "__index__" out_path_data = str(out_path / basename) logger.info(" getting excerpt to {}", out_path_data) @@ -292,8 +290,7 @@ def copy_excerpt(url: UrlEntry, data_dir: str, output_document: str): """Copy downloaded excerpt to output file.""" logger.info(" copying excerpt for {} to {}", url.url, output_document) in_path = pathlib.Path(data_dir) / url.hash - parsed = urllib.parse.urlparse(url.url) - basename = parsed.path.split("/")[-1] + basename = get_filename_from_url(url.url) or "__index__" excerpt_path = in_path / basename click.echo(err=True, message="copying {} => {}".format(excerpt_path, output_document)) if os.path.isdir(excerpt_path): From 7e8ffcc6ecbec69403f0d4a0be0898f3cf6ef70d Mon Sep 17 00:00:00 2001 From: Oliver Stolpe Date: Tue, 17 Jun 2025 08:35:17 +0200 Subject: [PATCH 13/15] Re-created file excerpts --- download_urls.yml | 34 ++++++++++++------- .../gnomad.exomes.v4.0.sites.chr13.vcf.bgz | 3 -- ...gnomad.exomes.v4.0.sites.chr13.vcf.bgz.tbi | 3 -- excerpt-data/0106e2c5435e5972/url.txt | 3 -- .../gnomad.exomes.r2.1.1.sites.5.vcf.bgz.tbi | 4 +-- .../03531c89f88e4ce8/genes_to_phenotype.txt | 3 ++ excerpt-data/03531c89f88e4ce8/url.txt | 3 ++ .../gnomad.genomes.v4.0.sites.chr1.vcf.bgz | 3 -- ...gnomad.genomes.v4.0.sites.chr1.vcf.bgz.tbi | 3 -- excerpt-data/03c9dba47d8d1fbc/url.txt | 3 -- ...gnomad.exomes.v4.0.sites.chr21.vcf.bgz.tbi | 3 -- excerpt-data/05d48443127f19c1/url.txt | 3 -- .../gnomad.v4.0.sv.chr4.vcf.gz | 3 -- .../gnomad.v4.0.sv.chr4.vcf.gz.tbi | 3 -- excerpt-data/05e93e6f1f5d60e6/url.txt | 3 -- .../mehari-data-txs-grch37-0.4.4.bin.zst | 3 -- excerpt-data/066e9189e40704c2/url.txt | 3 -- ...omad.genomes.v3.1.2.sites.chr7.vcf.bgz.tbi | 4 +-- .../gnomad.exomes.v4.0.sites.chr10.vcf.bgz | 3 -- ...gnomad.exomes.v4.0.sites.chr10.vcf.bgz.tbi | 3 -- excerpt-data/083f4075b9190a42/url.txt | 3 -- .../gnomad.exomes.r2.1.1.sites.3.vcf.bgz.tbi | 4 +-- ...r2.1.1.sites.1.liftover_grch38.vcf.bgz.tbi | 4 +-- ...r2.1.1.sites.1.liftover_grch38.vcf.bgz.tbi | 4 +-- .../gnomad.v4.0.sv.chr15.vcf.gz | 3 -- .../gnomad.v4.0.sv.chr15.vcf.gz.tbi | 3 -- excerpt-data/0be9b2561c9397f2/url.txt | 3 -- .../gnomad.genomes.r2.1.1.sites.1.vcf.bgz.tbi | 4 +-- ...mad.genomes.v3.1.2.sites.chr20.vcf.bgz.tbi | 4 +-- .../ClinGen_gene_curation_list_GRCh37.tsv | 3 -- excerpt-data/0e7eb7069eb4d354/url.txt | 3 -- ...mad.genomes.v3.1.2.sites.chr12.vcf.bgz.tbi | 4 +-- ...nomad.genomes.v4.0.sites.chr11.vcf.bgz.tbi | 3 -- excerpt-data/13652bb20d0252c1/url.txt | 3 -- ...nomad.genomes.v4.0.sites.chr22.vcf.bgz.tbi | 3 -- excerpt-data/13affcfaed12d83b/url.txt | 3 -- .../gnomad.v4.0.sv.chr3.vcf.gz | 3 -- .../gnomad.v4.0.sv.chr3.vcf.gz.tbi | 3 -- excerpt-data/13d4b1406e769b80/url.txt | 3 -- ...nomad.genomes.v4.0.sites.chr15.vcf.bgz.tbi | 3 -- excerpt-data/141f65a2d306a79f/url.txt | 3 -- .../whole_genome_SNVs_inclAnno.tsv.gz.tbi | 3 -- .../gnomad.exomes.v4.0.sites.chr19.vcf.bgz | 3 -- ...gnomad.exomes.v4.0.sites.chr19.vcf.bgz.tbi | 3 -- excerpt-data/172c2a003f154e5a/url.txt | 3 -- excerpt-data/17f0d5f9c4671d95/url.txt | 3 -- .../gnomad.v4.0.sv.chr5.vcf.gz | 3 -- .../gnomad.v4.0.sv.chr5.vcf.gz.tbi | 3 -- excerpt-data/182806147755e799/url.txt | 3 -- .../gnomad.genomes.v4.0.sites.chr19.vcf.bgz | 3 -- ...nomad.genomes.v4.0.sites.chr19.vcf.bgz.tbi | 3 -- excerpt-data/1853efeb3c05bb4f/url.txt | 3 -- .../gnomad.v4.0.sv.chr18.vcf.gz | 3 -- .../gnomad.v4.0.sv.chr18.vcf.gz.tbi | 3 -- excerpt-data/19a12d845df10514/url.txt | 3 -- .../gnomad.exomes.v4.0.sites.chr7.vcf.bgz | 3 -- .../gnomad.exomes.v4.0.sites.chr7.vcf.bgz.tbi | 3 -- excerpt-data/1bd50fbfec4be878/url.txt | 3 -- ...gnomad.genomes.r2.1.1.sites.17.vcf.bgz.tbi | 4 +-- ...omad.genomes.v3.1.2.sites.chr9.vcf.bgz.tbi | 4 +-- .../1eb8194e7c6b93b5/phenotype_to_genes.txt | 3 ++ excerpt-data/1eb8194e7c6b93b5/url.txt | 3 ++ ...2.1.1.sites.16.liftover_grch38.vcf.bgz.tbi | 4 +-- .../gnomad.genomes.r2.1.1.sites.6.vcf.bgz.tbi | 4 +-- .../gnomad.v4.0.sv.chrX.vcf.gz | 3 -- .../gnomad.v4.0.sv.chrX.vcf.gz.tbi | 3 -- excerpt-data/2245e9d640b3f206/url.txt | 3 -- ...gnomad.exomes.v4.0.sites.chr15.vcf.bgz.tbi | 3 -- excerpt-data/2254592ec259ff77/url.txt | 3 -- ...2.1.1.sites.17.liftover_grch38.vcf.bgz.tbi | 4 +-- ...nomad.genomes.v4.0.sites.chr10.vcf.bgz.tbi | 3 -- excerpt-data/2652aa710820a40c/url.txt | 3 -- ...gnomad.genomes.v4.0.sites.chr8.vcf.bgz.tbi | 3 -- excerpt-data/26c74484dfebfa98/url.txt | 3 -- excerpt-data/2706fba9e13b0fd5/mim2gene_medgen | 4 +-- ...r2.1.1.sites.3.liftover_grch38.vcf.bgz.tbi | 4 +-- excerpt-data/2814066cdd049594/hp.obo | 3 ++ excerpt-data/2814066cdd049594/url.txt | 3 ++ .../gnomad.genomes.v4.0.sites.chr2.vcf.bgz | 3 -- ...gnomad.genomes.v4.0.sites.chr2.vcf.bgz.tbi | 3 -- excerpt-data/28336ee11b96317b/url.txt | 3 -- ...omad.genomes.v3.1.2.sites.chr1.vcf.bgz.tbi | 4 +-- .../gnomad.genomes.v4.0.sites.chr7.vcf.bgz | 3 -- ...gnomad.genomes.v4.0.sites.chr7.vcf.bgz.tbi | 3 -- excerpt-data/2b63d07e3a1c8709/url.txt | 3 -- .../gnomad.exomes.r2.1.1.sites.12.vcf.bgz.tbi | 4 +-- .../gnomad.genomes.r2.1.1.sites.9.vcf.bgz.tbi | 4 +-- .../ClinGen_gene_curation_list_GRCh37.tsv | 3 ++ excerpt-data/2c7a6e7659001b2a/url.txt | 3 ++ ...gnomad.genomes.r2.1.1.sites.16.vcf.bgz.tbi | 4 +-- .../gnomad.exomes.r2.1.1.sites.2.vcf.bgz.tbi | 4 +-- .../gnomad.v2.1.1.lof_metrics.by_gene.txt.bgz | 2 +- ...rCNV_2022.dosage_sensitivity_scores.tsv.gz | 4 +-- .../AlphaMissense_hg19.tsv.gz | 4 +-- excerpt-data/32c97f6adaf88f01/hp.obo | 3 -- excerpt-data/32c97f6adaf88f01/url.txt | 3 -- .../gnomad.v4.0.sv.chr2.vcf.gz | 3 -- .../gnomad.v4.0.sv.chr2.vcf.gz.tbi | 3 -- excerpt-data/3390d9ca9ce97bac/url.txt | 3 -- ...nomad.genomes.v4.0.sites.chr17.vcf.bgz.tbi | 3 -- excerpt-data/34295f63bb863636/url.txt | 3 -- .../gnomad.genomes.v4.0.sites.chr9.vcf.bgz | 3 -- ...gnomad.genomes.v4.0.sites.chr9.vcf.bgz.tbi | 3 -- excerpt-data/351c2213184837e6/url.txt | 3 -- .../gnomad.genomes.v4.0.sites.chr18.vcf.bgz | 3 -- ...nomad.genomes.v4.0.sites.chr18.vcf.bgz.tbi | 3 -- excerpt-data/36e32020ce7f9934/url.txt | 3 -- .../gnomad.exomes.v4.0.sites.chr2.vcf.bgz | 3 -- .../gnomad.exomes.v4.0.sites.chr2.vcf.bgz.tbi | 3 -- excerpt-data/371f94dff12ce4fd/url.txt | 3 -- .../gnomad.exomes.r2.1.1.sites.17.vcf.bgz.tbi | 4 +-- .../gnomad.exomes.v4.0.sites.chrY.vcf.bgz.tbi | 3 -- excerpt-data/378fefd938740932/url.txt | 3 -- ...gnomad.exomes.v4.0.sites.chr17.vcf.bgz.tbi | 3 -- excerpt-data/392b43598966a31c/url.txt | 3 -- .../martservice | 0 excerpt-data/394e630f41014c0a/url.txt | 3 ++ .../gnomad.exomes.r2.1.1.sites.1.vcf.bgz.tbi | 4 +-- ...00001405.40_GRCh38.p14_assembly_report.txt | 2 +- .../gnomad.v4.0.sv.chrY.vcf.gz | 3 -- .../gnomad.v4.0.sv.chrY.vcf.gz.tbi | 3 -- excerpt-data/3b19a5df654e6b4f/url.txt | 3 -- ...r2.1.1.sites.8.liftover_grch38.vcf.bgz.tbi | 4 +-- excerpt-data/3c82362d005645e5/url.txt | 3 -- .../gnomad.genomes.r2.1.1.sites.2.vcf.bgz.tbi | 4 +-- .../gnomad.exomes.v4.0.sites.chr4.vcf.bgz.tbi | 3 -- excerpt-data/3e3d4b4d0a7b5028/url.txt | 3 -- .../gnomad.exomes.r2.1.1.sites.18.vcf.bgz.tbi | 4 +-- ...mad.genomes.v3.1.2.sites.chr10.vcf.bgz.tbi | 4 +-- .../gnomad.exomes.r2.1.1.sites.7.vcf.bgz.tbi | 4 +-- ...gnomad.genomes.r2.1.1.sites.17.vcf.bgz.tbi | 4 +-- excerpt-data/41961c7350780224/phenotype.hpoa | 3 -- excerpt-data/41961c7350780224/url.txt | 3 -- .../gnomad.genomes.r2.1.1.sites.X.vcf.bgz.tbi | 4 +-- .../gnomad.v4.0.sv.chr7.vcf.gz | 3 -- .../gnomad.v4.0.sv.chr7.vcf.gz.tbi | 3 -- excerpt-data/41e368687b2c69e4/url.txt | 3 -- .../gnomad.genomes.v4.0.sites.chr16.vcf.bgz | 3 -- ...nomad.genomes.v4.0.sites.chr16.vcf.bgz.tbi | 3 -- excerpt-data/426688069d57932a/url.txt | 3 -- .../gnomad.genomes.v4.0.sites.chr4.vcf.bgz | 3 -- ...gnomad.genomes.v4.0.sites.chr4.vcf.bgz.tbi | 3 -- excerpt-data/431f413816b6c200/url.txt | 3 -- ...r2.1.1.sites.2.liftover_grch38.vcf.bgz.tbi | 4 +-- ...2.1.1.sites.18.liftover_grch38.vcf.bgz.tbi | 4 +-- ...gnomad.genomes.r2.1.1.sites.10.vcf.bgz.tbi | 4 +-- .../gnomad.genomes.v4.0.sites.chr5.vcf.bgz | 3 -- ...gnomad.genomes.v4.0.sites.chr5.vcf.bgz.tbi | 3 -- excerpt-data/46dd4a494619d287/url.txt | 3 -- ...r2.1.1.sites.3.liftover_grch38.vcf.bgz.tbi | 4 +-- .../gnomad.exomes.r2.1.1.sites.8.vcf.bgz.tbi | 4 +-- ...gnomad.genomes.r2.1.1.sites.11.vcf.bgz.tbi | 4 +-- .../mehari-data-txs-grch38-0.4.4.bin.zst | 3 -- excerpt-data/48599d2a2461065d/url.txt | 3 -- ...2.1.1.sites.19.liftover_grch38.vcf.bgz.tbi | 4 +-- .../gnomad.genomes.r2.1.1.sites.7.vcf.bgz.tbi | 4 +-- ...omad.genomes.v3.1.2.sites.chr3.vcf.bgz.tbi | 4 +-- .../gnomad.exomes.v4.0.sites.chr4.vcf.bgz | 3 -- .../gnomad.exomes.v4.0.sites.chr4.vcf.bgz.tbi | 3 -- excerpt-data/4cb269f1b5d72987/url.txt | 3 -- .../gnomad.exomes.v4.0.sites.chr3.vcf.bgz | 3 -- .../gnomad.exomes.v4.0.sites.chr3.vcf.bgz.tbi | 3 -- excerpt-data/4ceaef4bafe4459e/url.txt | 3 -- ...gnomad.exomes.v4.0.sites.chr20.vcf.bgz.tbi | 3 -- excerpt-data/4dc077f61f3a5f1a/url.txt | 3 -- excerpt-data/4ec03f691a337110/dbscSNV1.1.zip | 3 -- excerpt-data/4ec03f691a337110/url.txt | 3 -- .../gnomad.genomes.v4.0.sites.chr6.vcf.bgz | 3 -- ...gnomad.genomes.v4.0.sites.chr6.vcf.bgz.tbi | 3 -- excerpt-data/4fec56d6c3eaa7a5/url.txt | 3 -- ...omad.genomes.v3.1.2.sites.chr8.vcf.bgz.tbi | 4 +-- .../AlphaMissense_gene_hg38.tsv.gz | 4 +-- .../gnomad.exomes.r2.1.1.sites.16.vcf.bgz.tbi | 4 +-- .../gnomad.exomes.v4.0.sites.chrX.vcf.bgz.tbi | 3 -- excerpt-data/53351bf97ac0cb1c/url.txt | 3 -- ...mad.genomes.v3.1.2.sites.chr20.vcf.bgz.tbi | 4 +-- ...2.1.1.sites.19.liftover_grch38.vcf.bgz.tbi | 4 +-- .../gnomad.v4.0.sv.chr11.vcf.gz | 3 -- .../gnomad.v4.0.sv.chr11.vcf.gz.tbi | 3 -- excerpt-data/555fd2fa82d1b73d/url.txt | 3 -- .../gnomad.genomes.v4.0.sites.chr15.vcf.bgz | 3 -- ...nomad.genomes.v4.0.sites.chr15.vcf.bgz.tbi | 3 -- excerpt-data/55e0a2317a683ab4/url.txt | 3 -- .../gnomad.genomes.r2.1.1.sites.8.vcf.bgz.tbi | 4 +-- ...mad.genomes.v3.1.2.sites.chr19.vcf.bgz.tbi | 4 +-- .../gnomad.exomes.r2.1.1.sites.4.vcf.bgz.tbi | 4 +-- ...r2.1.1.sites.7.liftover_grch38.vcf.bgz.tbi | 4 +-- ...mad.genomes.v3.1.2.sites.chr17.vcf.bgz.tbi | 4 +-- .../gnomad.exomes.r2.1.1.sites.19.vcf.bgz.tbi | 4 +-- ...r2.1.1.sites.5.liftover_grch38.vcf.bgz.tbi | 4 +-- .../GRCh37.nr_duplications.tsv.gz | 4 +-- .../gnomad.v4.0.sv.chr21.vcf.gz | 3 -- .../gnomad.v4.0.sv.chr21.vcf.gz.tbi | 3 -- excerpt-data/6433022d4690f461/url.txt | 3 -- ...nomad.genomes.v4.0.sites.chr18.vcf.bgz.tbi | 3 -- excerpt-data/657e4807c49e1004/url.txt | 3 -- ...gnomad.genomes.v4.0.sites.chr9.vcf.bgz.tbi | 3 -- excerpt-data/65907b0581a5b8d6/url.txt | 3 -- .../hg19.TADs.zip | 0 excerpt-data/669ec73ad3bcb2be/url.txt | 3 ++ .../gnomad.exomes.r2.1.1.sites.16.vcf.bgz.tbi | 4 +-- ...gnomad.exomes.v4.0.sites.chr18.vcf.bgz.tbi | 3 -- excerpt-data/67817771217df3b3/url.txt | 3 -- ...2.1.1.sites.16.liftover_grch38.vcf.bgz.tbi | 4 +-- .../gnomad.exomes.v4.0.sites.chrY.vcf.bgz | 3 -- .../gnomad.exomes.v4.0.sites.chrY.vcf.bgz.tbi | 3 -- excerpt-data/6a2ca4c3c4d56fcc/url.txt | 3 -- ...gnomad.exomes.v4.0.sites.chr11.vcf.bgz.tbi | 3 -- excerpt-data/6a5c9383a976f57c/url.txt | 3 -- ...omad.genomes.v3.1.2.sites.chr1.vcf.bgz.tbi | 4 +-- ...2.1.1.sites.12.liftover_grch38.vcf.bgz.tbi | 4 +-- ...r2.1.1.sites.6.liftover_grch38.vcf.bgz.tbi | 4 +-- .../gnomad.genomes.r2.1.1.sites.X.vcf.bgz.tbi | 4 +-- ...omad.genomes.v3.1.2.sites.chr2.vcf.bgz.tbi | 4 +-- .../gnomad.exomes.r2.1.1.sites.4.vcf.bgz.tbi | 4 +-- ...gnomad.genomes.r2.1.1.sites.20.vcf.bgz.tbi | 4 +-- .../gnomad.exomes.v4.0.sites.chr16.vcf.bgz | 3 -- ...gnomad.exomes.v4.0.sites.chr16.vcf.bgz.tbi | 3 -- excerpt-data/6eb8fbeb78d6a919/url.txt | 3 -- .../gnomad.v4.0.sv.chr13.vcf.gz | 3 -- .../gnomad.v4.0.sv.chr13.vcf.gz.tbi | 3 -- excerpt-data/6f337fba39cc4c2e/url.txt | 3 -- excerpt-data/6f378db589a4bbb9/orphacodes | 2 +- .../gnomad.exomes.r2.1.1.sites.3.vcf.bgz.tbi | 4 +-- ...gnomad.exomes.v4.0.sites.chr19.vcf.bgz.tbi | 3 -- excerpt-data/6fc9eec6a65511d7/url.txt | 3 -- .../gnomad.exomes.v4.0.sites.chr17.vcf.bgz | 3 -- ...gnomad.exomes.v4.0.sites.chr17.vcf.bgz.tbi | 3 -- excerpt-data/707cba867e038049/url.txt | 3 -- .../gnomad.genomes.r2.1.1.sites.1.vcf.bgz.tbi | 4 +-- ...nomad.genomes.v4.0.sites.chr14.vcf.bgz.tbi | 3 -- excerpt-data/7114d7c6dd665c88/url.txt | 3 -- .../gnomad.exomes.v4.0.sites.chr7.vcf.bgz.tbi | 3 -- excerpt-data/721f5e77ccd899f3/url.txt | 3 -- .../731d6d6a08727278/genomicSuperDups.txt.gz | 4 +-- .../gnomad.exomes.v4.0.sites.chr1.vcf.bgz.tbi | 3 -- excerpt-data/734dd2cf511bcc99/url.txt | 3 -- ...nomad.genomes.v4.0.sites.chr19.vcf.bgz.tbi | 3 -- excerpt-data/73709bf9797b788e/url.txt | 3 -- ...mad.genomes.v3.1.2.sites.chr18.vcf.bgz.tbi | 4 +-- excerpt-data/750c1a506ac33b85/__index__ | 3 ++ excerpt-data/750c1a506ac33b85/database | 3 -- ...0001405.15_GRCh38_full_analysis_set.fna.gz | 4 +-- ...r2.1.1.sites.4.liftover_grch38.vcf.bgz.tbi | 4 +-- .../gnomad.exomes.r2.1.1.sites.X.vcf.bgz.tbi | 4 +-- ...2.1.1.sites.20.liftover_grch38.vcf.bgz.tbi | 4 +-- .../ClinGen_region_curation_list_GRCh38.tsv | 3 -- excerpt-data/796c631dc892eda6/url.txt | 3 -- ...gnomad.exomes.v4.0.sites.chr20.vcf.bgz.tbi | 3 -- excerpt-data/7a4f4d0b825c6ee9/url.txt | 3 -- .../7aecff82421c0377/00-All.vcf.gz.tbi | 4 +-- excerpt-data/7c0ae83df129c4dc/rmsk.txt.gz | 4 +-- .../gnomad.genomes.v4.0.sites.chrY.vcf.bgz | 3 -- ...gnomad.genomes.v4.0.sites.chrY.vcf.bgz.tbi | 3 -- excerpt-data/7dc9a2d3e91f5ace/url.txt | 3 -- ...omad.genomes.v3.1.2.sites.chr5.vcf.bgz.tbi | 4 +-- ...gnomad.genomes.r2.1.1.sites.19.vcf.bgz.tbi | 4 +-- .../bvfzmkpgtphvbmmrvb2iyl2jl21o49kc | 3 -- excerpt-data/80731e6cc5c789f9/url.txt | 3 -- ...r2.1.1.sites.X.liftover_grch38.vcf.bgz.tbi | 4 +-- ...s-GRCh37-ensembl-and-refseq-0.10.3.bin.zst | 3 ++ excerpt-data/8158379cf97c7ea0/url.txt | 3 ++ ...r2.1.1.sites.5.liftover_grch38.vcf.bgz.tbi | 4 +-- .../gnomad.genomes.r2.1.1.sites.2.vcf.bgz.tbi | 4 +-- ...gnomad.genomes.v4.0.sites.chr7.vcf.bgz.tbi | 3 -- excerpt-data/82dc5a7f0fc84572/url.txt | 3 -- .../gnomad.exomes.r2.1.1.sites.5.vcf.bgz.tbi | 4 +-- ...r2.1.1.sites.4.liftover_grch38.vcf.bgz.tbi | 4 +-- .../gnomad.exomes.v4.0.sites.chr15.vcf.bgz | 3 -- ...gnomad.exomes.v4.0.sites.chr15.vcf.bgz.tbi | 3 -- excerpt-data/866263d22fc92d8d/url.txt | 3 -- .../HI_Predictions_Version3.bed.gz | 4 +-- ...gnomad.genomes.v4.0.sites.chr3.vcf.bgz.tbi | 3 -- excerpt-data/880883f1c30bcb54/url.txt | 3 -- ...mad.genomes.v3.1.2.sites.chr16.vcf.bgz.tbi | 4 +-- ...mad.genomes.v3.1.2.sites.chr11.vcf.bgz.tbi | 4 +-- .../gnomad.exomes.r2.1.1.sites.17.vcf.bgz.tbi | 4 +-- .../gnomad.exomes.v4.0.sites.chr9.vcf.bgz.tbi | 3 -- excerpt-data/8b3ea1c474bfca38/url.txt | 3 -- ...gnomad.exomes.v4.0.sites.chr13.vcf.bgz.tbi | 3 -- excerpt-data/8b7db3ddfc1330b8/url.txt | 3 -- excerpt-data/8bad0386c4cd562f/dbNSFP4.5c.zip | 3 -- excerpt-data/8bad0386c4cd562f/url.txt | 3 -- excerpt-data/8bc133d94c3b655e/__index__ | 3 ++ excerpt-data/8bc133d94c3b655e/alignments | 3 -- ...gnomad.genomes.v4.0.sites.chrX.vcf.bgz.tbi | 3 -- excerpt-data/8d2a1e4704172382/url.txt | 3 -- .../8d674ac6e66dc47b/altSeqLiftOverPsl.txt.gz | 4 +-- ...omad.genomes.v3.1.2.sites.chr8.vcf.bgz.tbi | 4 +-- .../gnomad.exomes.v4.0.sites.chr1.vcf.bgz | 3 -- .../gnomad.exomes.v4.0.sites.chr1.vcf.bgz.tbi | 3 -- excerpt-data/8e30e5e8bed1f86c/url.txt | 3 -- .../a84zcdlkx2asq2nxh6xr2gdb4csmyvhk | 3 -- excerpt-data/8e490bdeafb43ab4/url.txt | 3 -- excerpt-data/8ee47118be15da10/current_README | 3 -- excerpt-data/8ee47118be15da10/url.txt | 3 -- ...gnomad.genomes.r2.1.1.sites.18.vcf.bgz.tbi | 4 +-- ...omad.genomes.v3.1.2.sites.chr2.vcf.bgz.tbi | 4 +-- ...gnomad.genomes.v4.0.sites.chr2.vcf.bgz.tbi | 3 -- excerpt-data/90ea12206ce9b4d2/url.txt | 3 -- ...gnomad.genomes.r2.1.1.sites.16.vcf.bgz.tbi | 4 +-- ...2.1.1.sites.11.liftover_grch38.vcf.bgz.tbi | 4 +-- .../gnomad.genomes.v4.0.sites.chr10.vcf.bgz | 3 -- ...nomad.genomes.v4.0.sites.chr10.vcf.bgz.tbi | 3 -- excerpt-data/92a43e4e1c50a925/url.txt | 3 -- .../gnomad.exomes.r2.1.1.sites.11.vcf.bgz.tbi | 4 +-- .../GRCh38.nr_insertions.tsv.gz | 4 +-- .../gnomad.exomes.r2.1.1.sites.1.vcf.bgz.tbi | 4 +-- .../{release_notes => __index__} | 0 .../gnomad.genomes.r2.1.1.sites.6.vcf.bgz.tbi | 4 +-- .../97187ff23d7d2773/phenotype_to_genes.txt | 3 -- excerpt-data/97187ff23d7d2773/url.txt | 3 -- ...gnomad.genomes.v3.1.sites.chrM.vcf.bgz.tbi | 4 +-- .../gnomad.genomes.v4.0.sites.chr14.vcf.bgz | 3 -- ...nomad.genomes.v4.0.sites.chr14.vcf.bgz.tbi | 3 -- excerpt-data/9801d5503cc46d9d/url.txt | 3 -- ...GCF_000001405.40_GRCh38.p14_genomic.gff.gz | 4 +-- ...gnomad.genomes.v4.0.sites.chrY.vcf.bgz.tbi | 3 -- excerpt-data/98e0491a03063fc7/url.txt | 3 -- .../GRCh37.nr_deletions.tsv.gz | 4 +-- ...omad.genomes.v3.1.2.sites.chr7.vcf.bgz.tbi | 4 +-- .../gnomad.genomes.r2.1.1.sites.7.vcf.bgz.tbi | 4 +-- .../gnomad.v4.0.sv.chr10.vcf.gz | 3 -- .../gnomad.v4.0.sv.chr10.vcf.gz.tbi | 3 -- excerpt-data/9cc0f2ee73775510/url.txt | 3 -- ...mad.genomes.v3.1.2.sites.chr18.vcf.bgz.tbi | 4 +-- ...gnomad.genomes.r2.1.1.sites.20.vcf.bgz.tbi | 4 +-- ...r2.1.1.sites.X.liftover_grch38.vcf.bgz.tbi | 4 +-- .../gnomad.genomes.v4.0.sites.chr11.vcf.bgz | 3 -- ...nomad.genomes.v4.0.sites.chr11.vcf.bgz.tbi | 3 -- excerpt-data/9e6db9977f7e6ad4/url.txt | 3 -- .../gnomad.genomes.v4.0.sites.chrX.vcf.bgz | 3 -- ...gnomad.genomes.v4.0.sites.chrX.vcf.bgz.tbi | 3 -- excerpt-data/9f6844871f8cbbc9/url.txt | 3 -- .../gnomad.genomes.v4.0.sites.chr12.vcf.bgz | 3 -- ...nomad.genomes.v4.0.sites.chr12.vcf.bgz.tbi | 3 -- excerpt-data/9fb6d04c9311611b/url.txt | 3 -- .../gnomad.exomes.r2.1.1.sites.10.vcf.bgz.tbi | 4 +-- .../ORDO.csv.gz} | 4 +-- excerpt-data/a0f9f11118d32143/download | 3 -- ...gnomad.exomes.v4.0.sites.chr16.vcf.bgz.tbi | 3 -- excerpt-data/a17783212192968d/url.txt | 3 -- .../gnomad.v4.0.sv.chr16.vcf.gz | 3 -- .../gnomad.v4.0.sv.chr16.vcf.gz.tbi | 3 -- excerpt-data/a271968c7bf845c0/url.txt | 3 -- ...2.1.1.sites.20.liftover_grch38.vcf.bgz.tbi | 4 +-- .../gnomad.exomes.r2.1.1.sites.10.vcf.bgz.tbi | 4 +-- ...2.1.1.sites.11.liftover_grch38.vcf.bgz.tbi | 4 +-- .../hg38.TADs.zip | 0 excerpt-data/a7ad8838c57d30ac/url.txt | 3 ++ .../gnomad.exomes.r2.1.1.sites.6.vcf.bgz.tbi | 4 +-- .../gnomad.v4.0.sv.chr20.vcf.gz | 3 -- .../gnomad.v4.0.sv.chr20.vcf.gz.tbi | 3 -- excerpt-data/a83da02295a7ae02/url.txt | 3 -- ...gnomad.exomes.v4.0.sites.chr14.vcf.bgz.tbi | 3 -- excerpt-data/a9193d84c26ddae9/url.txt | 3 -- excerpt-data/a9229376a47367b7/__index__ | 3 ++ excerpt-data/a9229376a47367b7/database | 3 -- .../gnomad.genomes.r2.1.1.sites.8.vcf.bgz.tbi | 4 +-- excerpt-data/a9dd799550b2e5ae/url.txt | 3 -- ...gnomad.genomes.v4.0.sites.chr1.vcf.bgz.tbi | 3 -- excerpt-data/aabd3baf70c808d6/url.txt | 3 -- .../gnomad.genomes.r2.1.1.sites.4.vcf.bgz.tbi | 4 +-- .../gnomad.genomes.v4.0.sites.chr3.vcf.bgz | 3 -- ...gnomad.genomes.v4.0.sites.chr3.vcf.bgz.tbi | 3 -- excerpt-data/abee2d5809505f83/url.txt | 3 -- .../GRCh38.nr_deletions.tsv.gz | 4 +-- .../gnomad.exomes.v4.0.sites.chr3.vcf.bgz.tbi | 3 -- excerpt-data/ac63e43b6e0e1a0d/url.txt | 3 -- .../ac92d419f271d95f/genes_to_phenotype.txt | 3 -- excerpt-data/ac92d419f271d95f/url.txt | 3 -- .../gnomad.genomes.r2.1.1.sites.4.vcf.bgz.tbi | 4 +-- .../gnomad.exomes.r2.1.1.sites.9.vcf.bgz.tbi | 4 +-- ...nomad.genomes.v4.0.sites.chr21.vcf.bgz.tbi | 3 -- excerpt-data/ae03f6e3817a686d/url.txt | 3 -- .../gnomad.exomes.r2.1.1.sites.11.vcf.bgz.tbi | 4 +-- .../gnomad.v4.0.sv.chr6.vcf.gz | 3 -- .../gnomad.v4.0.sv.chr6.vcf.gz.tbi | 3 -- excerpt-data/aea53328ecd0b712/url.txt | 3 -- .../gnomad.exomes.v4.0.sites.chr18.vcf.bgz | 3 -- ...gnomad.exomes.v4.0.sites.chr18.vcf.bgz.tbi | 3 -- excerpt-data/af1389a40c2c79a3/url.txt | 3 -- .../whole_genome_SNVs_inclAnno.tsv.gz.tbi | 3 -- .../b07ff34b63faa235/knownGene.exonAA.fa.gz | 4 +-- ...omad.genomes.v3.1.2.sites.chr5.vcf.bgz.tbi | 4 +-- .../whole_genome_SNVs_inclAnno.tsv.gz.tbi | 3 -- .../gnomad.genomes.v4.0.sites.chr8.vcf.bgz | 3 -- ...gnomad.genomes.v4.0.sites.chr8.vcf.bgz.tbi | 3 -- excerpt-data/b1206087515a23c5/url.txt | 3 -- .../gnomad.exomes.v4.0.sites.chr5.vcf.bgz | 3 -- .../gnomad.exomes.v4.0.sites.chr5.vcf.bgz.tbi | 3 -- excerpt-data/b316bad6f6c5dce1/url.txt | 3 -- ...nomad.genomes.v4.0.sites.chr12.vcf.bgz.tbi | 3 -- excerpt-data/b49a230364ef590d/url.txt | 3 -- ...gnomad.genomes.r2.1.1.sites.19.vcf.bgz.tbi | 4 +-- ...gnomad.genomes.r2.1.1.sites.12.vcf.bgz.tbi | 4 +-- ...omad.genomes.v3.1.2.sites.chr4.vcf.bgz.tbi | 4 +-- .../gnomad.exomes.r2.1.1.sites.9.vcf.bgz.tbi | 4 +-- excerpt-data/b920970c3e3329fb/dbNSFP4.5a.zip | 3 -- excerpt-data/b920970c3e3329fb/url.txt | 3 -- .../gnomad.genomes.r2.1.1.sites.3.vcf.bgz.tbi | 4 +-- ...omad.genomes.v3.1.2.sites.chr4.vcf.bgz.tbi | 4 +-- .../ba0fabc633617321/genomicSuperDups.txt.gz | 4 +-- .../ba11237fa6ca916a/knownToEnsembl.txt.gz | 4 +-- .../gnomad.genomes.v4.0.sites.chr17.vcf.bgz | 3 -- ...nomad.genomes.v4.0.sites.chr17.vcf.bgz.tbi | 3 -- excerpt-data/bb10ab002f2bbfa6/url.txt | 3 -- .../gnomad.exomes.r2.1.1.sites.7.vcf.bgz.tbi | 4 +-- .../gnomad.v4.0.sv.chr17.vcf.gz | 3 -- .../gnomad.v4.0.sv.chr17.vcf.gz.tbi | 3 -- excerpt-data/bc6f1860df305e83/url.txt | 3 -- ...gnomad.exomes.v4.0.sites.chr12.vcf.bgz.tbi | 3 -- excerpt-data/bd5899bf92bede68/url.txt | 3 -- ...2.1.1.sites.10.liftover_grch38.vcf.bgz.tbi | 4 +-- ...r2.1.1.sites.2.liftover_grch38.vcf.bgz.tbi | 4 +-- .../gnomad.genomes.r2.1.1.sites.3.vcf.bgz.tbi | 4 +-- .../gnomad.exomes.v4.0.sites.chr5.vcf.bgz.tbi | 3 -- excerpt-data/c043ae02bae26d06/url.txt | 3 -- excerpt-data/c07b6193df69b9ec/phenotype.hpoa | 3 ++ excerpt-data/c07b6193df69b9ec/url.txt | 3 ++ ...GCF_000001405.40_GRCh38.p14_genomic.gtf.gz | 4 +-- .../gnomad.exomes.v4.0.sites.chr22.vcf.bgz | 3 -- ...gnomad.exomes.v4.0.sites.chr22.vcf.bgz.tbi | 3 -- excerpt-data/c2d4c9487692f853/url.txt | 3 -- ...nomad.genomes.v4.0.sites.chr16.vcf.bgz.tbi | 3 -- excerpt-data/c2e6fc096a06b889/url.txt | 3 -- .../c310c0509f957058/fixSeqLiftOverPsl.txt.gz | 4 +-- .../gnomad.exomes.v4.0.sites.chr8.vcf.bgz | 3 -- .../gnomad.exomes.v4.0.sites.chr8.vcf.bgz.tbi | 3 -- excerpt-data/c371f84b3aaba9a6/url.txt | 3 -- .../gnomad.exomes.r2.1.1.sites.6.vcf.bgz.tbi | 4 +-- .../gnomad.v4.0.sv.chr22.vcf.gz | 3 -- .../gnomad.v4.0.sv.chr22.vcf.gz.tbi | 3 -- excerpt-data/c3ce41a42c6319e0/url.txt | 3 -- ...r2.1.1.sites.6.liftover_grch38.vcf.bgz.tbi | 4 +-- excerpt-data/c47e38a1fc060f0d/hs37d5.fa.gz | 4 +-- .../AlphaMissense_hg38.tsv.gz | 4 +-- .../c4b3be274faf2078/00-All.vcf.gz.tbi | 4 +-- .../gnomad.genomes.v4.0.sites.chr20.vcf.bgz | 3 -- ...nomad.genomes.v4.0.sites.chr20.vcf.bgz.tbi | 3 -- excerpt-data/c54ea6487cf96fa6/url.txt | 3 -- ...gnomad.exomes.v4.0.sites.chr22.vcf.bgz.tbi | 3 -- excerpt-data/c6c81f5a54d459f6/url.txt | 3 -- ...nomad.genomes.v4.0.sites.chr20.vcf.bgz.tbi | 3 -- excerpt-data/c6d2ee4507003c81/url.txt | 3 -- ...gnomad.genomes.r2.1.1.sites.11.vcf.bgz.tbi | 4 +-- .../gnomad.exomes.v4.0.sites.chr2.vcf.bgz.tbi | 3 -- excerpt-data/c7bb18b598b575a4/url.txt | 3 -- .../gnomad.exomes.v4.0.sites.chr6.vcf.bgz.tbi | 3 -- excerpt-data/c87053220fdc1174/url.txt | 3 -- .../gnomad.exomes.r2.1.1.sites.8.vcf.bgz.tbi | 4 +-- .../ClinGen_region_curation_list_GRCh38.tsv | 3 ++ excerpt-data/c986b4cea56d610d/url.txt | 3 ++ excerpt-data/c9c7d6df0e24b954/__index__ | 4 +-- .../gnomad.exomes.r2.1.1.sites.18.vcf.bgz.tbi | 4 +-- .../gnomad.v4.0.sv.chr14.vcf.gz | 3 -- .../gnomad.v4.0.sv.chr14.vcf.gz.tbi | 3 -- excerpt-data/ca218c36ad8374d2/url.txt | 3 -- .../ClinGen_gene_curation_list_GRCh38.tsv | 3 -- excerpt-data/cb35d21dd121ab4b/url.txt | 3 -- ...gnomad.genomes.v4.0.sites.chr5.vcf.bgz.tbi | 3 -- excerpt-data/cbb0e0ed76762826/url.txt | 3 -- excerpt-data/cbdd7c59d9d96ca1/__index__ | 3 ++ excerpt-data/cbdd7c59d9d96ca1/url.txt | 3 ++ .../gnomad.genomes.r2.1.1.sites.5.vcf.bgz.tbi | 4 +-- .../gnomad.exomes.v4.0.sites.chr14.vcf.bgz | 3 -- ...gnomad.exomes.v4.0.sites.chr14.vcf.bgz.tbi | 3 -- excerpt-data/cd838d492c44ea50/url.txt | 3 -- .../gnomad.exomes.r2.1.1.sites.2.vcf.bgz.tbi | 4 +-- ...mad.genomes.v3.1.2.sites.chr12.vcf.bgz.tbi | 4 +-- excerpt-data/cdaaf7a3f7595d3d/__index__ | 4 +-- .../gnomad.exomes.v4.0.sites.chr9.vcf.bgz | 3 -- .../gnomad.exomes.v4.0.sites.chr9.vcf.bgz.tbi | 3 -- excerpt-data/d0035524d71f83de/url.txt | 3 -- excerpt-data/d0629254a46f570f/rmsk.txt.gz | 4 +-- ...gnomad.exomes.v4.0.sites.chr10.vcf.bgz.tbi | 3 -- excerpt-data/d11dec5f18b4da8c/url.txt | 3 -- .../gnomad.genomes.r2.1.1.sites.5.vcf.bgz.tbi | 4 +-- ...r2.1.1.sites.8.liftover_grch38.vcf.bgz.tbi | 4 +-- ...omad.genomes.v3.1.2.sites.chr9.vcf.bgz.tbi | 4 +-- ...gnomad.genomes.v4.0.sites.chr4.vcf.bgz.tbi | 3 -- excerpt-data/d40913abe5c0e1ec/url.txt | 3 -- .../gnomad.exomes.v4.0.sites.chr8.vcf.bgz.tbi | 3 -- excerpt-data/d4cfbcdd27126f48/url.txt | 3 -- .../gnomad.exomes.v4.0.sites.chr6.vcf.bgz | 3 -- .../gnomad.exomes.v4.0.sites.chr6.vcf.bgz.tbi | 3 -- excerpt-data/d4f5cd78830c9fba/url.txt | 3 -- .../{alignments => __index__} | 0 ...GCF_000001405.25_GRCh37.p13_genomic.gtf.gz | 4 +-- ...2.1.1.sites.12.liftover_grch38.vcf.bgz.tbi | 4 +-- ...gnomad.genomes.v4.0.sites.chr6.vcf.bgz.tbi | 3 -- 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excerpt-data/f6dd8a9ed4e56bd8/url.txt delete mode 100644 excerpt-data/f9589989663c494c/url.txt create mode 100644 excerpt-data/f9d35b112718de39/ClinGen_gene_curation_list_GRCh38.tsv create mode 100644 excerpt-data/f9d35b112718de39/url.txt delete mode 100644 excerpt-data/fcd2407818a70148/gnomad.genomes.v4.0.sites.chr13.vcf.bgz delete mode 100644 excerpt-data/fcd2407818a70148/gnomad.genomes.v4.0.sites.chr13.vcf.bgz.tbi delete mode 100644 excerpt-data/fcd2407818a70148/url.txt delete mode 100644 excerpt-data/fe2a55106424e727/gnomad.v4.0.sv.chr8.vcf.gz delete mode 100644 excerpt-data/fe2a55106424e727/gnomad.v4.0.sv.chr8.vcf.gz.tbi delete mode 100644 excerpt-data/fe2a55106424e727/url.txt diff --git a/download_urls.yml b/download_urls.yml index bb8cc9a..98f8462 100644 --- a/download_urls.yml +++ b/download_urls.yml @@ -66,6 +66,7 @@ excerpt_strategy: strategy: manual count: null +# dbscSNV v1.1 - url: https://usf.box.com/shared/static/ffwlywsat3q5ijypvunno3rg6steqfs8 skip_upstream_check: true # does not work reliably in tests excerpt_strategy: @@ -115,10 +116,10 @@ - url: https://www.deciphergenomics.org/files/downloads/HI_Predictions_Version3.bed.gz -- url: ftp://ftp.clinicalgenome.org/ClinGen_region_curation_list_GRCh37.tsv -- url: ftp://ftp.clinicalgenome.org/ClinGen_region_curation_list_GRCh38.tsv -- url: ftp://ftp.clinicalgenome.org/ClinGen_gene_curation_list_GRCh37.tsv -- url: ftp://ftp.clinicalgenome.org/ClinGen_gene_curation_list_GRCh38.tsv +- url: https://ftp.clinicalgenome.org/ClinGen_region_curation_list_GRCh37.tsv +- url: https://ftp.clinicalgenome.org/ClinGen_region_curation_list_GRCh38.tsv +- url: https://ftp.clinicalgenome.org/ClinGen_gene_curation_list_GRCh37.tsv +- url: https://ftp.clinicalgenome.org/ClinGen_gene_curation_list_GRCh38.tsv - url: https://storage.googleapis.com/adult-gtex/annotations/v8/metadata-files/GTEx_Analysis_v8_Annotations_SampleAttributesDS.txt excerpt_strategy: @@ -164,6 +165,15 @@ strategy: no-excerpt count: null +- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.10.3/mehari-data-txs-grch37-ensembl-and-refseq-0.10.3.bin.zst + excerpt_strategy: + strategy: no-excerpt + count: null +- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.10.3/mehari-data-txs-grch38-ensembl-and-refseq-0.10.3.bin.zst + excerpt_strategy: + strategy: no-excerpt + count: null + - url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.10.3/mehari-data-txs-grch37-ensembl-0.10.3.bin.zst excerpt_strategy: strategy: no-excerpt @@ -173,24 +183,24 @@ strategy: no-excerpt count: null -- url: https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2024-01-16/hp.obo +- url: https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2025-03-03/hp.obo excerpt_strategy: strategy: no-excerpt count: null -- url: https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2024-01-16/phenotype.hpoa +- url: https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2025-03-03/phenotype.hpoa excerpt_strategy: strategy: no-excerpt count: null -- url: https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2024-01-16/phenotype_to_genes.txt +- url: https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2025-03-03/phenotype_to_genes.txt excerpt_strategy: strategy: no-excerpt count: null -- url: https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2024-01-16/genes_to_phenotype.txt +- url: https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2025-03-03/genes_to_phenotype.txt excerpt_strategy: strategy: no-excerpt count: null -- url: https://ftp.ensembl.org/pub/current_README +- url: https://may2024.archive.ensembl.org/pub/current_README - comment: The UCSC listing is used for checking the versions for GRCh37. url: https://hgdownload.cse.ucsc.edu/goldenpath/hg19/database @@ -217,11 +227,11 @@ count: 10000 - url: https://hgdownload.cse.ucsc.edu/goldenpath/hg38/multiz100way/alignments/knownGene.exonAA.fa.gz -- url: http://3dgenome.fsm.northwestern.edu/downloads/hg19.TADs.zip +- url: https://3dgenome.fsm.northwestern.edu/downloads/hg19.TADs.zip excerpt_strategy: strategy: no-excerpt count: null -- url: http://3dgenome.fsm.northwestern.edu/downloads/hg38.TADs.zip +- url: https://3dgenome.fsm.northwestern.edu/downloads/hg38.TADs.zip excerpt_strategy: strategy: no-excerpt count: null @@ -268,7 +278,7 @@ strategy: head count: 10000 -- url: 'https://ensembl.org/biomart/martservice?query=' +- url: 'https://may2024.archive.ensembl.org/biomart/martservice?query=' - url: 'https://storage.googleapis.com/public-download-files/hgnc/json/json/hgnc_complete_set.json' skip_upstream_check: true # does not work reliably in tests excerpt_strategy: diff --git a/excerpt-data/0106e2c5435e5972/gnomad.exomes.v4.0.sites.chr13.vcf.bgz b/excerpt-data/0106e2c5435e5972/gnomad.exomes.v4.0.sites.chr13.vcf.bgz deleted file mode 100644 index 3d17d22..0000000 --- a/excerpt-data/0106e2c5435e5972/gnomad.exomes.v4.0.sites.chr13.vcf.bgz +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:f1d6df639dc72c846543b41e1567b70a1d737804dfffd7e5f7b27a5c90f8056f -size 122388 diff --git a/excerpt-data/0106e2c5435e5972/gnomad.exomes.v4.0.sites.chr13.vcf.bgz.tbi b/excerpt-data/0106e2c5435e5972/gnomad.exomes.v4.0.sites.chr13.vcf.bgz.tbi deleted file mode 100644 index cb2f357..0000000 --- a/excerpt-data/0106e2c5435e5972/gnomad.exomes.v4.0.sites.chr13.vcf.bgz.tbi +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:d08cce697eb2c1dd4f717e7b61f9f1ed3fb2566e11c2c448f325320fda582715 -size 155 diff --git a/excerpt-data/0106e2c5435e5972/url.txt b/excerpt-data/0106e2c5435e5972/url.txt deleted file mode 100644 index 830b58e..0000000 --- a/excerpt-data/0106e2c5435e5972/url.txt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:6fdeef96865f27baf3b9934c1977b17864ace5dc6e21c5aaaca1e365e5c6d6de -size 111 diff --git a/excerpt-data/02b0e15df1b90b86/gnomad.exomes.r2.1.1.sites.5.vcf.bgz.tbi b/excerpt-data/02b0e15df1b90b86/gnomad.exomes.r2.1.1.sites.5.vcf.bgz.tbi index 08c3d4d..5979c3e 100644 --- a/excerpt-data/02b0e15df1b90b86/gnomad.exomes.r2.1.1.sites.5.vcf.bgz.tbi +++ b/excerpt-data/02b0e15df1b90b86/gnomad.exomes.r2.1.1.sites.5.vcf.bgz.tbi @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:c5fa1573e146186f868370d1c92d4b831e4f1b9ba20aae2719cb1fa7d0fbeb68 -size 115 +oid sha256:7126f3f5de124ba0ec07e906a0dde6a9fb243a1a528616b1f2c327728574e2b0 +size 107 diff --git a/excerpt-data/03531c89f88e4ce8/genes_to_phenotype.txt b/excerpt-data/03531c89f88e4ce8/genes_to_phenotype.txt new file mode 100644 index 0000000..5eff2a1 --- /dev/null +++ b/excerpt-data/03531c89f88e4ce8/genes_to_phenotype.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:72fcbfd67a331aa0622f206817c38e14abbbfe11806024e6f9e1f1f37db02891 +size 19753823 diff --git a/excerpt-data/03531c89f88e4ce8/url.txt b/excerpt-data/03531c89f88e4ce8/url.txt new file mode 100644 index 0000000..1b1d952 --- /dev/null +++ b/excerpt-data/03531c89f88e4ce8/url.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d0d572517d885b4d3819bde28b8d3691a45d57686df3914b7b60a6ac07abf370 +size 110 diff --git a/excerpt-data/03c9dba47d8d1fbc/gnomad.genomes.v4.0.sites.chr1.vcf.bgz b/excerpt-data/03c9dba47d8d1fbc/gnomad.genomes.v4.0.sites.chr1.vcf.bgz deleted file mode 100644 index 1a375af..0000000 --- a/excerpt-data/03c9dba47d8d1fbc/gnomad.genomes.v4.0.sites.chr1.vcf.bgz +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:5957d79427b4451425dd7d289dabece128719a7524d896ccb78d7807ed737da0 -size 90430 diff --git a/excerpt-data/03c9dba47d8d1fbc/gnomad.genomes.v4.0.sites.chr1.vcf.bgz.tbi 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b/excerpt-data/fe2a55106424e727/gnomad.v4.0.sv.chr8.vcf.gz deleted file mode 100644 index 94dbf3d..0000000 --- a/excerpt-data/fe2a55106424e727/gnomad.v4.0.sv.chr8.vcf.gz +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:f5eff7946221bb0a00e6341e8c5da2c0afef2a9dd7f7c9afdb4be25683c19e76 -size 6524856 diff --git a/excerpt-data/fe2a55106424e727/gnomad.v4.0.sv.chr8.vcf.gz.tbi b/excerpt-data/fe2a55106424e727/gnomad.v4.0.sv.chr8.vcf.gz.tbi deleted file mode 100644 index 2e273a7..0000000 --- a/excerpt-data/fe2a55106424e727/gnomad.v4.0.sv.chr8.vcf.gz.tbi +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:1f375aba79bd150d346e029ffcb2a6b512203ea9f58e5eab28d84d66ddefcf50 -size 1998 diff --git a/excerpt-data/fe2a55106424e727/url.txt b/excerpt-data/fe2a55106424e727/url.txt deleted file mode 100644 index 9a3557b..0000000 --- a/excerpt-data/fe2a55106424e727/url.txt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:e291188c0c9535412c6ce64394db72a771b3a12c5742f3ad831b1b019c5e28d4 -size 104 diff --git a/rules/output/annonars/regions.smk b/rules/output/annonars/regions.smk index fc17892..d6d4b11 100644 --- a/rules/output/annonars/regions.smk +++ b/rules/output/annonars/regions.smk @@ -13,7 +13,7 @@ rule work_annonars_regions_download: # -- download clingen regions fi wget -O {output} \ - ftp://ftp.clinicalgenome.org/ClinGen_region_curation_list_$GENOME.tsv + https://ftp.clinicalgenome.org/ClinGen_region_curation_list_$GENOME.tsv """ diff --git a/rules/work/genes/clingen.smk b/rules/work/genes/clingen.smk index d075f43..6288339 100644 --- a/rules/work/genes/clingen.smk +++ b/rules/work/genes/clingen.smk @@ -13,7 +13,7 @@ rule clingen_gene_download: # -- download files fi wget -O {output.tsv} \ - ftp://ftp.clinicalgenome.org/ClinGen_gene_curation_list_{wildcards.genome_release}.tsv + https://ftp.clinicalgenome.org/ClinGen_gene_curation_list_{wildcards.genome_release}.tsv md5sum {output.tsv} > {output.tsv}.md5 """ diff --git a/rules/work/genes/ensembl.smk b/rules/work/genes/ensembl.smk index dfb3ea4..73a40a4 100644 --- a/rules/work/genes/ensembl.smk +++ b/rules/work/genes/ensembl.smk @@ -9,12 +9,6 @@ rule genes_ensembl_create_xlink: # -- create ENSEMBL gene information xlink tab r""" # Check wehther ensembl version is correct. export TMPDIR=$(mktemp -d) - trap "rm -rf $TMPDIR" EXIT - wget --no-check-certificate \ - -O $TMPDIR/current_README \ - https://may2024.archive.ensembl.org/pub/current_README - grep "The current release is Ensembl {DV.ensembl}" $TMPDIR/current_README \ - || (echo "WARNING: Ensembl version is not {DV.ensembl}.") echo -e "ensembl_gene_id\tensembl_transcript_id\tentrez_id\tgene_symbol" \ >{output.tsv} diff --git a/varfish_db_downloader/wget.py b/varfish_db_downloader/wget.py index 73872a4..151d162 100644 --- a/varfish_db_downloader/wget.py +++ b/varfish_db_downloader/wget.py @@ -22,6 +22,19 @@ from loguru import logger +def get_proxies_from_env() -> dict[str, str]: + proxies = {} + ftp_proxy = os.environ.get("ftp_proxy") or os.environ.get("FTP_PROXY") + no_proxy = os.environ.get("no_proxy") or os.environ.get("NO_PROXY") + if ftp_proxy: + proxies["ftp"] = ftp_proxy + if no_proxy: + # If no_proxy is set, we need to ensure it is in the right format + # for requests, which expects a comma-separated list. + proxies["no_proxy"] = no_proxy.replace(",", ";") + return proxies or {} + + def get_filename_from_url(url: str) -> str | None: """ Extracts the filename from a URL. @@ -79,10 +92,11 @@ def no_excerpt(url: str, path_out: str, count: int): """Do not excerpt, use all.""" logger.info(" (strategy no-excerpt from {} to {})", url, path_out) _ = count + proxies = get_proxies_from_env() with open(path_out, "wb") as outputf: requests_ftp.monkeypatch_session() s = requests.Session() - r = s.get(url, allow_redirects=True) + r = s.get(url, proxies=proxies, allow_redirects=True) outputf.write(r.content) @@ -97,15 +111,18 @@ def decompress_stream(stream): def excerpt_head(url: str, path_out: str, count: int): """Excerpt a plaint-text file by copying lines.""" logger.info(" (strategy head from {} to {})", url, path_out) - try_gzip = url.endswith(".gz") or url.endswith(".bgz") + is_gz = url.endswith(".gz") + is_bgz = url.endswith(".bgz") + try_gzip = is_gz or is_bgz if try_gzip: opener = gzip.open else: opener = open + proxies = get_proxies_from_env() with opener(path_out, "wb") as f_out: requests_ftp.monkeypatch_session() s = requests.Session() - r = s.get(url, stream=True) + r = s.get(url, proxies=proxies, stream=True) # First, attempt to read line by line which should work if requests is # correctly identifying gzip compression. is_raw_gzip = False @@ -132,7 +149,7 @@ def excerpt_head(url: str, path_out: str, count: int): break f_out.write(line.encode("utf-8")) f_out.write(b"\n") - if try_gzip: + if is_gz: # Fixup resulting compressed files so they are proper bgzip. subprocess.check_call(["gzip", "-d", path_out]) subprocess.check_call(["bgzip", path_out.replace(".gz", "")]) From 07717e8ef55546ec921e04252978fa0b60d1e993 Mon Sep 17 00:00:00 2001 From: Oliver Stolpe Date: Tue, 17 Jun 2025 08:41:56 +0200 Subject: [PATCH 14/15] Removed obsolete URL --- download_urls.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/download_urls.yml b/download_urls.yml index 98f8462..5990fda 100644 --- a/download_urls.yml +++ b/download_urls.yml @@ -200,8 +200,6 @@ strategy: no-excerpt count: null -- url: https://may2024.archive.ensembl.org/pub/current_README - - comment: The UCSC listing is used for checking the versions for GRCh37. url: https://hgdownload.cse.ucsc.edu/goldenpath/hg19/database excerpt_strategy: From 4105766d126debef2b15c3445bf94d6a264c49ce Mon Sep 17 00:00:00 2001 From: Oliver Stolpe Date: Tue, 17 Jun 2025 09:31:19 +0200 Subject: [PATCH 15/15] Fixing tbi excerpts --- .../whole_genome_SNVs_inclAnno.tsv.gz.tbi | 3 +++ .../gnomad.genomes.r3.0.indel_inclAnno.tsv.gz.tbi | 4 ++-- .../whole_genome_SNVs_inclAnno.tsv.gz.tbi | 3 +++ .../whole_genome_SNVs_inclAnno.tsv.gz.tbi | 3 +++ .../da7bef2de1acf04b/InDels_inclAnno.tsv.gz.tbi | 3 +++ .../gnomad.genomes.r3.0.indel_inclAnno.tsv.gz.tbi | 4 ++-- varfish_db_downloader/wget.py | 10 ++++++---- 7 files changed, 22 insertions(+), 8 deletions(-) create mode 100644 excerpt-data/15476a18eb31d5b1/whole_genome_SNVs_inclAnno.tsv.gz.tbi create mode 100644 excerpt-data/b02019ea774c7a5c/whole_genome_SNVs_inclAnno.tsv.gz.tbi create mode 100644 excerpt-data/b0cf111416acb4da/whole_genome_SNVs_inclAnno.tsv.gz.tbi create mode 100644 excerpt-data/da7bef2de1acf04b/InDels_inclAnno.tsv.gz.tbi diff --git a/excerpt-data/15476a18eb31d5b1/whole_genome_SNVs_inclAnno.tsv.gz.tbi b/excerpt-data/15476a18eb31d5b1/whole_genome_SNVs_inclAnno.tsv.gz.tbi new file mode 100644 index 0000000..e032d06 --- /dev/null +++ b/excerpt-data/15476a18eb31d5b1/whole_genome_SNVs_inclAnno.tsv.gz.tbi @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b6f4a4487f2a1f8505a29e4fade9597c3d95aef0d8af631cc7557dadc2fba59f +size 2797112 diff --git a/excerpt-data/827362e8dc9b273a/gnomad.genomes.r3.0.indel_inclAnno.tsv.gz.tbi b/excerpt-data/827362e8dc9b273a/gnomad.genomes.r3.0.indel_inclAnno.tsv.gz.tbi index 6cda014..699628e 100644 --- a/excerpt-data/827362e8dc9b273a/gnomad.genomes.r3.0.indel_inclAnno.tsv.gz.tbi +++ b/excerpt-data/827362e8dc9b273a/gnomad.genomes.r3.0.indel_inclAnno.tsv.gz.tbi @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:e2c267f56991d4259604465c7a109deb84f99f429fb4cf46377f05ae00af74a6 -size 108 +oid sha256:bab69d147944e5ea4ef2169ccd8d776e6f42b6ce7dc3a6115342f6fd543995c5 +size 2605990 diff --git a/excerpt-data/b02019ea774c7a5c/whole_genome_SNVs_inclAnno.tsv.gz.tbi b/excerpt-data/b02019ea774c7a5c/whole_genome_SNVs_inclAnno.tsv.gz.tbi new file mode 100644 index 0000000..e032d06 --- /dev/null +++ b/excerpt-data/b02019ea774c7a5c/whole_genome_SNVs_inclAnno.tsv.gz.tbi @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b6f4a4487f2a1f8505a29e4fade9597c3d95aef0d8af631cc7557dadc2fba59f +size 2797112 diff --git a/excerpt-data/b0cf111416acb4da/whole_genome_SNVs_inclAnno.tsv.gz.tbi b/excerpt-data/b0cf111416acb4da/whole_genome_SNVs_inclAnno.tsv.gz.tbi new file mode 100644 index 0000000..68515bd --- /dev/null +++ b/excerpt-data/b0cf111416acb4da/whole_genome_SNVs_inclAnno.tsv.gz.tbi @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a2795bdb82fe94942a1337589a4e3c9762fd532d9ac28f2f1035490a49e88c95 +size 2723850 diff --git a/excerpt-data/da7bef2de1acf04b/InDels_inclAnno.tsv.gz.tbi b/excerpt-data/da7bef2de1acf04b/InDels_inclAnno.tsv.gz.tbi new file mode 100644 index 0000000..2576bdc --- /dev/null +++ b/excerpt-data/da7bef2de1acf04b/InDels_inclAnno.tsv.gz.tbi @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b74518ec6ca1cd6d607382ebd08cd74082fc5ef2adbb96b80386faed0380206a +size 2425682 diff --git a/excerpt-data/e85bb0a95e708ef3/gnomad.genomes.r3.0.indel_inclAnno.tsv.gz.tbi b/excerpt-data/e85bb0a95e708ef3/gnomad.genomes.r3.0.indel_inclAnno.tsv.gz.tbi index 6cda014..699628e 100644 --- a/excerpt-data/e85bb0a95e708ef3/gnomad.genomes.r3.0.indel_inclAnno.tsv.gz.tbi +++ b/excerpt-data/e85bb0a95e708ef3/gnomad.genomes.r3.0.indel_inclAnno.tsv.gz.tbi @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:e2c267f56991d4259604465c7a109deb84f99f429fb4cf46377f05ae00af74a6 -size 108 +oid sha256:bab69d147944e5ea4ef2169ccd8d776e6f42b6ce7dc3a6115342f6fd543995c5 +size 2605990 diff --git a/varfish_db_downloader/wget.py b/varfish_db_downloader/wget.py index 151d162..49bbef4 100644 --- a/varfish_db_downloader/wget.py +++ b/varfish_db_downloader/wget.py @@ -157,16 +157,18 @@ def excerpt_head(url: str, path_out: str, count: int): def excerpt_copy_tbi(url: str, path_out: str, count: int): """Copy ``.tbi`` file from the (previously downloaded) ``.vcf.gz`` file.)""" + logger.info(" (performing download before COPY-TSV from {} to {})", url, path_out) + no_excerpt(url, path_out, count) _ = count vcf_url = url[:-4] vcf_file = vcf_url.split("/")[-1] vcf_url_hash = hash_url(vcf_url) base_path = os.path.dirname(os.path.dirname(path_out)) vcf_tbi_path = f"{base_path}/{vcf_url_hash}/{vcf_file}.tbi" - logger.info(" (strategy COPY_TBI from {} to {})", vcf_tbi_path, path_out) - if not os.path.exists(vcf_tbi_path): - raise RuntimeError(f"File {vcf_tbi_path} does not exist (strategy COPY-TBI)") - shutil.copy(vcf_tbi_path, path_out) + if not os.path.exists(path_out): + raise RuntimeError(f"File {path_out} does not exist (strategy COPY-TBI)") + logger.info(" (strategy COPY_TBI from {} to {})", path_out, vcf_tbi_path) + shutil.copy(path_out, vcf_tbi_path) def excerpt_vcf_head(url: str, path_out: str, count: int):