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Pull requests: broadinstitute/viral-pipelines

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Pull requests list

Upgrade WDL from 1.0 to 1.1
#635 opened Feb 3, 2026 by dpark01 Loading…
1 of 6 tasks
2
Add Kallisto and VirNucPro WDL pipelines
#632 opened Jan 23, 2026 by carze Loading…
57
scaffold_and_refine_multitaxa usability improvements: try obtaining e-mail address via Terra env introspection; allow taxid_to_ref_accessions_tsv to originate from an http[s] URL
#591 opened Mar 26, 2025 by tomkinsc Loading…
add exclude parameter to filter_subsample_sequences task and augur_from_msa workflow; improve handling of whitespace, empty lines, or absent last-line trailing newline in input include/exclude files
#586 opened Mar 5, 2025 by tomkinsc Loading…
initial WIP commit of a task and workflow to run delphy
#560 opened Oct 10, 2024 by tomkinsc Loading…
Adding Kraken to Krona conversion to blastoff.wdl
#544 opened Jun 25, 2024 by golu099 Loading…
19
in create_or_update_sample_tables, use the sample_original from demux as the key value for rows rather than sample (i.e. use IDs with forward slashes not dashes)
#539 opened May 15, 2024 by tomkinsc Loading…
add workflow to download multiple SRA accessions to multiple bams: fetch_multiple_sra_to_bams
#537 opened May 3, 2024 by tomkinsc Loading…
1
In align_and_count, change default to count only properly-paired reads
#534 opened Apr 24, 2024 by tomkinsc Loading…
parameterize table names in create_or_update_sample_tables task
#533 opened Apr 23, 2024 by tomkinsc Loading…
bugfix output location of fasta in download_annotations; pass NCBI API key to tasks: download_fasta, download_annotations
#481 opened Aug 10, 2023 by tomkinsc Loading…
add workflow: fetch_sra_bams_for_genbank_accession
#475 opened Jul 6, 2023 by tomkinsc • Draft
Integration of taxonomic classifier trainer wdl
#459 opened Mar 24, 2023 by golu099 Loading…
@golu099
16
include generate_author_sbt in sarscov2_illumina_full wdl workflow
#259 opened Apr 14, 2021 by tomkinsc Loading…
allow custom placeholder for missing data in tsv_join task
#227 opened Mar 11, 2021 by tomkinsc Loading…
3
merge_bams_bulk
#6 opened Dec 15, 2019 by lakras Loading…
12
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