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Now using multiMap and regexp for post-fix removal #9287

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Merged
merged 1 commit into from
Oct 29, 2025
Merged

Now using multiMap and regexp for post-fix removal #9287

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67 changes: 42 additions & 25 deletions subworkflows/nf-core/fasta_gxf_busco_plot/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -26,22 +26,22 @@ workflow FASTA_GXF_BUSCO_PLOT {
val_busco_cleanup // val(boolean); Set to true to remove BUSCO intermediate files

main:
ch_versions = Channel.empty()
ch_versions = channel.empty()
ch_db_path = val_busco_lineages_path
? Channel.of(file(val_busco_lineages_path, checkIfExists: true))
: Channel.of( [ [] ] )
? channel.of(file(val_busco_lineages_path, checkIfExists: true))
: channel.of( [ [] ] )
ch_config_path = val_busco_config
? Channel.of(file(val_busco_config, checkIfExists: true))
: Channel.of( [ [] ] )
ch_busco_cleanup = Channel.of([val_busco_cleanup])
? channel.of(file(val_busco_config, checkIfExists: true))
: channel.of( [ [] ] )
ch_busco_cleanup = channel.of([val_busco_cleanup])

// MODULE: BUSCO_BUSCO as BUSCO_ASSEMBLY
ch_busco_assembly_inputs = ch_fasta
| combine(
Channel.of(val_mode)
channel.of(val_mode)
)
| combine(
Channel.fromList(val_lineages)
channel.fromList(val_lineages)
)
| map { meta, fasta, mode, lineage ->
[
Expand All @@ -58,14 +58,22 @@ workflow FASTA_GXF_BUSCO_PLOT {
| combine(
ch_busco_cleanup
)
| multiMap { meta, fasta, mode, lineage, db, config, cleanup ->
fasta: [ meta, fasta ]
mode: mode
lineage: lineage
db: db
config: config
cleanup: cleanup
}

BUSCO_ASSEMBLY(
ch_busco_assembly_inputs.map { meta, fasta, _mode, _lineage, _db, _config, _cleanup -> [ meta, fasta ] },
ch_busco_assembly_inputs.map { _meta, _fasta, mode, _lineage, _db, _config, _cleanup -> mode },
ch_busco_assembly_inputs.map { _meta, _fasta, _mode, lineage, _db, _config, _cleanup -> lineage },
ch_busco_assembly_inputs.map { _meta, _fasta, _mode, _lineage, db, _config, _cleanup -> db },
ch_busco_assembly_inputs.map { _meta, _fasta, _mode, _lineage, _db, config, _cleanup -> config },
ch_busco_assembly_inputs.map { _meta, _fasta, _mode, _lineage, _db, _config, cleanup -> cleanup }
ch_busco_assembly_inputs.fasta,
ch_busco_assembly_inputs.mode,
ch_busco_assembly_inputs.lineage,
ch_busco_assembly_inputs.db,
ch_busco_assembly_inputs.config,
ch_busco_assembly_inputs.cleanup
)

ch_assembly_batch_summary = BUSCO_ASSEMBLY.out.batch_summary
Expand All @@ -77,7 +85,7 @@ workflow FASTA_GXF_BUSCO_PLOT {
// MODULE: BUSCO_GENERATEPLOT as PLOT_ASSEMBLY
ch_assembly_plot_summary = ch_assembly_short_summaries_txt
| map { meta, txt ->
def lineage_name = meta.lineage - '_odb'
def lineage_name = meta.lineage - ~/'_odb[0-9]+$'/
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@GallVp GallVp Oct 28, 2025

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This should work for _odb12, etc.

[
"short_summary.specific.${meta.lineage}.${meta.id}_${lineage_name}.txt",
txt.text
Expand All @@ -92,7 +100,7 @@ workflow FASTA_GXF_BUSCO_PLOT {

// MODULE: GFFREAD as EXTRACT_PROTEINS
ch_gffread_inputs = val_mode !in [ 'geno', 'genome' ]
? Channel.empty()
? channel.empty()
: ch_fasta
| map { meta, fasta -> [ meta.id, meta, fasta ] }
| join(
Expand All @@ -112,10 +120,10 @@ workflow FASTA_GXF_BUSCO_PLOT {
// MODULE: BUSCO_BUSCO as BUSCO_ANNOTATION
ch_busco_annotation_inputs = ch_proteins
| combine(
Channel.of('proteins')
channel.of('proteins')
)
| combine(
Channel.fromList(val_lineages)
channel.fromList(val_lineages)
)
| map { meta, fasta, mode, lineage ->
[
Expand All @@ -132,14 +140,23 @@ workflow FASTA_GXF_BUSCO_PLOT {
| combine(
ch_busco_cleanup
)
| multiMap { meta, fasta, mode, lineage, db, config, cleanup ->
fasta: [ meta, fasta ]
mode: mode
lineage: lineage
db: db
config: config
cleanup: cleanup
}


BUSCO_ANNOTATION(
ch_busco_annotation_inputs.map { meta, fasta, _mode, _lineage, _db, _config, _cleanup -> [ meta, fasta ] },
ch_busco_annotation_inputs.map { _meta, _fasta, mode, _lineage, _db, _config, _cleanup -> mode },
ch_busco_annotation_inputs.map { _meta, _fasta, _mode, lineage, _db, _config, _cleanup -> lineage },
ch_busco_annotation_inputs.map { _meta, _fasta, _mode, _lineage, db, _config, _cleanup -> db },
ch_busco_annotation_inputs.map { _meta, _fasta, _mode, _lineage, _db, config, _cleanup -> config },
ch_busco_annotation_inputs.map { _meta, _fasta, _mode, _lineage, _db, _config, cleanup -> cleanup }
ch_busco_annotation_inputs.fasta,
ch_busco_annotation_inputs.mode,
ch_busco_annotation_inputs.lineage,
ch_busco_annotation_inputs.db,
ch_busco_annotation_inputs.config,
ch_busco_annotation_inputs.cleanup
)

ch_annotation_batch_summary = BUSCO_ANNOTATION.out.batch_summary
Expand All @@ -151,7 +168,7 @@ workflow FASTA_GXF_BUSCO_PLOT {
// MODULE: BUSCO_GENERATEPLOT as PLOT_ANNOTATION
ch_annotation_plot_summary = ch_annotation_short_summaries_txt
| map { meta, txt ->
def lineage_name = meta.lineage - '_odb'
def lineage_name = meta.lineage - ~/'_odb[0-9]+$'/
[
"short_summary.specific.${meta.lineage}.${meta.id}_${lineage_name}.proteins.txt",
txt.text
Expand Down
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