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Merged
mribeirodantas merged 4 commits into from
Oct 29, 2025
Merged

Topics/samtools view #9301

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df6753d
topics bamstats generalstats
nvnieuwk Oct 28, 2025
2e2aaaf
fix version
nvnieuwk Oct 28, 2025
605d083
update samtools/view to use topics
nvnieuwk Oct 29, 2025
c19fb75
Merge branch 'topics-adoption' into topics/samtools-view
nvnieuwk Oct 29, 2025
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12 changes: 1 addition & 11 deletions modules/nf-core/samtools/view/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ process SAMTOOLS_VIEW {
tuple val(meta), path("${prefix}.${file_type}.crai"), emit: crai, optional: true
tuple val(meta), path("${prefix}.unselected.${file_type}"), emit: unselected, optional: true
tuple val(meta), path("${prefix}.unselected.${file_type}.{csi,crai}"), emit: unselected_index, optional: true
path "versions.yml", emit: versions
tuple val("${task.process}"), val('samtools'), eval('samtools --version | head -1 | sed -e "s/samtools //"'), emit: versions_samtools, topic: versions

when:
task.ext.when == null || task.ext.when
Expand Down Expand Up @@ -60,11 +60,6 @@ process SAMTOOLS_VIEW {
-o ${output_file} \\
$input \\
$args2

cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""

stub:
Expand Down Expand Up @@ -95,10 +90,5 @@ process SAMTOOLS_VIEW {
${index}
${unselected}
${unselected_index}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}
30 changes: 23 additions & 7 deletions modules/nf-core/samtools/view/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -140,13 +140,29 @@ output:
description: index for the "unselected" file
pattern: "*.unselected.{csi,crai}"
ontologies: []
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
ontologies:
- edam: http://edamontology.org/format_3750 # YAML
versions_samtools:
- - ${task.process}:
type: string
description: Name of the process
- samtools:
type: string
description: Name of the tool
- samtools --version | head -1 | sed -e "s/samtools //:
type: string
description: Version of samtools used

topics:
- versions:
- - process:
type: string
description: The process the versions were collected from
- tool:
type: string
description: The tool name
- version:
type: string
description: The version of the tool

authors:
- "@drpatelh"
- "@joseespinosa"
Expand Down
77 changes: 10 additions & 67 deletions modules/nf-core/samtools/view/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -29,13 +29,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(file(process.out.bam[0][1]).name).match("bam_bam") },
{ assert snapshot(process.out.bai).match("bam_bai") },
{ assert snapshot(process.out.crai).match("bam_crai") },
{ assert snapshot(process.out.cram).match("bam_cram") },
{ assert snapshot(process.out.csi).match("bam_csi") },
{ assert snapshot(process.out.sam).match("bam_sam") },
{ assert snapshot(process.out.versions).match("bam_versions") }
{ assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam"])).match()}
)
}
}
Expand All @@ -62,11 +56,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(
file(process.out.bam[0][1]).name,
file(process.out.csi[0][1]).name,
process.out.versions).match()
}
{ assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam", "csi"])).match()}
)
}
}
Expand All @@ -93,10 +83,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(
file(process.out.bam[0][1]).name,
file(process.out.bai[0][1]).name,
process.out.versions).match() }
{ assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam", "bai"])).match()}
)
}
}
Expand Down Expand Up @@ -124,13 +111,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(
file(process.out.bam[0][1]).name,
file(process.out.bai[0][1]).name,
file(process.out.unselected[0][1]).name,
file(process.out.unselected_index[0][1]).name,
process.out.versions).match()
}
{ assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam", "bai", "unselected", "unselected_index"])).match()}
)
}
}
Expand Down Expand Up @@ -158,13 +139,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(
file(process.out.cram[0][1]).name,
file(process.out.crai[0][1]).name,
file(process.out.unselected[0][1]).name,
file(process.out.unselected_index[0][1]).name,
process.out.versions).match()
}
{ assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam", "bai", "unselected", "unselected_index", "crai"])).match()}
)
}
}
Expand Down Expand Up @@ -192,13 +167,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(file(process.out.cram[0][1]).name).match("cram_cram") },
{ assert snapshot(process.out.bai).match("cram_bai") },
{ assert snapshot(process.out.bam).match("cram_bam") },
{ assert snapshot(process.out.crai).match("cram_crai") },
{ assert snapshot(process.out.csi).match("cram_csi") },
{ assert snapshot(process.out.sam).match("cram_sam") },
{ assert snapshot(process.out.versions).match("cram_versions") }
{ assert snapshot(sanitizeOutput(process.out, unstableKeys: ["cram"])).match()}
)
}
}
Expand Down Expand Up @@ -228,13 +197,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(file(process.out.bam[0][1]).name).match("cram_to_bam_bam") },
{ assert snapshot(process.out.bai).match("cram_to_bam_bai") },
{ assert snapshot(process.out.crai).match("cram_to_bam_crai") },
{ assert snapshot(process.out.cram).match("cram_to_bam_cram") },
{ assert snapshot(process.out.csi).match("cram_to_bam_csi") },
{ assert snapshot(process.out.sam).match("cram_to_bam_sam") },
{ assert snapshot(process.out.versions).match("cram_to_bam_versions") }
{ assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam"])).match()}
)
}
}
Expand Down Expand Up @@ -264,13 +227,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(file(process.out.bam[0][1]).name).match("cram_to_bam_index_bam") },
{ assert snapshot(file(process.out.csi[0][1]).name).match("cram_to_bam_index_csi") },
{ assert snapshot(process.out.bai).match("cram_to_bam_index_bai") },
{ assert snapshot(process.out.crai).match("cram_to_bam_index_crai") },
{ assert snapshot(process.out.cram).match("cram_to_bam_index_cram") },
{ assert snapshot(process.out.sam).match("cram_to_bam_index_sam") },
{ assert snapshot(process.out.versions).match("cram_to_bam_index_versions") }
{ assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam", "csi"])).match()}
)
}
}
Expand Down Expand Up @@ -300,15 +257,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(file(process.out.bam[0][1]).name).match("cram_to_bam_index_qname_bam") },
{ assert snapshot(file(process.out.csi[0][1]).name).match("cram_to_bam_index_qname_csi") },
{ assert snapshot(process.out.bai).match("cram_to_bam_index_qname_bai") },
{ assert snapshot(process.out.crai).match("cram_to_bam_index_qname_crai") },
{ assert snapshot(process.out.cram).match("cram_to_bam_index_qname_cram") },
{ assert snapshot(process.out.sam).match("cram_to_bam_index_qname_sam") },
{ assert snapshot(file(process.out.unselected[0][1]).name).match("cram_to_bam_index_qname_unselected") },
{ assert snapshot(file(process.out.unselected_index[0][1]).name).match("cram_to_bam_index_qname_unselected_csi") },
{ assert snapshot(process.out.versions).match("cram_to_bam_index_qname_versions") }
{ assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam", "bai", "unselected", "unselected_index"])).match()}
)
}
}
Expand Down Expand Up @@ -336,13 +285,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(file(process.out.bam[0][1]).name).match("bam_stub_bam") },
{ assert snapshot(file(process.out.csi[0][1]).name).match("bam_stub_csi") },
{ assert snapshot(process.out.bai).match("bam_stub_bai") },
{ assert snapshot(process.out.crai).match("bam_stub_crai") },
{ assert snapshot(process.out.cram).match("bam_stub_cram") },
{ assert snapshot(process.out.sam).match("bam_stub_sam") },
{ assert snapshot(process.out.versions).match("bam_stub_versions") }
{ assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam", "csi"])).match()}
)
}
}
Expand Down
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