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--output-unselected option in samtools view #2674

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merged 15 commits into from
Jun 21, 2024
Merged

--output-unselected option in samtools view #2674

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6ad23a7
add unoutput option
priyanka-surana Dec 16, 2022
45bddda
trying to fix emit
priyanka-surana Dec 16, 2022
15d6bed
Merge branch 'master' into samtools_view
priyanka-surana Dec 16, 2022
a21f2e1
CI fixed, tests still incorrect
priyanka-surana Dec 16, 2022
a2240e4
Fixed the checksums
muffato Sep 4, 2023
542deb1
Merge branch 'master' into samtools_view
muffato Sep 8, 2023
83dfaf5
Fixed the syntax
muffato Sep 4, 2023
d86bb73
Call this "unselected" rather than "unoutput"
muffato Sep 11, 2023
f699546
Merge branch 'master' into samtools_view
muffato Jun 21, 2024
b1c2b54
Alignment rocks
muffato Jun 21, 2024
bb0910f
bugfix: the variable needs to be visible by the output declaration
muffato Jun 21, 2024
95523fb
bugfix: this was not the regular file name
muffato Jun 21, 2024
047741e
Updated the test case
muffato Jun 21, 2024
bd6a527
fixup! Alignment rocks
muffato Jun 21, 2024
194ec39
Updated the meta.yml
muffato Jun 21, 2024
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40 changes: 21 additions & 19 deletions modules/nf-core/samtools/view/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -13,27 +13,29 @@ process SAMTOOLS_VIEW {
path qname

output:
tuple val(meta), path("*.bam"), emit: bam, optional: true
tuple val(meta), path("*.cram"), emit: cram, optional: true
tuple val(meta), path("*.sam"), emit: sam, optional: true
tuple val(meta), path("*.bai"), emit: bai, optional: true
tuple val(meta), path("*.csi"), emit: csi, optional: true
tuple val(meta), path("*.crai"), emit: crai, optional: true
path "versions.yml", emit: versions
tuple val(meta), path("${prefix}.bam"), emit: bam, optional: true
tuple val(meta), path("${prefix}.cram"), emit: cram, optional: true
tuple val(meta), path("${prefix}.sam"), emit: sam, optional: true
tuple val(meta), path("${prefix}.${file_type}.bai"), emit: bai, optional: true
tuple val(meta), path("${prefix}.${file_type}.csi"), emit: csi, optional: true
tuple val(meta), path("${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}.{bai,csi,crsi}"), emit: unselected_index, optional: true
path "versions.yml", emit: versions

when:
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
prefix = task.ext.prefix ?: "${meta.id}"
def reference = fasta ? "--reference ${fasta}" : ""
def readnames = qname ? "--qname-file ${qname}": ""
def file_type = args.contains("--output-fmt sam") ? "sam" :
args.contains("--output-fmt bam") ? "bam" :
args.contains("--output-fmt cram") ? "cram" :
input.getExtension()
file_type = args.contains("--output-fmt sam") ? "sam" :
args.contains("--output-fmt bam") ? "bam" :
args.contains("--output-fmt cram") ? "cram" :
input.getExtension()
readnames = qname ? "--qname-file ${qname} --output-unselected ${prefix}.unselected.${file_type}": ""
if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
"""
samtools \\
Expand All @@ -54,14 +56,14 @@ process SAMTOOLS_VIEW {

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def file_type = args.contains("--output-fmt sam") ? "sam" :
args.contains("--output-fmt bam") ? "bam" :
args.contains("--output-fmt cram") ? "cram" :
input.getExtension()
prefix = task.ext.prefix ?: "${meta.id}"
file_type = args.contains("--output-fmt sam") ? "sam" :
args.contains("--output-fmt bam") ? "bam" :
args.contains("--output-fmt cram") ? "cram" :
input.getExtension()
if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"

def index = args.contains("--write-index") ? "touch ${prefix}.csi" : ""
def index = args.contains("--write-index") ? "touch ${prefix}.${file_type}.csi" : ""

"""
touch ${prefix}.${file_type}
Expand Down
9 changes: 9 additions & 0 deletions modules/nf-core/samtools/view/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -73,6 +73,15 @@ output:
type: file
description: optional CRAM file index
pattern: "*.{crai}"
# unselected and unselected_index are created when passing a qname
- unselected:
type: file
description: optional file with unselected alignments
pattern: "*.unselected.{bam,cram,sam}"
- unselected_index:
type: file
description: index for the "unselected" file
pattern: "*.unselected.{bai,csi,crai}"
- versions:
type: file
description: File containing software versions
Expand Down
2 changes: 2 additions & 0 deletions modules/nf-core/samtools/view/tests/main.nf.test
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Expand Up @@ -172,6 +172,8 @@ nextflow_process {
{ 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") }
)
}
Expand Down
22 changes: 21 additions & 1 deletion modules/nf-core/samtools/view/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -355,6 +355,26 @@
},
"timestamp": "2024-02-12T19:38:23.322874"
},
"cram_to_bam_index_qname_unselected": {
"content": [
"test.unselected.bam"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.04.3"
},
"timestamp": "2024-02-12T19:38:23.322874"
},
"cram_to_bam_index_qname_unselected_csi": {
"content": [
"test.unselected.bam.csi"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.04.3"
},
"timestamp": "2024-02-12T19:38:23.328458"
},
"bam_versions": {
"content": [
[
Expand Down Expand Up @@ -477,7 +497,7 @@
},
"bam_stub_csi": {
"content": [
"test.csi"
"test.bam.csi"
],
"meta": {
"nf-test": "0.8.4",
Expand Down
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