samtools/*stats*: use prefix for outputs (#1788)

* use prefix in flagstat

* use prefix in idxstats

* use prefix in stats

* update test.yml
This commit is contained in:
Matthias De Smet 2022-06-16 13:42:01 +02:00 committed by GitHub
parent 052b9f2fe9
commit ecece498f1
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GPG key ID: 4AEE18F83AFDEB23
6 changed files with 23 additions and 19 deletions

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@ -19,12 +19,13 @@ process SAMTOOLS_FLAGSTAT {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
samtools \\
flagstat \\
--threads ${task.cpus-1} \\
$bam \\
> ${bam}.flagstat
> ${prefix}.flagstat
cat <<-END_VERSIONS > versions.yml
"${task.process}":

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@ -19,11 +19,13 @@ process SAMTOOLS_IDXSTATS {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
samtools \\
idxstats \\
$bam \\
> ${bam}.idxstats
> ${prefix}.idxstats
cat <<-END_VERSIONS > versions.yml
"${task.process}":

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@ -8,7 +8,7 @@ process SAMTOOLS_STATS {
'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
input:
tuple val(meta), path(input), path(input_index)
tuple val(meta), path(bam), path(bai)
path fasta
output:
@ -20,14 +20,15 @@ process SAMTOOLS_STATS {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def reference = fasta ? "--reference ${fasta}" : ""
"""
samtools \\
stats \\
--threads ${task.cpus-1} \\
${reference} \\
${input} \\
> ${input}.stats
${bam} \\
> ${prefix}.stats
cat <<-END_VERSIONS > versions.yml
"${task.process}":
@ -38,7 +39,7 @@ process SAMTOOLS_STATS {
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${input}.stats
touch ${prefix}.stats
cat <<-END_VERSIONS > versions.yml
"${task.process}":

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@ -1,8 +1,8 @@
- name: samtools flagstat
command: nextflow run ./tests/modules/samtools/flagstat -entry test_samtools_flagstat -c ./tests/config/nextflow.config -c ./tests/modules/samtools/flagstat/nextflow.config
- name: samtools flagstat test_samtools_flagstat
command: nextflow run ./tests/modules/samtools/flagstat -entry test_samtools_flagstat -c ./tests/config/nextflow.config -c ./tests/modules/samtools/flagstat/nextflow.config
tags:
- samtools
- samtools/flagstat
files:
- path: ./output/samtools/test.paired_end.sorted.bam.flagstat
- path: output/samtools/test.flagstat
md5sum: 4f7ffd1e6a5e85524d443209ac97d783

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@ -1,8 +1,8 @@
- name: samtools idxstats
command: nextflow run ./tests/modules/samtools/idxstats -entry test_samtools_idxstats -c ./tests/config/nextflow.config -c ./tests/modules/samtools/idxstats/nextflow.config
- name: samtools idxstats test_samtools_idxstats
command: nextflow run ./tests/modules/samtools/idxstats -entry test_samtools_idxstats -c ./tests/config/nextflow.config -c ./tests/modules/samtools/idxstats/nextflow.config
tags:
- samtools
- samtools/idxstats
- samtools
files:
- path: ./output/samtools/test.paired_end.sorted.bam.idxstats
- path: output/samtools/test.idxstats
md5sum: df60a8c8d6621100d05178c93fb053a2

View file

@ -1,17 +1,17 @@
- name: samtools stats test_samtools_stats
command: nextflow run ./tests/modules/samtools/stats -entry test_samtools_stats -c ./tests/config/nextflow.config -c ./tests/modules/samtools/stats/nextflow.config
command: nextflow run ./tests/modules/samtools/stats -entry test_samtools_stats -c ./tests/config/nextflow.config -c ./tests/modules/samtools/stats/nextflow.config
tags:
- samtools/stats
- samtools
- samtools/stats
files:
- path: output/samtools/test.paired_end.sorted.bam.stats
- path: output/samtools/test.stats
md5sum: c1e9ad551281b0bca32be1c832d125af
- name: samtools stats test_samtools_stats_cram
command: nextflow run ./tests/modules/samtools/stats -entry test_samtools_stats_cram -c ./tests/config/nextflow.config -c ./tests/modules/samtools/stats/nextflow.config
command: nextflow run ./tests/modules/samtools/stats -entry test_samtools_stats_cram -c ./tests/config/nextflow.config -c ./tests/modules/samtools/stats/nextflow.config
tags:
- samtools/stats
- samtools
- samtools/stats
files:
- path: output/samtools/test.paired_end.recalibrated.sorted.cram.stats
- path: output/samtools/test.stats
md5sum: 103cd7b19743c42dab9ce570144c6f36