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Add option -p to set the # of cpus on stringtie (#601)

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* Add option -p  to set  the # of cpus on stringtie

* Bump version 2.1.7 to stringtie modules

* Output stringtie/merge version

* Fix padding

* Apply suggestions from code review

* Defining software variable

* Fix test, gff can't be md5 check, contains instead

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
Jose Espinosa-Carrasco 2021-07-21 15:38:40 +02:00 committed by GitHub
parent a0019d4175
commit 217303f5c1
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GPG key ID: 4AEE18F83AFDEB23
3 changed files with 20 additions and 9 deletions
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10
modules/stringtie/merge/main.nf
View file

@ -11,11 +11,11 @@ process STRINGTIE_MERGE {
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
// Note: 2.7X indices incompatible with AWS iGenomes. // Note: 2.7X indices incompatible with AWS iGenomes.
conda (params.enable_conda ? "bioconda::stringtie=2.1.4" : null) conda (params.enable_conda ? "bioconda::stringtie=2.1.7" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/stringtie:2.1.4--h7e0af3c_0" container "https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0"
} else { } else {
container "quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0" container "quay.io/biocontainers/stringtie:2.1.7--h978d192_0"
} }
input: input:
@ -24,12 +24,16 @@ process STRINGTIE_MERGE {
output: output:
path "stringtie.merged.gtf", emit: gtf path "stringtie.merged.gtf", emit: gtf
path "*.version.txt" , emit: version
script: script:
def software = getSoftwareName(task.process)
""" """
stringtie \\ stringtie \\
--merge $stringtie_gtf \\ --merge $stringtie_gtf \\
-G $annotation_gtf \\ -G $annotation_gtf \\
-o stringtie.merged.gtf -o stringtie.merged.gtf
echo \$(stringtie --version 2>&1) > ${software}.version.txt
""" """
} }

9
modules/stringtie/stringtie/main.nf
View file

@ -11,11 +11,11 @@ process STRINGTIE {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::stringtie=2.1.4" : null) conda (params.enable_conda ? "bioconda::stringtie=2.1.7" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/stringtie:2.1.4--h7e0af3c_0" container "https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0"
} else { } else {
container "quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0" container "quay.io/biocontainers/stringtie:2.1.7--h978d192_0"
} }
input: input:
@ -48,8 +48,9 @@ process STRINGTIE {
-A ${prefix}.gene.abundance.txt \\ -A ${prefix}.gene.abundance.txt \\
-C ${prefix}.coverage.gtf \\ -C ${prefix}.coverage.gtf \\
-b ${prefix}.ballgown \\ -b ${prefix}.ballgown \\
-p $task.cpus \\
$options.args $options.args
stringtie --version > ${software}.version.txt echo \$(stringtie --version 2>&1) > ${software}.version.txt
""" """
} }

10
tests/modules/stringtie/merge/test.yml
View file

@ -5,7 +5,10 @@
- stringtie/merge - stringtie/merge
files: files:
- path: ./output/test_stringtie_forward_merge/stringtie.merged.gtf - path: ./output/test_stringtie_forward_merge/stringtie.merged.gtf
md5sum: 676aa20a2d7a3db18136cdc7ba183099 contains:
- 'stringtie'
- 'merge'
- 'chr22'
- name: stringtie reverse-strand merge - name: stringtie reverse-strand merge
command: nextflow run ./tests/modules/stringtie/merge/ -entry test_stringtie_reverse_merge -c tests/config/nextflow.config command: nextflow run ./tests/modules/stringtie/merge/ -entry test_stringtie_reverse_merge -c tests/config/nextflow.config
@ -14,4 +17,7 @@
- stringtie/merge - stringtie/merge
files: files:
- path: ./output/test_stringtie_reverse_merge/stringtie.merged.gtf - path: ./output/test_stringtie_reverse_merge/stringtie.merged.gtf
md5sum: 67e5102722ecaeea1fb44d1ec0953474 contains:
- 'stringtie'
- 'merge'
- 'chr22'