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Update DIAMOND module to output log file (#1879)

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* Update DIAMOND module to output log file

* Updating DIAMOND module to output log file - with jfy133 suggestions

Co-authored-by: Mahwash Jamy <mahwashjamy@n183-p186.eduroam.kth.se>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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Mahwash Jamy 2022-07-14 16:18:28 +02:00 committed by GitHub
parent 013035eb5c
commit 3531824af8
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3 changed files with 18 additions and 6 deletions
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6
modules/diamond/blastx/main.nf
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@ -21,6 +21,7 @@ process DIAMOND_BLASTX {
tuple val(meta), path('*.sam') , optional: true, emit: sam tuple val(meta), path('*.sam') , optional: true, emit: sam
tuple val(meta), path('*.tsv') , optional: true, emit: tsv tuple val(meta), path('*.tsv') , optional: true, emit: tsv
tuple val(meta), path('*.paf') , optional: true, emit: paf tuple val(meta), path('*.paf') , optional: true, emit: paf
tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
when: when:
@ -54,7 +55,10 @@ process DIAMOND_BLASTX {
--query $fasta \\ --query $fasta \\
--outfmt ${outfmt} ${columns} \\ --outfmt ${outfmt} ${columns} \\
$args \\ $args \\
--out ${prefix}.${out_ext} --out ${prefix}.${out_ext} \\
--log
mv diamond.log ${prefix}.log
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

5
modules/diamond/blastx/meta.yml
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@ -70,7 +70,12 @@ output:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- log:
type: file
description: Log file containing stdout information
pattern: "*.{log}"
authors: authors:
- "@spficklin" - "@spficklin"
- "@jfy133" - "@jfy133"
- "@mjamy"

13
tests/modules/diamond/blastx/test.yml
View file

@ -1,18 +1,21 @@
- name: diamond blastx test_diamond_blastx - name: diamond blastx test_diamond_blastx
command: nextflow run tests/modules/diamond/blastx -entry test_diamond_blastx -c tests/config/nextflow.config command: nextflow run ./tests/modules/diamond/blastx -entry test_diamond_blastx -c ./tests/config/nextflow.config -c ./tests/modules/diamond/blastx/nextflow.config
tags: tags:
- diamond - diamond
- diamond/blastx - diamond/blastx
files: files:
- path: output/diamond/proteome.fasta.dmnd
- path: output/diamond/test.diamond_blastx.log
contains: ["queries aligned"]
- path: output/diamond/test.diamond_blastx.txt - path: output/diamond/test.diamond_blastx.txt
- path: output/diamond/versions.yml
- name: diamond blastx test_diamond_blastx_daa - name: diamond blastx test_diamond_blastx_daa
command: nextflow run tests/modules/diamond/blastx -entry test_diamond_blastx_daa -c tests/config/nextflow.config command: nextflow run ./tests/modules/diamond/blastx -entry test_diamond_blastx_daa -c ./tests/config/nextflow.config -c ./tests/modules/diamond/blastx/nextflow.config
tags: tags:
- diamond - diamond
- diamond/blastx - diamond/blastx
files: files:
- path: output/diamond/proteome.fasta.dmnd
- path: output/diamond/test.diamond_blastx.daa - path: output/diamond/test.diamond_blastx.daa
md5sum: 0df4a833408416f32981415873facc11 - path: output/diamond/test.diamond_blastx.log
- path: output/diamond/versions.yml contains: ["queries aligned"]