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Merge pull request #105 from genomic-medicine-sweden/diamond-update

Update the dev branch with the DIAMOND module update
This commit is contained in:
Mahwash Jamy 2022-07-28 17:21:59 +02:00 committed by GitHub
commit 06298e867c
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5 changed files with 13 additions and 3 deletions

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@ -387,7 +387,7 @@ process {
publishDir = [
path: { "${params.outdir}/diamond/${meta.db_name}" },
mode: params.publish_dir_mode,
pattern: '*.{blast,xml,txt,daa,sam,tsv,paf}'
pattern: '*.{blast,xml,txt,daa,sam,tsv,paf,log}'
]
}

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@ -28,7 +28,7 @@
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"diamond/blastx": {
"git_sha": "bd3bfe0817246082525ab93707976676b1fe208b"
"git_sha": "3531824af826c16cd252bc5aa82ae169b244ebaa"
},
"fastp": {
"git_sha": "d0a1cbb703a130c19f6796c3fce24fbe7dfce789"

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@ -21,6 +21,7 @@ process DIAMOND_BLASTX {
tuple val(meta), path('*.sam') , optional: true, emit: sam
tuple val(meta), path('*.tsv') , optional: true, emit: tsv
tuple val(meta), path('*.paf') , optional: true, emit: paf
tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions
when:
@ -54,7 +55,10 @@ process DIAMOND_BLASTX {
--query $fasta \\
--outfmt ${outfmt} ${columns} \\
$args \\
--out ${prefix}.${out_ext}
--out ${prefix}.${out_ext} \\
--log
mv diamond.log ${prefix}.log
cat <<-END_VERSIONS > versions.yml
"${task.process}":

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

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@ -208,6 +208,7 @@ workflow PROFILING {
DIAMOND_BLASTX ( ch_input_for_diamond.reads, ch_input_for_diamond.db, ch_diamond_reads_format , [] )
ch_versions = ch_versions.mix( DIAMOND_BLASTX.out.versions.first() )
ch_raw_profiles = ch_raw_profiles.mix( DIAMOND_BLASTX.out.tsv )
ch_multiqc_files = ch_multiqc_files.mix( DIAMOND_BLASTX.out.log )
}