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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:
commit
06298e867c
5 changed files with 13 additions and 3 deletions
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@ -387,7 +387,7 @@ process {
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publishDir = [
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path: { "${params.outdir}/diamond/${meta.db_name}" },
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mode: params.publish_dir_mode,
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pattern: '*.{blast,xml,txt,daa,sam,tsv,paf}'
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pattern: '*.{blast,xml,txt,daa,sam,tsv,paf,log}'
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]
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}
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@ -28,7 +28,7 @@
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"diamond/blastx": {
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"git_sha": "bd3bfe0817246082525ab93707976676b1fe208b"
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"git_sha": "3531824af826c16cd252bc5aa82ae169b244ebaa"
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},
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"fastp": {
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"git_sha": "d0a1cbb703a130c19f6796c3fce24fbe7dfce789"
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6
modules/nf-core/modules/diamond/blastx/main.nf
generated
6
modules/nf-core/modules/diamond/blastx/main.nf
generated
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@ -21,6 +21,7 @@ process DIAMOND_BLASTX {
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tuple val(meta), path('*.sam') , optional: true, emit: sam
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tuple val(meta), path('*.tsv') , optional: true, emit: tsv
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tuple val(meta), path('*.paf') , optional: true, emit: paf
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tuple val(meta), path("*.log") , emit: log
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path "versions.yml" , emit: versions
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when:
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@ -54,7 +55,10 @@ process DIAMOND_BLASTX {
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--query $fasta \\
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--outfmt ${outfmt} ${columns} \\
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$args \\
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--out ${prefix}.${out_ext}
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--out ${prefix}.${out_ext} \\
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--log
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mv diamond.log ${prefix}.log
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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5
modules/nf-core/modules/diamond/blastx/meta.yml
generated
5
modules/nf-core/modules/diamond/blastx/meta.yml
generated
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@ -70,7 +70,12 @@ output:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- log:
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type: file
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description: Log file containing stdout information
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pattern: "*.{log}"
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authors:
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- "@spficklin"
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- "@jfy133"
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- "@mjamy"
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@ -208,6 +208,7 @@ workflow PROFILING {
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DIAMOND_BLASTX ( ch_input_for_diamond.reads, ch_input_for_diamond.db, ch_diamond_reads_format , [] )
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ch_versions = ch_versions.mix( DIAMOND_BLASTX.out.versions.first() )
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ch_raw_profiles = ch_raw_profiles.mix( DIAMOND_BLASTX.out.tsv )
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ch_multiqc_files = ch_multiqc_files.mix( DIAMOND_BLASTX.out.log )
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}
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