mirror of
https://github.com/MillironX/taxprofiler.git
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Merge remote-tracking branch 'origin/dev' into porechop-log
This commit is contained in:
commit
873a13e028
7 changed files with 21 additions and 10 deletions
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@ -145,7 +145,7 @@ process {
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publishDir = [
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path: { "${params.outdir}/filtlong" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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pattern: '*.{fastq.gz,log}',
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enabled: params.save_preprocessed_reads
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]
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}
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@ -347,6 +347,7 @@ process {
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}
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withName: CENTRIFUGE_KREPORT {
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errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'}
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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@ -386,7 +387,7 @@ process {
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publishDir = [
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path: { "${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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@ -22,13 +22,13 @@
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"git_sha": "d2726fcf75063960f06b36d2229a4c0966614108"
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},
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"centrifuge/kreport": {
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"git_sha": "be4ae28c3c95b3c4047a7d9fb4cb0ed749631cea"
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"git_sha": "734d0db6079a4aa43b6509b207e5d6feb35d4838"
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},
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"custom/dumpsoftwareversions": {
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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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@ -8,7 +8,7 @@ process CENTRIFUGE_KREPORT {
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'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }"
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input:
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tuple val(meta), path(results)
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tuple val(meta), path(report)
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path db
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output:
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@ -23,7 +23,7 @@ process CENTRIFUGE_KREPORT {
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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db_name=`find -L ${db} -name "*.1.cf" -not -name "._*" | sed 's/.1.cf//'`
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centrifuge-kreport -x \$db_name ${results} > ${prefix}.txt
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centrifuge-kreport -x \$db_name ${report} > ${prefix}.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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@ -15,9 +15,9 @@ input:
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- results:
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- report:
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type: file
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description: File containing the centrifuge classification results
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description: File containing the centrifuge classification report
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pattern: "*.{txt}"
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output:
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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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@ -148,7 +148,7 @@ workflow PROFILING {
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}
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CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_reads, params.centrifuge_save_reads, params.centrifuge_save_reads )
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CENTRIFUGE_KREPORT (CENTRIFUGE_CENTRIFUGE.out.results, ch_input_for_centrifuge.db)
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CENTRIFUGE_KREPORT (CENTRIFUGE_CENTRIFUGE.out.report, ch_input_for_centrifuge.db)
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ch_versions = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
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ch_raw_classifications = ch_raw_classifications.mix( CENTRIFUGE_CENTRIFUGE.out.results )
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ch_raw_profiles = ch_raw_profiles.mix( CENTRIFUGE_KREPORT.out.kreport )
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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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