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Merge pull request #104 from nf-core/motus-profile-update
Update mOTUs profile module and mix log for multiqc
This commit is contained in:
commit
d7ca3df160
5 changed files with 11 additions and 3 deletions
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@ -391,6 +391,7 @@ process {
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}
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withName: MOTUS_PROFILE {
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/motus/${meta.db_name}" },
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mode: params.publish_dir_mode
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@ -79,7 +79,7 @@
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"motus/profile": {
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"git_sha": "6b960f0e75bbb4d5bd301cd3875fa078d0eab4d1"
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"git_sha": "b6ed584443ad68ac41e6975994139454a4f23c18"
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},
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"multiqc": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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6
modules/nf-core/modules/motus/profile/main.nf
generated
6
modules/nf-core/modules/motus/profile/main.nf
generated
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@ -15,6 +15,7 @@ process MOTUS_PROFILE {
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tuple val(meta), path("*.out"), emit: out
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tuple val(meta), path("*.bam"), optional: true, emit: bam
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tuple val(meta), path("*.mgc"), optional: true, emit: mgc
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tuple val(meta), path("*.log") , emit: log
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path "versions.yml" , emit: versions
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when:
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@ -36,7 +37,8 @@ process MOTUS_PROFILE {
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$refdb \\
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-t $task.cpus \\
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-n $prefix \\
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-o ${prefix}.out
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-o ${prefix}.out \\
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2> ${prefix}.log
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## mOTUs version number is not available from command line.
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## mOTUs save the version number in index database folder.
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@ -48,7 +50,7 @@ process MOTUS_PROFILE {
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fi
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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mOTUs: \$VERSION
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motus: \$VERSION
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END_VERSIONS
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"""
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}
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4
modules/nf-core/modules/motus/profile/meta.yml
generated
4
modules/nf-core/modules/motus/profile/meta.yml
generated
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@ -56,6 +56,10 @@ output:
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type: file
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description: Optional intermediate mgc read count table file saved with `-M`.
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pattern: "*.{mgc}"
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- log:
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type: file
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description: Standard error logging file containing summary statistics
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pattern: "*.log"
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authors:
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- "@jianhong"
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@ -227,6 +227,7 @@ workflow PROFILING {
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MOTUS_PROFILE ( ch_input_for_motus.reads, ch_input_for_motus.db )
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ch_versions = ch_versions.mix( MOTUS_PROFILE.out.versions.first() )
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ch_raw_profiles = ch_raw_profiles.mix( MOTUS_PROFILE.out.out )
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ch_multiqc_files = ch_multiqc_files.mix( MOTUS_PROFILE.out.log.map{it[1]} )
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}
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