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https://github.com/MillironX/taxprofiler.git
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Make parameter naming more consistent for clipmerge
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parent
51a0acd05b
commit
8012998542
4 changed files with 20 additions and 15 deletions
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@ -41,7 +41,7 @@ process {
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// TODO also include option to NOT merge
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ext.args = [
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{ ${meta.single_end} } == 0 ? "-m" : '',
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params.fastp_exclude_unmerged ? '' : "--include_unmerged"
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params.shortread_excludeunmerged ? '' : "--include_unmerged"
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].join(' ').trim()
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publishDir = [
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path: { "${params.outdir}/fastp" },
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@ -84,7 +84,7 @@ process {
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pattern: '*.{rma6,tab,text,sam,log}'
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]
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ext.args = { "${meta.db_params}" }
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ext.when = params.run_malt
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ext.prefix = { "${meta.id}-${meta.db_name}" }
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}
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withName: KRAKEN2_KRAKEN2 {
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@ -94,7 +94,6 @@ process {
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pattern: '.{fastq.gz,txt}'
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]
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ext.args = { "${meta.db_params}" }
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ext.when = params.run_kraken2
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ext.prefix = { "${meta.id}-${meta.db_name}" }
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}
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@ -55,9 +55,9 @@ params {
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databases = null
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// FASTQ preprocessing
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fastp_clip_merge = false
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fastp_exclude_unmerged = true
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remove_adapters = false
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shortread_clipmerge = false
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shortread_excludeunmerged = true
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longread_clip = false
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// MALT
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run_malt = false
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@ -23,7 +23,7 @@ workflow SHORTREAD_PREPROCESSING {
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// TODO move to subworkflow
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if ( params.fastp_clip_merge ) {
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if ( params.shortread_clipmerge ) {
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ch_input_for_fastp = reads
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.dump(tag: "pre-fastp_branch")
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@ -100,17 +100,14 @@ workflow TAXPROFILER {
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//
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// PERFORM PREPROCESSING
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//
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if ( params.fastp_clip_merge ) {
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if ( params.shortread_clipmerge ) {
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SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq )
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}
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ch_multiqc_files = Channel.empty()
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if ( params.remove_adapters ) {
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if ( params.longread_clip ) {
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ch_longreads_preprocessed = LONGREAD_PREPROCESSING ( INPUT_CHECK.out.nanopore ).reads
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.map { it -> [ it[0], [it[1]] ] }
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ch_versions = ch_versions.mix(LONGREAD_PREPROCESSING.out.versions.first())
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ch_multiqc_files = ch_multiqc_files.mix(LONGREAD_PREPROCESSING.out.mqc)
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} else {
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ch_longreads_preprocessed = INPUT_CHECK.out.nanopore
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}
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@ -187,9 +184,13 @@ workflow TAXPROFILER {
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//
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// RUN PROFILING
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//
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MALT_RUN ( ch_input_for_malt.reads, params.malt_mode, ch_input_for_malt.db )
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KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db )
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if ( params.run_malt ) {
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MALT_RUN ( ch_input_for_malt.reads, params.malt_mode, ch_input_for_malt.db )
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}
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if ( params.run_kraken2 ) {
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KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db )
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}
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//
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// MODULE: MultiQC
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@ -197,14 +198,19 @@ workflow TAXPROFILER {
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workflow_summary = WorkflowTaxprofiler.paramsSummaryMultiqc(workflow, summary_params)
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ch_workflow_summary = Channel.value(workflow_summary)
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ch_multiqc_files = Channel.empty()
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ch_multiqc_files = ch_multiqc_files.mix(Channel.from(ch_multiqc_config))
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ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([]))
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ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
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ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
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ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
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if (params.fastp_clip_merge) {
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if (params.shortread_clipmerge) {
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ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_PREPROCESSING.out.mqc)
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}
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if (params.longread_clip) {
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ch_multiqc_files = ch_multiqc_files.mix(LONGREAD_PREPROCESSING.out.mqc)
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}
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if (params.run_kraken2) {
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ch_multiqc_files = ch_multiqc_files.mix(KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([]))
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ch_versions = ch_versions.mix(KRAKEN2_KRAKEN2.out.versions.first())
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