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https://github.com/MillironX/taxprofiler.git
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Start working getting kraken and centrifuge working in MQC
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parent
1fe9c133f1
commit
e76b299705
3 changed files with 37 additions and 4 deletions
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@ -13,3 +13,35 @@ export_plots: true
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custom_logo: "nf-core-taxprofiler_logo_custom_light.png"
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custom_logo_url: https://nf-co.re/taxprofiler
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custom_logo_title: "nf-core/taxprofiler"
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run_modules:
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- fastqc
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- adapterRemoval
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- fastp
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- bowtie2
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- kraken
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- malt
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#extra_fn_clean_exts:
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# - '_fastp'
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# - '.pe.settings'
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# - '.se.settings'
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top_modules:
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- 'fastqc':
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name: "FastQC (pre-processing)"
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path_filters:
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- '*_raw.zip'
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- 'fastp'
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- 'fastqc':
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name: "FastQC (post-processing)"
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path_filters:
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- '*_processed.zip'
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- 'kraken':
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name: "Kraken"
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path_filters:
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- '*kraken.report'
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- 'kraken':
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name: Centrifuge"
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path_filters:
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- '*centrifuge.kreport'
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@ -285,7 +285,7 @@ process {
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withName: KRAKEN2_KRAKEN2 {
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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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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.kraken" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.kraken" }
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publishDir = [
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path: { "${params.outdir}/kraken2/${meta.db_name}" },
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mode: params.publish_dir_mode,
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@ -343,12 +343,12 @@ process {
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pattern: '*.{txt,sam,gz}'
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]
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.centrifuge" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.centrifuge" }
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}
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withName: CENTRIFUGE_KREPORT {
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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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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.centrifuge" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.centrifuge" }
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publishDir = [
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path: { "${params.outdir}/centrifuge/${meta.db_name}" },
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mode: params.publish_dir_mode,
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@ -127,7 +127,7 @@ workflow PROFILING {
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}
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KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db, params.kraken2_save_reads, params.kraken2_save_readclassification )
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ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report.collect{it[1]}.ifEmpty([]) )
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ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report )
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ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
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ch_raw_classifications = ch_raw_classifications.mix( KRAKEN2_KRAKEN2.out.classified_reads_assignment )
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ch_raw_profiles = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.report )
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@ -152,6 +152,7 @@ workflow PROFILING {
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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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ch_multiqc_files = ch_multiqc_files.mix( CENTRIFUGE_KREPORT.out.kreport )
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}
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