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Merge pull request #109 from nf-core/centrifuge_mqc
Trying to get Centrifuge output into MQC
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commit
de70b0a01d
3 changed files with 42 additions and 3 deletions
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@ -13,3 +13,41 @@ 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-Trimming)"
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path_filters:
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- "*raw_*fastqc.zip"
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- "fastp"
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- "adapterRemoval"
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- "fastqc":
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name: "FastQC (post-Trimming)"
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path_filters:
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- "*raw_*processed.zip"
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- "kraken":
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name: "Kraken"
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path_filters:
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- "*.kraken2.report.txt"
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- "kraken":
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name: "Centrifuge"
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anchor: "centrifuge"
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target: "Centrifuge"
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doi: "10.1101/gr.210641.116"
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info: "is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index. Note: Figure title"
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extra: "Note: plot title will say Kraken2 due to Centrifuge producing the same output format as Kraken. If activated, see the actual Kraken2 results in the section above."
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path_filters:
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- "*.centrifuge.txt"
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@ -343,13 +343,13 @@ 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}-${meta.db_name}.centrifuge" }
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}
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withName: CENTRIFUGE_KREPORT {
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errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'}
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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ext.prefix = params.perform_runmerging ? { "${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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@ -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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@ -185,7 +186,7 @@ workflow PROFILING {
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KAIJU_KAIJU ( ch_input_for_kaiju.reads, ch_input_for_kaiju.db)
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KAIJU_KAIJU2TABLE (KAIJU_KAIJU.out.results, ch_input_for_kaiju.db, params.kaiju_taxon_name)
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ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary )
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ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary )
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ch_versions = ch_versions.mix( KAIJU_KAIJU.out.versions.first() )
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ch_raw_classifications = ch_raw_classifications.mix( KAIJU_KAIJU.out.results )
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ch_raw_profiles = ch_raw_profiles.mix( KAIJU_KAIJU2TABLE.out.summary )
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