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Merge pull request #109 from nf-core/centrifuge_mqc

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Trying to get Centrifuge output into MQC
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James A. Fellows Yates 2022-07-29 13:36:25 +02:00 committed by GitHub
commit de70b0a01d
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3 changed files with 42 additions and 3 deletions
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38
assets/multiqc_config.yml
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@ -13,3 +13,41 @@ export_plots: true
custom_logo: "nf-core-taxprofiler_logo_custom_light.png"
custom_logo_url: https://nf-co.re/taxprofiler
custom_logo_title: "nf-core/taxprofiler"
run_modules:
- fastqc
- adapterRemoval
- fastp
- bowtie2
- kraken
- malt
#extra_fn_clean_exts:
# - '_fastp'
# - '.pe.settings'
# - '.se.settings'
top_modules:
- "fastqc":
name: "FastQC (pre-Trimming)"
path_filters:
- "*raw_*fastqc.zip"
- "fastp"
- "adapterRemoval"
- "fastqc":
name: "FastQC (post-Trimming)"
path_filters:
- "*raw_*processed.zip"
- "kraken":
name: "Kraken"
path_filters:
- "*.kraken2.report.txt"
- "kraken":
name: "Centrifuge"
anchor: "centrifuge"
target: "Centrifuge"
doi: "10.1101/gr.210641.116"
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"
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."
path_filters:
- "*.centrifuge.txt"

4
conf/modules.config
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@ -343,13 +343,13 @@ process {
pattern: '*.{txt,sam,gz}'
]
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.centrifuge" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.centrifuge" }
}
withName: CENTRIFUGE_KREPORT {
errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'}
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.centrifuge" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.centrifuge" }
publishDir = [
path: { "${params.outdir}/centrifuge/${meta.db_name}" },
mode: params.publish_dir_mode,

3
subworkflows/local/profiling.nf
View file

@ -152,6 +152,7 @@ workflow PROFILING {
ch_versions = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
ch_raw_classifications = ch_raw_classifications.mix( CENTRIFUGE_CENTRIFUGE.out.results )
ch_raw_profiles = ch_raw_profiles.mix( CENTRIFUGE_KREPORT.out.kreport )
ch_multiqc_files = ch_multiqc_files.mix( CENTRIFUGE_KREPORT.out.kreport )
}
@ -185,7 +186,7 @@ workflow PROFILING {
KAIJU_KAIJU ( ch_input_for_kaiju.reads, ch_input_for_kaiju.db)
KAIJU_KAIJU2TABLE (KAIJU_KAIJU.out.results, ch_input_for_kaiju.db, params.kaiju_taxon_name)
ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary )
ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary )
ch_versions = ch_versions.mix( KAIJU_KAIJU.out.versions.first() )
ch_raw_classifications = ch_raw_classifications.mix( KAIJU_KAIJU.out.results )
ch_raw_profiles = ch_raw_profiles.mix( KAIJU_KAIJU2TABLE.out.summary )