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Start working getting kraken and centrifuge working in MQC

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This commit is contained in:
James A. Fellows Yates 2022-07-26 08:18:54 +00:00
parent 1fe9c133f1
commit e76b299705
3 changed files with 37 additions and 4 deletions
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32
assets/multiqc_config.yml
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@ -13,3 +13,35 @@ 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-processing)"
path_filters:
- '*_raw.zip'
- 'fastp'
- 'fastqc':
name: "FastQC (post-processing)"
path_filters:
- '*_processed.zip'
- 'kraken':
name: "Kraken"
path_filters:
- '*kraken.report'
- 'kraken':
name: Centrifuge"
path_filters:
- '*centrifuge.kreport'

6
conf/modules.config
View file

@ -285,7 +285,7 @@ process {
withName: KRAKEN2_KRAKEN2 {
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}.kraken" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.kraken" }
publishDir = [
path: { "${params.outdir}/kraken2/${meta.db_name}" },
mode: params.publish_dir_mode,
@ -343,12 +343,12 @@ process {
pattern: '*.{txt,sam,gz}'
]
ext.args = { "${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 {
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

@ -127,7 +127,7 @@ workflow PROFILING {
}
KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db, params.kraken2_save_reads, params.kraken2_save_readclassification )
ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report.collect{it[1]}.ifEmpty([]) )
ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report )
ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
ch_raw_classifications = ch_raw_classifications.mix( KRAKEN2_KRAKEN2.out.classified_reads_assignment )
ch_raw_profiles = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.report )
@ -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 )
}