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revert spacing
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ftabaro committed Nov 28, 2024
1 parent df9ec1e commit 62e6e7f
Showing 1 changed file with 13 additions and 4 deletions.
17 changes: 13 additions & 4 deletions modules/local/multiqc.nf
Original file line number Diff line number Diff line change
Expand Up @@ -10,45 +10,54 @@ process MULTIQC {
path multiqc_config
path mqc_custom_config
path logo

path 'fastqc/*'
path 'trimgalore/fastqc/*'
path 'trimgalore/*'

path 'alignment/library/*'
path 'alignment/library/*'
path 'alignment/library/*'

path 'alignment/merged_library/unfiltered/*'
path 'alignment/merged_library/unfiltered/*'
path 'alignment/merged_library/unfiltered/*'
path 'alignment/merged_library/unfiltered/picard_metrics/*'

path 'alignment/merged_library/filtered/*'
path 'alignment/merged_library/filtered/*'
path 'alignment/merged_library/filtered/*'
path 'alignment/merged_library/filtered/picard_metrics/*'

path 'preseq/*'

path 'deeptools/*'
path 'deeptools/*'

path 'phantompeakqualtools/*'
path 'phantompeakqualtools/*'
path 'phantompeakqualtools/*'
path 'phantompeakqualtools/*'

path 'macs3/peaks/*'
path 'macs3/peaks/*'
path 'macs3/annotation/*'
path 'macs3/featurecounts/*'

path 'deseq2/*'
path 'deseq2/*'

output:
path "*multiqc_report.html", emit: report
path "*_data", emit: data
path "*_plots", optional: true, emit: plots
path "versions.yml", emit: versions
path "*_data" , emit: data
path "*_plots" , optional: true, emit: plots
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ''
def args = task.ext.args ?: ''
def custom_config = params.multiqc_config ? "--config ${mqc_custom_config}" : ''
"""
multiqc \\
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