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Fix multiqc shared mem error #436

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Fix multiqc shared mem error #436

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52931d7
update multiqc module
ftabaro Nov 21, 2024
92da3ac
update multiqc local module
ftabaro Nov 21, 2024
df9ec1e
Merge branch 'dev' into fix-multiqc-shared-mem-error
ftabaro Nov 28, 2024
62e6e7f
revert spacing
ftabaro Nov 28, 2024
1b7b81e
update CHANGELOG.md
ftabaro Nov 28, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [[PR #434](https://github.com/nf-core/chipseq/pull/434)] - Prevent pipeline fails from erroneous param validation when igenomes is used.
- [[#432](https://github.com/nf-core/chipseq/issues/432)] - Fix `GFFREAD` call to have the two expected input channels.
- [[#428](https://github.com/nf-core/chipseq/issues/428)] - Bump MultiQC version to 1.25.1

### Parameters

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71 changes: 35 additions & 36 deletions modules/local/multiqc.nf
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@@ -1,70 +1,69 @@
process MULTIQC {
label 'process_medium'

conda "bioconda::multiqc=1.23"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/multiqc:1.23--pyhdfd78af_0' :
'biocontainers/multiqc:1.23--pyhdfd78af_0' }"
conda "bioconda::multiqc=1.25.1"
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0'
: 'biocontainers/multiqc:1.25.1--pyhdfd78af_0'}"

input:
path workflow_summary
path multiqc_config
path mqc_custom_config
path logo

path ('fastqc/*')
path ('trimgalore/fastqc/*')
path ('trimgalore/*')
path 'fastqc/*'
path 'trimgalore/fastqc/*'
path 'trimgalore/*'
Comment on lines +14 to +16
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Actually, to be more consistent with standard modules implementation I would suggest this instead:

Suggested change
path 'fastqc/*'
path 'trimgalore/fastqc/*'
path 'trimgalore/*'
path "fastqc/*"
path "trimgalore/fastqc/*"
path "trimgalore/*"


path ('alignment/library/*')
path ('alignment/library/*')
path ('alignment/library/*')
path 'alignment/library/*'
path 'alignment/library/*'
path 'alignment/library/*'
Comment on lines +18 to +20
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Suggested change
path 'alignment/library/*'
path 'alignment/library/*'
path 'alignment/library/*'
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/unfiltered/*'
path 'alignment/merged_library/unfiltered/*'
path 'alignment/merged_library/unfiltered/*'
path 'alignment/merged_library/unfiltered/picard_metrics/*'
Comment on lines +22 to +25
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Suggested change
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/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 'alignment/merged_library/filtered/*'
path 'alignment/merged_library/filtered/*'
path 'alignment/merged_library/filtered/*'
path 'alignment/merged_library/filtered/picard_metrics/*'
Comment on lines +27 to +30
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Suggested change
path 'alignment/merged_library/filtered/*'
path 'alignment/merged_library/filtered/*'
path 'alignment/merged_library/filtered/*'
path 'alignment/merged_library/filtered/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 'preseq/*'
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Suggested change
path 'preseq/*'
path "preseq/*"


path ('deeptools/*')
path ('deeptools/*')
path 'deeptools/*'
path 'deeptools/*'
Comment on lines +34 to +35
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Suggested change
path 'deeptools/*'
path 'deeptools/*'
path "deeptools/*"
path "deeptools/*"


path ('phantompeakqualtools/*')
path ('phantompeakqualtools/*')
path ('phantompeakqualtools/*')
path ('phantompeakqualtools/*')
path 'phantompeakqualtools/*'
path 'phantompeakqualtools/*'
path 'phantompeakqualtools/*'
path 'phantompeakqualtools/*'
Comment on lines +37 to +40
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Suggested change
path 'phantompeakqualtools/*'
path 'phantompeakqualtools/*'
path 'phantompeakqualtools/*'
path 'phantompeakqualtools/*'
path "phantompeakqualtools/*"
path "phantompeakqualtools/*"
path "phantompeakqualtools/*"
path "phantompeakqualtools/*"


path ('macs3/peaks/*')
path ('macs3/peaks/*')
path ('macs3/annotation/*')
path ('macs3/featurecounts/*')
path 'macs3/peaks/*'
path 'macs3/peaks/*'
path 'macs3/annotation/*'
path 'macs3/featurecounts/*'
Comment on lines +42 to +45
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Suggested change
path 'macs3/peaks/*'
path 'macs3/peaks/*'
path 'macs3/annotation/*'
path 'macs3/featurecounts/*'
path "macs3/peaks/*"
path "macs3/peaks/*"
path "macs3/annotation/*"
path "macs3/featurecounts/*"


path ('deseq2/*')
path ('deseq2/*')
path 'deseq2/*'
path 'deseq2/*'
Comment on lines +47 to +48
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Suggested change
path 'deseq2/*'
path 'deseq2/*'
path "deseq2/*"
path "deseq2/*"


output:
path "*multiqc_report.html", emit: report
path "*_data" , emit: data
path "*_plots" , optional:true, emit: plots
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 custom_config = params.multiqc_config ? "--config $mqc_custom_config" : ''
def custom_config = params.multiqc_config ? "--config ${mqc_custom_config}" : ''
"""
multiqc \\
-f \\
$args \\
$custom_config \\
${args} \\
${custom_config} \\
.

cat <<-END_VERSIONS > versions.yml
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