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https://github.com/MillironX/taxprofiler.git
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Fix MultiQC
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parent
d11257b330
commit
fc26948950
5 changed files with 15 additions and 13 deletions
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@ -12,7 +12,7 @@
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params {
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config_profile_name = 'Test profile'
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config_profile_description = 'Minimal test dataset without performing any preprocessing nor profiling to check pipeline function. Useful when you only wish to test a single profiler without having to 'opt-out' of all the others'
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config_profile_description = "Minimal test dataset without performing any preprocessing nor profiling to check pipeline function. Useful when you only wish to test a single profiler without having to 'opt-out' of all the others"
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// Limit resources so that this can run on GitHub Actions
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max_cpus = 2
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@ -115,7 +115,7 @@
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},
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"multiqc": {
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"branch": "master",
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"git_sha": "5138acca0985ca01c38a1c4fba917d83772b1106"
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"git_sha": "16eee433b87b303bda650131ac5a0b1ad725e166"
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},
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"porechop": {
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"branch": "master",
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3
modules/nf-core/modules/multiqc/main.nf
generated
3
modules/nf-core/modules/multiqc/main.nf
generated
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@ -8,7 +8,8 @@ process MULTIQC {
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input:
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path multiqc_files, stageAs: "?/*"
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tuple path(multiqc_config), path(multiqc_logo)
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path(multiqc_config)
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path(multiqc_logo)
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output:
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path "*multiqc_report.html", emit: report
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7
modules/nf-core/modules/multiqc/meta.yml
generated
7
modules/nf-core/modules/multiqc/meta.yml
generated
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@ -12,6 +12,7 @@ tools:
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homepage: https://multiqc.info/
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documentation: https://multiqc.info/docs/
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licence: ["GPL-3.0-or-later"]
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input:
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- multiqc_files:
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type: file
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@ -19,12 +20,13 @@ input:
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List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
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- multiqc_config:
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type: file
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description: Config yml for MultiQC
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description: Optional config yml for MultiQC
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pattern: "*.{yml,yaml}"
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- multiqc_logo:
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type: file
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description: Logo file for MultiQC
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description: Optional logo file for MultiQC
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pattern: "*.{png}"
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output:
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- report:
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type: file
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@ -46,3 +48,4 @@ authors:
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- "@abhi18av"
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- "@bunop"
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- "@drpatelh"
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- "@jfy133"
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@ -42,8 +42,7 @@ if (params.run_malt && params.run_krona && !params.krona_taxonomy_directory) log
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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ch_multiqc_config = file("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
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ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
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ch_multiqc_config = params.multiqc_config ? file( params.multiqc_config, checkIfExists: true ) : file("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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@ -93,7 +92,7 @@ def multiqc_report = []
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workflow TAXPROFILER {
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ch_versions = Channel.empty()
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ch_taxprofiler_logo = Channel.fromPath("$projectDir/docs/images/nf-core-taxprofiler_logo_custom_light.png")
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ch_multiqc_logo= Channel.fromPath("$projectDir/docs/images/nf-core-taxprofiler_logo_custom_light.png")
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/*
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SUBWORKFLOW: Read in samplesheet, validate and stage input files
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@ -241,14 +240,11 @@ workflow TAXPROFILER {
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ch_workflow_summary = Channel.value(workflow_summary)
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ch_multiqc_files = Channel.empty()
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ch_multiqc_files = ch_multiqc_files.mix(Channel.from(ch_multiqc_config))
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ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([]))
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ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
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ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
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ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
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ch_multiqc_files = ch_multiqc_files.mix(ch_taxprofiler_logo.ifEmpty([]))
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if (params.perform_shortread_qc) {
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ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
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}
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@ -269,7 +265,9 @@ workflow TAXPROFILER {
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// TODO create multiQC module for metaphlan
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MULTIQC (
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ch_multiqc_files.collect(), [[], []]
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ch_multiqc_files.collect(),
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ch_multiqc_config,
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ch_multiqc_logo
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)
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multiqc_report = MULTIQC.out.report.toList()
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ch_versions = ch_versions.mix(MULTIQC.out.versions)
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