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Update MultiQC to re-add staging logos as a separate input channel (#2032)

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* Update main.nf

* Update meta.yml

* Re-add logos as not staged in a way that works with MultiQC config files
This commit is contained in:
James A. Fellows Yates 2022-09-08 12:36:15 +02:00 committed by GitHub
parent 8d2fedadff
commit 16eee433b8
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3 changed files with 8 additions and 3 deletions
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1
modules/multiqc/main.nf
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@ -9,6 +9,7 @@ process MULTIQC {
input: input:
path multiqc_files, stageAs: "?/*" path multiqc_files, stageAs: "?/*"
path(multiqc_config) path(multiqc_config)
path(multiqc_logo)
output: output:
path "*multiqc_report.html", emit: report path "*multiqc_report.html", emit: report

4
modules/multiqc/meta.yml
View file

@ -22,6 +22,10 @@ input:
type: file type: file
description: Optional config yml for MultiQC description: Optional config yml for MultiQC
pattern: "*.{yml,yaml}" pattern: "*.{yml,yaml}"
- multiqc_logo:
type: file
description: Optional logo file for MultiQC
pattern: "*.{png}"
output: output:
- report: - report:

6
tests/modules/multiqc/main.nf
View file

@ -13,7 +13,7 @@ workflow test_multiqc {
] ]
FASTQC ( input ) FASTQC ( input )
MULTIQC ( FASTQC.out.zip.collect { it[1] }, [] ) MULTIQC ( FASTQC.out.zip.collect { it[1] }, [], [] )
} }
workflow test_multiqc_fn_collision { workflow test_multiqc_fn_collision {
@ -29,7 +29,7 @@ workflow test_multiqc_fn_collision {
FASTQC2 ( fqc_input ) FASTQC2 ( fqc_input )
mqc_input = mqc_input.mix(FASTQC2.out.zip.collect { it[1] }) mqc_input = mqc_input.mix(FASTQC2.out.zip.collect { it[1] })
MULTIQC ( mqc_input, [] ) MULTIQC ( mqc_input, [], [] )
} }
workflow test_multiqc_config { workflow test_multiqc_config {
@ -41,5 +41,5 @@ workflow test_multiqc_config {
mqc_input = Channel.empty() mqc_input = Channel.empty()
FASTQC ( input ) FASTQC ( input )
MULTIQC ( FASTQC.out.zip.collect { it[1] }, mqc_config ) MULTIQC ( FASTQC.out.zip.collect { it[1] }, mqc_config, [] )
} }