From 3e89a9e146706e3e5228d7da54b712ac9ef92664 Mon Sep 17 00:00:00 2001 From: ggabernet Date: Sat, 1 Oct 2022 16:31:09 +0200 Subject: [PATCH 1/3] fix template --- nf_core/pipeline-template/workflows/pipeline.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index 83d49a327b..51baff1cc2 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -91,7 +91,7 @@ workflow {{ short_name|upper }} { workflow_summary = Workflow{{ short_name[0]|upper }}{{ short_name[1:] }}.paramsSummaryMultiqc(workflow, summary_params) ch_workflow_summary = Channel.value(workflow_summary) - methods_description = WorkflowTestpipeline.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description) + methods_description = Workflow{{ short_name[0]|upper }}{{ short_name[1:] }}.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description) ch_methods_description = Channel.value(methods_description) ch_multiqc_files = Channel.empty() From f8c0cef932cf33802d8b4d43e3e190a364b0344f Mon Sep 17 00:00:00 2001 From: ggabernet Date: Sat, 1 Oct 2022 17:01:08 +0200 Subject: [PATCH 2/3] fix multiqc not run --- nf_core/pipeline-template/workflows/pipeline.nf | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index 51baff1cc2..74ed67a3bc 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -23,9 +23,9 @@ if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input sample ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -ch_multiqc_config = file("$projectDir/assets/multiqc_config.yml", checkIfExists: true) -ch_multiqc_custom_config = params.multiqc_config ? file( params.multiqc_config, checkIfExists: true ) : Channel.empty() -ch_multiqc_logo = params.multiqc_logo ? file( params.multiqc_logo, checkIfExists: true ) : Channel.empty() +ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) +ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty() +ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty() ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) /* @@ -102,9 +102,9 @@ workflow {{ short_name|upper }} { MULTIQC ( ch_multiqc_files.collect(), - ch_multiqc_config, - ch_multiqc_custom_config, - ch_multiqc_logo + ch_multiqc_config.collect().ifEmpty([]), + ch_multiqc_custom_config.collect().ifEmpty([]), + ch_multiqc_logo.collect().ifEmpty([]) ) multiqc_report = MULTIQC.out.report.toList() ch_versions = ch_versions.mix(MULTIQC.out.versions) From cd5a32b5b3de614ba524c0397b4c6f0927e068ee Mon Sep 17 00:00:00 2001 From: ggabernet Date: Sat, 1 Oct 2022 19:32:44 +0200 Subject: [PATCH 3/3] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1b1c0f7854..5b238a419f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ - Update MultiQC module, update supplying MultiQC default and custom config and logo files to module - Add a 'recommend' methods description text to MultiQC to help pipeline users report pipeline usage in publications ([#1749](https://github.com/nf-core/tools/pull/1749)) - Fix template spacing modified by JINJA ([#1830](https://github.com/nf-core/tools/pull/1830)) +- Fix MultiQC execution on template [#1855](https://github.com/nf-core/tools/pull/1855) ### Linting