From 18300758c839d07c06303ea8b48c2c92ef276291 Mon Sep 17 00:00:00 2001 From: Regina Reynolds Date: Wed, 1 Feb 2023 19:15:53 +0000 Subject: [PATCH 1/3] fix: `--skip_fastqc` error Enabling `--skip_fastqc` resulted in the error `Access to 'FASTQC.out' is undefined since the workflow 'FASTQC' has not been invoked before accessing the output attribute`. Fixed by initiating empty channel wherein FASTQC output can be stored if FASTQC run. Otherwise channel remains empty. # --- workflows/dragen.nf | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/workflows/dragen.nf b/workflows/dragen.nf index 3b8141b..be28045 100644 --- a/workflows/dragen.nf +++ b/workflows/dragen.nf @@ -84,11 +84,13 @@ workflow DRAGEN { // // MODULE: Run FastQC // + ch_multiqc_fastqc = Channel.empty() if (!params.skip_fastqc) { FASTQC ( INPUT_CHECK.out.reads ) ch_versions = ch_versions.mix(FASTQC.out.versions.first()) + ch_multiqc_fastqc = FASTQC.out.zip } if (!params.skip_dragen) { @@ -155,7 +157,7 @@ workflow DRAGEN { ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) - ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_fastqc.collect{it[1]}.ifEmpty([])) MULTIQC ( ch_multiqc_files.collect() From e0b78cd59a6d478f9c73d7e9b446822874a73eab Mon Sep 17 00:00:00 2001 From: Regina Reynolds Date: Wed, 1 Feb 2023 19:24:15 +0000 Subject: [PATCH 2/3] docs: add fix to changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 029cab9..e75c44a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,8 @@ Initial release of nf-core/dragen, created with the [nf-core](https://nf-co.re/) ### `Fixed` +- Fixed error `Access to 'FASTQC_CHECK.out' is undefined since the workflow 'FASTQC_CHECK' has not been invoked before accessing the output attribute` when `-skip_fastqc` enabled by adjusting channel generation + ### `Dependencies` ### `Deprecated` From 0090138a3db0123e547775ffd5c11119b308869a Mon Sep 17 00:00:00 2001 From: Regina Reynolds Date: Wed, 1 Feb 2023 19:30:23 +0000 Subject: [PATCH 3/3] docs: add fix to changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e75c44a..fa8d993 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,7 +11,7 @@ Initial release of nf-core/dragen, created with the [nf-core](https://nf-co.re/) ### `Fixed` -- Fixed error `Access to 'FASTQC_CHECK.out' is undefined since the workflow 'FASTQC_CHECK' has not been invoked before accessing the output attribute` when `-skip_fastqc` enabled by adjusting channel generation +- Fixed error `Access to 'FASTQC.out' is undefined since the workflow 'FASTQC' has not been invoked before accessing the output attribute` when `-skip_fastqc` enabled by adjusting channel generation ### `Dependencies`