From 163611504031a81e609ed950824a9efb5e091ddb Mon Sep 17 00:00:00 2001 From: peterpru Date: Tue, 17 Dec 2024 15:42:06 +0100 Subject: [PATCH 1/2] add haplocheck to multiqc --- assets/multiqc_config.yml | 3 +++ workflows/raredisease.nf | 1 + 2 files changed, 4 insertions(+) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 9f87335c..53538d6c 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -19,6 +19,7 @@ export_plots: true run_modules: - fastqc - fastp + - haplocheck - qualimap - picard - mosdepth @@ -39,6 +40,8 @@ module_order: name: "fastp" - mosdepth: name: "Mosdepth" + - haplocheck: + name: "haplocheck" - ngsbits: name: "ngsbits" - peddy: diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 8e7257c6..66624349 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -902,6 +902,7 @@ workflow RAREDISEASE { ) ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(HAPLOCHECK.out.txt.map){it[1]}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.fastp_json.map{it[1]}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.sex_check.map{it[1]}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.multiple_metrics.map{it[1]}.collect().ifEmpty([])) From e071e58d952aa5c71bf1172b424eef10feed56aa Mon Sep 17 00:00:00 2001 From: peterpru Date: Wed, 18 Dec 2024 06:03:20 +0100 Subject: [PATCH 2/2] fix typo and add changelog --- CHANGELOG.md | 1 + workflows/raredisease.nf | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d68b0072..d1bb3e17 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - A new analysis option `mito` to call and annotate only mitochondrial variants [#608](https://github.com/nf-core/raredisease/pull/608) - An option to restrict analysis to specific contigs [#644](https://github.com/nf-core/raredisease/pull/644) - Fastp and ngsbits output files as input of MultiQC [#647](https://github.com/nf-core/raredisease/pull/647/). +- Haplocheck output files as input of MultiQC [#653]](https://github.com/nf-core/raredisease/pull/653) ### `Changed` diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 66624349..63974a8c 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -902,7 +902,7 @@ workflow RAREDISEASE { ) ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(HAPLOCHECK.out.txt.map){it[1]}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(HAPLOCHECK.out.txt.map{it[1]}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.fastp_json.map{it[1]}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.sex_check.map{it[1]}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.multiple_metrics.map{it[1]}.collect().ifEmpty([]))