From 2ffdf56c657d26bd23a21469489271a9c9bd2e82 Mon Sep 17 00:00:00 2001 From: Matthijs van Niekerk Date: Thu, 17 Oct 2024 13:45:05 +0200 Subject: [PATCH 1/3] Do not emit aligner input bams as markdups outputs --- modules/local/markdups/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/markdups/main.nf b/modules/local/markdups/main.nf index 93e791bc..d309219a 100644 --- a/modules/local/markdups/main.nf +++ b/modules/local/markdups/main.nf @@ -17,8 +17,8 @@ process MARKDUPS { val has_umis output: - tuple val(meta), path('*bam'), path('*bai'), emit: bam - path 'versions.yml' , emit: versions + tuple val(meta), path('*.markdups.bam'), path('*.markdups.bai'), emit: bam + path 'versions.yml' , emit: versions path '*.tsv' when: From d64a54f797dfe38d7927d084d0502a9cb4175fcc Mon Sep 17 00:00:00 2001 From: Matthijs van Niekerk Date: Fri, 18 Oct 2024 10:23:20 +0200 Subject: [PATCH 2/3] fix markdups bai file pattern --- modules/local/markdups/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/markdups/main.nf b/modules/local/markdups/main.nf index d309219a..5b0d37a2 100644 --- a/modules/local/markdups/main.nf +++ b/modules/local/markdups/main.nf @@ -17,8 +17,8 @@ process MARKDUPS { val has_umis output: - tuple val(meta), path('*.markdups.bam'), path('*.markdups.bai'), emit: bam - path 'versions.yml' , emit: versions + tuple val(meta), path('*.markdups.bam'), path('*.markdups.bam.bai'), emit: bam + path 'versions.yml' , emit: versions path '*.tsv' when: From 52064e827fc6d6e11f296b52cc94e30d5b36a6f4 Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Wed, 30 Oct 2024 10:41:48 +1100 Subject: [PATCH 3/3] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 302b4829..b9802b0d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) ## [dev] +- [105](https://github.com/nf-core/oncoanalyser/pull/105) - Adjust MarkDups outputs to improve efficiency with k8s - [98](https://github.com/nf-core/oncoanalyser/pull/98) - Fix typos in error messages for process and run mode check - [96](https://github.com/nf-core/oncoanalyser/pull/96) - Added missing type field to an entry in the nextflow_schema.json - [95](https://github.com/nf-core/oncoanalyser/pull/95) - Post-release bump