From dc6c09e0838735d6716474474bc4c6382b7b89a7 Mon Sep 17 00:00:00 2001 From: WackerO Date: Sat, 11 Jun 2022 13:32:53 +0200 Subject: [PATCH 1/2] samtools mpileup now bgzips mpileup files --- modules/samtools/mpileup/main.nf | 3 ++- tests/modules/samtools/mpileup/test.yml | 8 ++++---- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/modules/samtools/mpileup/main.nf b/modules/samtools/mpileup/main.nf index fcd498be..550c7921 100644 --- a/modules/samtools/mpileup/main.nf +++ b/modules/samtools/mpileup/main.nf @@ -11,7 +11,7 @@ process SAMTOOLS_MPILEUP { path fasta output: - tuple val(meta), path("*.mpileup"), emit: mpileup + tuple val(meta), path("*.mpileup.gz"), emit: mpileup path "versions.yml" , emit: versions when: @@ -27,6 +27,7 @@ process SAMTOOLS_MPILEUP { --output ${prefix}.mpileup \\ $args \\ $input + bgzip ${prefix}.mpileup cat <<-END_VERSIONS > versions.yml "${task.process}": samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') diff --git a/tests/modules/samtools/mpileup/test.yml b/tests/modules/samtools/mpileup/test.yml index c3d794d0..8834f639 100644 --- a/tests/modules/samtools/mpileup/test.yml +++ b/tests/modules/samtools/mpileup/test.yml @@ -4,8 +4,8 @@ - samtools - samtools/mpileup files: - - path: output/samtools/test.mpileup - md5sum: 958e6bead4103d72026f80153b6b5150 + - path: output/samtools/test.mpileup.gz + md5sum: 29455c36377196e8bc9cf831cf17b5dc - path: output/samtools/versions.yml - name: samtools mpileup test_samtools_mpileup_intervals @@ -14,6 +14,6 @@ - samtools - samtools/mpileup files: - - path: output/samtools/test.mpileup - md5sum: 958e6bead4103d72026f80153b6b5150 + - path: output/samtools/test.mpileup.gz + md5sum: 29455c36377196e8bc9cf831cf17b5dc - path: output/samtools/versions.yml From 24e05f6097a5dde57dd80d33295ed120f1b81aef Mon Sep 17 00:00:00 2001 From: WackerO <43847497+WackerO@users.noreply.github.com> Date: Mon, 13 Jun 2022 09:35:34 +0200 Subject: [PATCH 2/2] Update modules/samtools/mpileup/main.nf Co-authored-by: FriederikeHanssen --- modules/samtools/mpileup/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/samtools/mpileup/main.nf b/modules/samtools/mpileup/main.nf index 550c7921..cfab5c98 100644 --- a/modules/samtools/mpileup/main.nf +++ b/modules/samtools/mpileup/main.nf @@ -12,7 +12,7 @@ process SAMTOOLS_MPILEUP { output: tuple val(meta), path("*.mpileup.gz"), emit: mpileup - path "versions.yml" , emit: versions + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when