Updated modules (ca92a9b8) · Commits · Chaos / Cutandrun

CHANGELOG.md

+1 −1

Original line number	Diff line number	Diff line
		@@ -98,7 +98,7 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
		\| ---------- \| ----------- \| ----------- \|
		\| `samtools` \| 1.14 \| 1.15.1 \|
		\| `bowtie2` \| 2.4.2 \| 2.4.4 \|
		\| `picard` \| 2.25.7 \| 2.27.1 \|
		\| `picard` \| 2.25.7 \| 2.27.2 \|

		> NB: Dependency has been updated if both old and new version information is present.
		> NB: Dependency has been added if just the new version information is present.

+2 −2

Original line number	Diff line number	Diff line
		@@ -46,7 +46,7 @@
		"git_sha": "f0800157544a82ae222931764483331a81812012"
		},
		"picard/markduplicates": {
		"git_sha": "20ebb89ff97a2665106be9cace5ccb9aa4eed1be"
		"git_sha": "63db63757cab03cfa7a02c0d0f134b66fbfadea6"
		},
		"samtools/flagstat": {
		"git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
		@@ -76,7 +76,7 @@
		"git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
		},
		"untar": {
		"git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"
		"git_sha": "51be617b1ca9bff973655eb899d591ed6ab253b5"
		}
		}
		}

+3 −3

Original line number	Diff line number	Diff line
		@@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES {
		tag "$meta.id"
		label 'process_medium'

		conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
		conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
		container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
		'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
		'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
		'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
		'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"

		input:
		tuple val(meta), path(bam)

+7 −1

Original line number	Diff line number	Diff line
		@@ -21,12 +21,18 @@ process UNTAR {
		def args = task.ext.args ?: ''
		def args2 = task.ext.args2 ?: ''
		untar = archive.toString() - '.tar.gz'

		"""
		mkdir output

		tar \\
		-C output --strip-components 1 \\
		-xzvf \\
		$args \\
		$archive \\
		$args2 \\
		$args2

		mv output ${untar}

		cat <<-END_VERSIONS > versions.yml
		"${task.process}":

Original line number	Diff line number	Diff line
		@@ -98,7 +98,7 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
		\| ---------- \| ----------- \| ----------- \|
		\| `samtools` \| 1.14 \| 1.15.1 \|
		\| `bowtie2` \| 2.4.2 \| 2.4.4 \|
		\| `picard` \| 2.25.7 \| 2.27.1 \|
		\| `picard` \| 2.25.7 \| 2.27.2 \|

		> NB: Dependency has been updated if both old and new version information is present.
		> NB: Dependency has been added if just the new version information is present.