Updated modules (e32038ec) · Commits · Chaos / Cutandrun

modules.json

+13 −13

Original line number	Diff line number	Diff line
		@@ -19,16 +19,16 @@
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
		},
		"bowtie2/align": {
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
		"git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
		},
		"bowtie2/build": {
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
		},
		"cat/fastq": {
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
		"git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"
		},
		"custom/getchromsizes": {
		"git_sha": "950700bcdc0e9a2b6883d40d2c51c6fc435cd714"
		"git_sha": "213403187932dbbdd936a04474cc8cd8abae7a08"
		},
		"deeptools/computematrix": {
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
		@@ -37,34 +37,34 @@
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
		},
		"fastqc": {
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
		"git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe"
		},
		"gunzip": {
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
		"git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"
		},
		"macs2/callpeak": {
		"git_sha": "f0800157544a82ae222931764483331a81812012"
		},
		"picard/markduplicates": {
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
		"git_sha": "20ebb89ff97a2665106be9cace5ccb9aa4eed1be"
		},
		"samtools/flagstat": {
		"git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"
		"git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
		},
		"samtools/idxstats": {
		"git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"
		"git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
		},
		"samtools/index": {
		"git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"
		"git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
		},
		"samtools/sort": {
		"git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"
		"git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
		},
		"samtools/stats": {
		"git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"
		"git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
		},
		"samtools/view": {
		"git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"
		"git_sha": "6b64f9cb6c3dd3577931cc3cd032d6fb730000ce"
		},
		"seacr/callpeak": {
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
		@@ -76,7 +76,7 @@
		"git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
		},
		"untar": {
		"git_sha": "7ec09d0ef4df89617baacc9b2dafcddb7cd4b05a"
		"git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"
		}
		}
		}

modules/nf-core/modules/bowtie2/align/main.nf

+3 −3

Original line number	Diff line number	Diff line
		@@ -2,10 +2,10 @@ process BOWTIE2_ALIGN {
		tag "$meta.id"
		label 'process_high'

		conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4 bioconda::samtools=1.14 conda-forge::pigz=2.6' : null)
		conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6' : null)
		container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
		'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:4d235f41348a00533f18e47c9669f1ecb327f629-0' :
		'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:4d235f41348a00533f18e47c9669f1ecb327f629-0' }"
		'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0' :
		'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0' }"

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

modules/nf-core/modules/cat/fastq/main.nf

+2 −2

Original line number	Diff line number	Diff line
		@@ -4,8 +4,8 @@ process CAT_FASTQ {

		conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
		container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
		'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
		'biocontainers/biocontainers:v1.2.0_cv1' }"
		'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
		'ubuntu:20.04' }"

		input:
		tuple val(meta), path(reads, stageAs: "input/")

modules/nf-core/modules/custom/getchromsizes/main.nf

+3 −3

Original line number	Diff line number	Diff line
		@@ -2,10 +2,10 @@ process CUSTOM_GETCHROMSIZES {
		tag "$fasta"
		label 'process_low'

		conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
		conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
		container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
		'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
		'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
		'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
		'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"

		input:
		path fasta

modules/nf-core/modules/fastqc/main.nf

+12 −0

Original line number	Diff line number	Diff line
		@@ -44,4 +44,16 @@ process FASTQC {
		END_VERSIONS
		"""
		}

		stub:
		def prefix = task.ext.prefix ?: "${meta.id}"
		"""
		touch ${prefix}.html
		touch ${prefix}.zip

		cat <<-END_VERSIONS > versions.yml
		"${task.process}":
		fastqc: \$( fastqc --version \| sed -e "s/FastQC v//g" )
		END_VERSIONS
		"""
		}

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