Merge branch 'chris_feat' into dev (f8eeaf45) · Commits · Chaos / Cutandrun

.github/workflows/awsfulltest.yml

+0 −3

Original line number	Diff line number	Diff line
		@@ -15,9 +15,6 @@ jobs:
		steps:
		- name: Launch workflow via tower
		uses: nf-core/tower-action@master
		# TODO nf-core: You can customise AWS full pipeline tests as required
		# Add full size test data (but still relatively small datasets for few samples)
		# on the `test_full.config` test runs with only one set of parameters

		with:
		workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}

bin/scrape_software_versions.py

100755 → 100644

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File mode changed from 100755 to 100644.

View file

conf/base.config

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Original line number	Diff line number	Diff line
		@@ -9,8 +9,6 @@
		*/

		process {

		// TODO nf-core: Check the defaults for all processes
		cpus = { check_max( 1 * task.attempt, 'cpus' ) }
		memory = { check_max( 6.GB * task.attempt, 'memory' ) }
		time = { check_max( 4.h * task.attempt, 'time' ) }
		@@ -19,13 +17,6 @@ process {
		maxRetries = 1
		maxErrors = '-1'

		// Process-specific resource requirements
		// NOTE - Please try and re-use the labels below as much as possible.
		// These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
		// If possible, it would be nice to keep the same label naming convention when
		// adding in your local modules too.
		// TODO nf-core: Customise requirements for specific processes.
		// See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
		withLabel:process_low {
		cpus = { check_max( 2 * task.attempt, 'cpus' ) }
		memory = { check_max( 12.GB * task.attempt, 'memory' ) }

modules.json

+15 −12

Original line number	Diff line number	Diff line
		@@ -4,28 +4,28 @@
		"repos": {
		"nf-core/modules": {
		"bedtools/bamtobed": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		},
		"bedtools/genomecov": {
		"git_sha": "e8b33e6eb1be2a03abdd2c06068f9a5cebc02bb4"
		},
		"bedtools/intersect": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		},
		"bedtools/merge": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		},
		"bedtools/sort": {
		"git_sha": "2959b4ba070d138d1577acc48d35cc669fbef972"
		},
		"bowtie2/align": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		},
		"bowtie2/build": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		},
		"cat/fastq": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		},
		"deeptools/computematrix": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		@@ -34,28 +34,31 @@
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"fastqc": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		},
		"gunzip": {
		"git_sha": "e560fbbc3ed68e62bc810a50f552394056f81762"
		},
		"picard/markduplicates": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		},
		"samtools/flagstat": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"samtools/idxstats": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		},
		"samtools/index": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"samtools/sort": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		},
		"samtools/stats": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"samtools/view": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		"git_sha": "ac1e6df076195cec553a2079c9cebd94026a0d47"
		},
		"seacr/callpeak": {
		"git_sha": "4d89d6b2f0c478ac7ef80ece5cad44fdf7ffd614"
		@@ -67,7 +70,7 @@
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"untar": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		}
		}
		}

modules/local/get_chrom_sizes.nf

+3 −3

Original line number	Diff line number	Diff line
		@@ -14,11 +14,11 @@ process GET_CHROM_SIZES {
		mode: params.publish_dir_mode,
		saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:"genome", publish_id:'') }

		conda (params.enable_conda ? "bioconda::samtools=1.13" : null)
		conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
		if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
		container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
		container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
		} else {
		container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
		container "quay.io/biocontainers/samtools:1.14--hb421002_0"
		}

		input:

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