Merge branch 'dev' into chris-feat (bae63c19) · Commits · Chaos / Cutandrun

.github/workflows/branch.yml

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		@@ -43,4 +43,3 @@ jobs:
		Thanks again for your contribution!
		repo-token: ${{ secrets.GITHUB_TOKEN }}
		allow-repeats: false

.github/workflows/ci.yml

+3 −3

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		@@ -39,7 +39,7 @@ jobs:
		sudo mv nextflow /usr/local/bin/

		# Work around for the unexpected end of file error that github actions seems to get when downloading compressed
		# files during pipelie execution
		# files during pipelie execution
		- name: Download data
		run: \|
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz
		@@ -81,7 +81,7 @@ jobs:
		sudo mv nextflow /usr/local/bin/

		# Work around for the unexpected end of file error that github actions seems to get when downloading compressed
		# files during pipelie execution
		# files during pipelie execution
		- name: Download data
		run: \|
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz
		@@ -121,7 +121,7 @@ jobs:
		nextflow self-update

		# Work around for the unexpected end of file error that github actions seems to get when downloading compressed
		# files during pipelie execution
		# files during pipelie execution
		- name: Download data
		run: \|
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz

.github/workflows/linting.yml

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		@@ -138,4 +138,3 @@ jobs:
		lint_log.txt
		lint_results.md
		PR_number.txt

.github/workflows/linting_comment.yml

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Original line number	Diff line number	Diff line

		name: nf-core linting comment
		# This workflow is triggered after the linting action is complete
		# It posts an automated comment to the PR, even if the PR is coming from a fork
		@@ -27,4 +26,3 @@ jobs:
		GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
		number: ${{ steps.pr_number.outputs.pr_number }}
		path: linting-logs/lint_results.md

conf/resources.config

0 → 100644

+170 −0

Original line number	Diff line number	Diff line
		/*
		========================================================================================
		nf-core/cutandrun Nextflow resource config file
		========================================================================================
		Minimal and process-specific resource allocation.
		----------------------------------------------------------------------------------------
		*/

		/*
		========================================================================================
		MINIMAL AND ULTRA LOW RESOURCE ALLOCATION
		========================================================================================
		*/

		process {
		withLabel:process_min {
		cpus = { check_max( 1 * task.attempt, 'cpus' ) }
		memory = { check_max( 2.GB * task.attempt, 'memory' ) }
		time = { check_max( 1.h * task.attempt, 'time' ) }
		}

		withLabel:process_ultralow {
		cpus = { check_max( 2 * task.attempt, 'cpus' ) }
		memory = { check_max( 8.GB * task.attempt, 'memory' ) }
		time = { check_max( 4.h * task.attempt, 'time' ) }
		}
		}

		/*
		========================================================================================
		MODULE-SPECIFIC RESOURCE ALLOCATION
		========================================================================================
		*/

		process {
		withName: '.*:ALIGN_BOWTIE2:BOWTIE2_ALIGN' {
		cpus = { check_max( 32 * task.attempt, 'cpus' ) }
		memory = { check_max( 64.GB * task.attempt, 'memory' ) }
		time = { check_max( 4.h * task.attempt, 'time' ) }
		}

		withName: '.*:ALIGN_BOWTIE2:BOWTIE2_SPIKEIN_ALIGN' {
		cpus = { check_max( 32 * task.attempt, 'cpus' ) }
		memory = { check_max( 64.GB * task.attempt, 'memory' ) }
		time = { check_max( 4.h * task.attempt, 'time' ) }
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_COMPUTEMATRIX_GENE' {
		cpus = { check_max( 16 * task.attempt, 'cpus' ) }
		memory = { check_max( 32.GB * task.attempt, 'memory' ) }
		time = { check_max( 4.h * task.attempt, 'time' ) }
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_COMPUTEMATRIX_PEAKS' {
		cpus = { check_max( 16 * task.attempt, 'cpus' ) }
		memory = { check_max( 32.GB * task.attempt, 'memory' ) }
		time = { check_max( 4.h * task.attempt, 'time' ) }
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:CUSTOM_DUMPSOFTWAREVERSIONS' {
		cpus = { check_max( 1 * task.attempt, 'cpus' ) }
		memory = { check_max( 2.GB * task.attempt, 'memory' ) }
		time = { check_max( 1.h * task.attempt, 'time' ) }
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:.*:SAMTOOLS_INDEX' {
		cpus = { check_max( 1 * task.attempt, 'cpus' ) }
		memory = { check_max( 2.GB * task.attempt, 'memory' ) }
		time = { check_max( 1.h * task.attempt, 'time' ) }
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:.*:SAMTOOLS_STATS' {
		cpus = { check_max( 1 * task.attempt, 'cpus' ) }
		memory = { check_max( 2.GB * task.attempt, 'memory' ) }
		time = { check_max( 1.h * task.attempt, 'time' ) }
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:.*:SAMTOOLS_STATS' {
		cpus = { check_max( 1 * task.attempt, 'cpus' ) }
		memory = { check_max( 2.GB * task.attempt, 'memory' ) }
		time = { check_max( 1.h * task.attempt, 'time' ) }
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:.*:SAMTOOLS_IDXSTATS' {
		cpus = { check_max( 1 * task.attempt, 'cpus' ) }
		memory = { check_max( 2.GB * task.attempt, 'memory' ) }
		time = { check_max( 1.h * task.attempt, 'time' ) }
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:.*:SAMTOOLS_FLAGSTAT' {
		cpus = { check_max( 1 * task.attempt, 'cpus' ) }
		memory = { check_max( 2.GB * task.attempt, 'memory' ) }
		time = { check_max( 1.h * task.attempt, 'time' ) }
		}

		withName: '.*CHROMSIZES' {
		cpus = { check_max( 1 * task.attempt, 'cpus' ) }
		memory = { check_max( 2.GB * task.attempt, 'memory' ) }
		time = { check_max( 1.h * task.attempt, 'time' ) }
		}

		// 1 CPU 8 GB
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_PEAKCALLING:BEDTOOLS_GENOMECOV' {
		cpus = { check_max( 1 * task.attempt, 'cpus' ) }
		memory = { check_max( 8.GB * task.attempt, 'memory' ) }
		time = { check_max( 4.h * task.attempt, 'time' ) }
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_PEAKCALLING:BEDTOOLS_SORT' {
		cpus = { check_max( 1 * task.attempt, 'cpus' ) }
		memory = { check_max( 8.GB * task.attempt, 'memory' ) }
		time = { check_max( 4.h * task.attempt, 'time' ) }
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_PEAKCALLING:UCSC_BEDGRAPHTOBIGWIG' {
		cpus = { check_max( 1 * task.attempt, 'cpus' ) }
		memory = { check_max( 8.GB * task.attempt, 'memory' ) }
		time = { check_max( 4.h * task.attempt, 'time' ) }
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:BEDTOOLS_INTERSECT' {
		cpus = { check_max( 1 * task.attempt, 'cpus' ) }
		memory = { check_max( 8.GB * task.attempt, 'memory' ) }
		time = { check_max( 4.h * task.attempt, 'time' ) }
		}

		withName: '.:CONSENSUS_PEAKS:BEDTOOLS_MERGE\|.:CONSENSUS_PEAKS_ALL:BEDTOOLS_MERGE' {
		cpus = { check_max( 1 * task.attempt, 'cpus' ) }
		memory = { check_max( 8.GB * task.attempt, 'memory' ) }
		time = { check_max( 4.h * task.attempt, 'time' ) }
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_PEAKCALLING:UCSC_BEDCLIP' {
		cpus = { check_max( 1 * task.attempt, 'cpus' ) }
		memory = { check_max( 8.GB * task.attempt, 'memory' ) }
		time = { check_max( 4.h * task.attempt, 'time' ) }
		}

		// ultralow
		withName: '.*:CALCULATE_FRAGMENTS:BEDTOOLS_BAMTOBED' {
		cpus = { check_max( 2 * task.attempt, 'cpus' ) }
		memory = { check_max( 8.GB * task.attempt, 'memory' ) }
		time = { check_max( 4.h * task.attempt, 'time' ) }
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:SEACR_CALLPEAK' {
		cpus = { check_max( 2 * task.attempt, 'cpus' ) }
		memory = { check_max( 8.GB * task.attempt, 'memory' ) }
		time = { check_max( 4.h * task.attempt, 'time' ) }
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:FASTQC_TRIMGALORE:FASTQC' {
		cpus = { check_max( 2 * task.attempt, 'cpus' ) }
		memory = { check_max( 8.GB * task.attempt, 'memory' ) }
		time = { check_max( 4.h * task.attempt, 'time' ) }
		}

		// memory
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_PLOTHEATMAP_PEAKS' {
		cpus = { check_max( 1 * task.attempt, 'cpus' ) }
		memory = { check_max( 32.GB * task.attempt, 'memory' ) }
		time = { check_max( 4.h * task.attempt, 'time' ) }
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:.*:SAMTOOLS_VIEW' {
		cpus = { check_max( 1 * task.attempt, 'cpus' ) }
		memory = { check_max( 32.GB * task.attempt, 'memory' ) }
		time = { check_max( 4.h * task.attempt, 'time' ) }
		}
		}
		No newline at end of file

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