Merge pull request #18 from luslab/dev (678fa5e6) · Commits · Chaos / Cutandrun

.github/workflows/ci.yml

+12 −7

Original line number	Diff line number	Diff line
		@@ -10,7 +10,7 @@ on:

		jobs:
		test:
		name: Run workflow tests
		name: Run standard pipeline test
		# Only run on push if this is the nf-core dev branch (merged PRs)
		if: ${{ github.event_name != 'push' \|\| (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }}
		runs-on: ubuntu-latest
		@@ -33,14 +33,19 @@ jobs:
		- name: Run pipeline with test data
		run: \|
		nextflow run ${GITHUB_WORKSPACE} -profile test,docker

		sra_download:
		name: Test downloading of public data
		if: ${{ github.event_name != 'push' \|\| (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
		# ---------------------------------------------------------------------
		test_no_igg:
		name: Run pipeline test with no IgG
		# Only run on push if this is the nf-core dev branch (merged PRs)
		if: ${{ github.event_name != 'push' \|\| (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }}
		runs-on: ubuntu-latest
		env:
		NXF_VER: ${{ matrix.nxf_ver }}
		NXF_ANSI_LOG: false
		strategy:
		matrix:
		# Nextflow versions: check pipeline minimum and current latest
		nxf_ver: ["21.04.0", ""]
		steps:
		- name: Check out pipeline code
		uses: actions/checkout@v2
		@@ -50,6 +55,6 @@ jobs:
		wget -qO- get.nextflow.io \| bash
		sudo mv nextflow /usr/local/bin/

		- name: Run pipeline to download public data
		- name: Run pipeline with test data
		run: \|
		nextflow run ${GITHUB_WORKSPACE} -profile test_sra,docker
		nextflow run ${GITHUB_WORKSPACE} -profile test_no_igg,docker

bin/lib/reports.py

+4 −4

Original line number	Diff line number	Diff line
		@@ -71,8 +71,8 @@ class Reports:
		frag_base_i = os.path.basename(dt_frag_list[i])
		sample_id = frag_base_i.split(".")[0]
		sample_id_split = sample_id.rsplit("_", 1)
		rep_i = sample_id_split[len(sample_id_split)-1]
		group_i ="_".join(sample_id_split[0:(len(sample_id_split)-1)])
		rep_i = sample_id_split[1]
		group_i = sample_id_split[0]

		# create long forms of fragment histograms
		dt_frag_i_long = np.repeat(dt_frag_i['Size'].values, dt_frag_i['Occurrences'].values)
		@@ -134,8 +134,8 @@ class Reports:
		bed_base_i = os.path.basename(seacr_bed_list[i])
		sample_id = bed_base_i.split(".")[0]
		sample_id_split = sample_id.rsplit("_", 1)
		rep_i = sample_id_split[len(sample_id_split)-1]
		group_i ="_".join(sample_id_split[0:(len(sample_id_split)-1)])
		rep_i = sample_id_split[1]
		group_i = sample_id_split[0]
		seacr_bed_i['group'] = np.repeat(group_i, seacr_bed_i.shape[0])
		seacr_bed_i['replicate'] = np.repeat(rep_i, seacr_bed_i.shape[0])

conf/test_no_igg.config

0 → 100644

+26 −0

Original line number	Diff line number	Diff line
		/*
		========================================================================================
		Nextflow config file for running minimal tests
		========================================================================================
		Defines input files and everything required to run a more robust test.

		Use as follows:
		nextflow run nf-core/cutandrun -profile test_hg38_chr7,<docker/singularity>

		----------------------------------------------------------------------------------------
		*/

		params {
		config_profile_name = 'GSE145187 hg38-chr7'
		config_profile_description = 'Runs on full data for GSE145187 but just on chr7 of hg38 and no IgG control'

		// Limit resources so that this can run CI
		max_cpus = 2
		max_memory = 6.GB
		max_time = 6.h

		genome = 'GRCh38'
		input = 'https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-noigg-small.csv'
		fasta = 'https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/reference/genomes/hg38-chr7.fa.gz'
		igg_control = false
		}

lib/WorkflowMain.groovy

+6 −2

Original line number	Diff line number	Diff line
		@@ -83,7 +83,9 @@ class WorkflowMain {
		//
		public static String getGenomeAttribute(params, attribute) {
		def val = ''
		if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
		if (params.attribute) {
		val = params.attribute
		} else if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
		if (params.genomes[ params.genome ].containsKey(attribute)) {
		val = params.genomes[ params.genome ][ attribute ]
		}
		@@ -96,7 +98,9 @@ class WorkflowMain {
		//
		public static String getGenomeAttributeSpikeIn(params, attribute) {
		def val = ''
		if (params.genomes && params.spikein_genome && params.genomes.containsKey(params.spikein_genome)) {
		if (params.attribute) {
		val = params.attribute
		} else if (params.genomes && params.spikein_genome && params.genomes.containsKey(params.spikein_genome)) {
		if (params.genomes[ params.spikein_genome ].containsKey(attribute)) {
		val = params.genomes[ params.spikein_genome ][ attribute ]
		}

main.nf

+11 −7

Original line number	Diff line number	Diff line
		@@ -17,11 +17,13 @@ nextflow.enable.dsl = 2
		========================================================================================
		*/

		params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
		params.gtf = WorkflowMain.getGenomeAttribute(params, 'gtf')
		params.gene_bed = WorkflowMain.getGenomeAttribute(params, 'bed12')
		params.blacklist = WorkflowMain.getGenomeAttribute(params, 'blacklist')
		params.bowtie2 = WorkflowMain.getGenomeAttribute(params, 'bowtie2')
		if (!params.fasta) {
		params.bowtie2 = params.bowtie2 ?: WorkflowMain.getGenomeAttribute(params, 'bowtie2')
		}
		params.fasta = params.fasta ?: WorkflowMain.getGenomeAttribute(params, 'fasta')
		params.gtf = params.gtf ?: WorkflowMain.getGenomeAttribute(params, 'gtf')
		params.gene_bed = params.gene_bed ?: WorkflowMain.getGenomeAttribute(params, 'bed12')
		params.blacklist = params.blacklist ?: WorkflowMain.getGenomeAttribute(params, 'blacklist')

		/*
		========================================================================================
		@@ -29,8 +31,10 @@ params.bowtie2 = WorkflowMain.getGenomeAttribute(params, 'bowtie2')
		========================================================================================
		*/

		params.spikein_fasta = WorkflowMain.getGenomeAttributeSpikeIn(params, 'fasta')
		params.spikein_bowtie2 = WorkflowMain.getGenomeAttributeSpikeIn(params, 'bowtie2')
		if (!params.spikein_fasta) {
		params.spikein_bowtie2 = params.spikein_bowtie2 ?: WorkflowMain.getGenomeAttributeSpikeIn(params, 'bowtie2')
		}
		params.spikein_fasta = params.spikein_fasta ?: WorkflowMain.getGenomeAttributeSpikeIn(params, 'fasta')

		/*
		========================================================================================

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