Updated local zip to extended test (da203048) · Commits · Chaos / Cutandrun

.github/workflows/ci.yml

+26 −2

Original line number	Diff line number	Diff line
		@@ -72,9 +72,21 @@ jobs:
		wget -qO- get.nextflow.io \| bash
		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
		- name: Download data
		run: \|
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.bed.gz
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz

		- name: Run pipeline with test data
		run: \|
		nextflow run ${GITHUB_WORKSPACE} -profile docker,test_full_small
		nextflow run ${GITHUB_WORKSPACE} -profile docker,test_full_small_local_zip

		#####################################
		### EDGE VERSION INTEGRATION TEST ###
		#####################################
		@@ -97,9 +109,21 @@ jobs:
		sudo mv nextflow /usr/local/bin/
		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
		- name: Download data
		run: \|
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.bed.gz
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz

		- name: Run pipeline with test data
		run: \|
		nextflow run ${GITHUB_WORKSPACE} -profile docker,test
		nextflow run ${GITHUB_WORKSPACE} -profile docker,test_local_zip

		##############################
		### UNIT TESTS ###
		##############################

conf/test_full_small_local_zip.config

+23 −0

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		params {
		config_profile_name = 'Test profile'
		config_profile_description = 'Minimal test dataset to check pipeline function'

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

		// Input data
		input = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet/test-GSE145187-all-small.csv'

		// Genome references
		fasta = '/home/runner/work/cutandrun/cutandrun/hg38-chr20.fa.gz'
		bowtie2 = '/home/runner/work/cutandrun/cutandrun/hg38-chr20-bowtie2.tar.gz'
		gtf = '/home/runner/work/cutandrun/cutandrun/hg38-chr20-genes.gtf.gz'
		gene_bed = '/home/runner/work/cutandrun/cutandrun/hg38-chr20-genes.bed.gz'
		blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
		spikein_fasta = '/home/runner/work/cutandrun/cutandrun/e_coli_U00096_3.fa.gz'
		spikein_bowtie2 = '/home/runner/work/cutandrun/cutandrun/e_coli_U00096_3.tar.gz'

		minimum_alignment_q_score = 10
		}

nextflow.config

+10 −9

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		@@ -181,7 +181,8 @@ profiles {
		test_no_igg { includeConfig "conf/test_no_igg.config" } // Runs a single sample with NO IgG control
		test_full { includeConfig "conf/test_full.config" } // Runs a full experimental dataset
		test_full_multi { includeConfig "conf/test_full_multi.config" } // Runs a full experimental dataset with extra fake replicates to enable full reporting functionality
		test_local_zip { includeConfig "conf/test_local_zip.config" } // Runs a single sample with an IgG control but that targets local already downloaded compressed input files
		test_local_zip { includeConfig "conf/test_local_zip.config" } // Runs a single sample with an IgG control but that targets local, already downloaded compressed input files
		test_full_small_local_zip { includeConfig "conf/test_full_small_local_zip.config" } // Runs a full experimental configuration but with a small dataset but that targets local, already downloaded compressed input files
		}

		// Load igenomes.config if required

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