Fixed control selection for peak calling and added more tests (b3988e03) · Commits · Chaos / Cutandrun

subworkflows/local/input_check.nf

+1 −1

Original line number	Diff line number	Diff line
		@@ -27,9 +27,9 @@ def get_samplesheet_paths(LinkedHashMap row) {
		meta.id = row.id
		meta.group = row.group
		meta.replicate = row.replicate.toInteger()
		meta.control_group = row.control
		meta.single_end = row.single_end.toBoolean()
		meta.is_control = row.is_control.toBoolean()
		meta.control_group = meta.is_control ? meta.group : row.control

		def array = []
		if (!file(row.fastq_1).exists()) {

tests/test_peak_callers.yml

+22 −0

Original line number	Diff line number	Diff line
		@@ -47,3 +47,25 @@
		files:
		- path: results/03_peak_calling/04_called_peaks/h3k27me3_R1.seacr.peaks.bed.stringent.bed
		- path: results/03_peak_calling/04_called_peaks/h3k27me3_R1.macs2.peaks.bed_summits.bed

		- name: test_peak_callers_seacr_single_ctrl_multi_rep
		command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --peakcaller seacr --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-all-multi-rep-single-ctrl.csv -c tests/config/nextflow.config
		tags:
		- test_peak_callers
		- test_peak_callers_seacr
		files:
		- path: results/03_peak_calling/04_called_peaks/h3k4me3_R1.seacr.peaks.bed.stringent.bed
		- path: results/03_peak_calling/04_called_peaks/h3k4me3_R2.seacr.peaks.bed.stringent.bed
		- path: results/03_peak_calling/04_called_peaks/h3k27me3_R1.seacr.peaks.bed.stringent.bed
		- path: results/03_peak_calling/04_called_peaks/h3k27me3_R2.seacr.peaks.bed.stringent.bed

		- name: test_peak_callers_seacr_multi_single_ctrl_multi_rep
		command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --peakcaller seacr --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-all-multi-rep-multi-single-ctrl.csv -c tests/config/nextflow.config
		tags:
		- test_peak_callers
		- test_peak_callers_seacr
		files:
		- path: results/03_peak_calling/04_called_peaks/h3k4me3_R1.seacr.peaks.bed.stringent.bed
		- path: results/03_peak_calling/04_called_peaks/h3k4me3_R2.seacr.peaks.bed.stringent.bed
		- path: results/03_peak_calling/04_called_peaks/h3k27me3_R1.seacr.peaks.bed.stringent.bed
		- path: results/03_peak_calling/04_called_peaks/h3k27me3_R2.seacr.peaks.bed.stringent.bed

tests/test_samplesheet_check.yml

+16 −0

Original line number	Diff line number	Diff line
		@@ -167,3 +167,19 @@
		- test_samplesheet
		files:
		- path: results/pipeline_info/samplesheet.valid.csv

		# Test all multi-rep single-ctrl
		- name: test_samplesheet_multi_rep_single_ctrl
		command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-all-multi-rep-single-ctrl.csv -c tests/config/nextflow.config
		tags:
		- test_samplesheet
		files:
		- path: results/pipeline_info/samplesheet.valid.csv

		# Test all multi-rep multi-single-ctrl
		- name: test_samplesheet_multi_rep_multi_single_ctrl
		command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-all-multi-rep-multi-single-ctrl.csv -c tests/config/nextflow.config
		tags:
		- test_samplesheet
		files:
		- path: results/pipeline_info/samplesheet.valid.csv

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