Merge pull request #43 from luslab/dev (bde3c9f5) · Commits · Chaos / Cutandrun

bin/lib/reports.py

+3 −0

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		@@ -343,6 +343,9 @@ class Reports:
		self.load_data()
		self.annotate_data_table()

		# Sort tables
		self.data_table = self.data_table.sort_values('group')

		# Plot 1
		multi_plot, data1 = self.alignment_summary()
		plots["01_01_seq_depth"] = multi_plot[0]

+2 −2

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		@@ -205,12 +205,12 @@ params {
		}

		"dt_compute_mat_gene" {
		args = "scale-regions --beforeRegionStartLength 3000 --regionBodyLength 5000 --afterRegionStartLength 3000 --skipZeros"
		args = "scale-regions --beforeRegionStartLength 3000 --regionBodyLength 5000 --afterRegionStartLength 3000 --skipZeros --missingDataAsZero"
		publish_dir = "04_reporting/heatmaps/gene"
		}

		"dt_compute_mat_peaks" {
		args = "reference-point -a 3000 -b 3000 --referencePoint center --skipZeros"
		args = "reference-point -a 3000 -b 3000 --referencePoint center --skipZeros --missingDataAsZero"
		publish_dir = "04_reporting/heatmaps/peaks"
		}

+1 −1

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		@@ -27,7 +27,7 @@ params {
		bowtie2 = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz'
		gtf = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz'
		gene_bed = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.bed.gz'
		blacklist = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed"
		blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
		spikein_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz'
		spikein_bowtie2 = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz'

0 → 100644

+20 −0

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		params {
		config_profile_name = 'Test profile'
		config_profile_description = 'Minimal test dataset to check pipeline function with custom genome files except fasta and bt index'

		// 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-small.csv'

		// Genome references
		fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz'
		bowtie2 = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz'
		spikein_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz'
		spikein_bowtie2 = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz'

		minimum_alignment_q_score = 10
		}
		No newline at end of file

+1 −0

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		@@ -16,5 +16,6 @@ params {

		genome = 'GRCh38'
		input = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet/test-GSE145187-all.csv'

		minimum_alignment_q_score = 10
		}
		No newline at end of file