Merge pull request #46 from luslab/dev (fd6aa8e8) · Commits · Chaos / Cutandrun

.gitignore

+3 −0

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		@@ -19,3 +19,6 @@ dev/docker/static_reports/test_output/*
		!dev/docker/static_reports/test_output/_dummy.txt

		!tests/data/

		.vscode/
		profile.svg

.vscode/settings.json

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+0 −8

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		{
		"python.pythonPath": "/usr/local/Caskroom/miniconda/base/envs/cutrun/bin/python",
		"editor.tabSize": 4,
		"editor.insertSpaces": true,
		"editor.detectIndentation": false,
		"editor.renderWhitespace": "all",
		"editor.renderFinalNewline": true
		}

assets/blacklists/GRCh37-blacklist.bed

deleted100644 → 0

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		Y 27167859 27206241 BSR/Beta 1000 .
		Y 27206778 27229502 BSR/Beta 1000 .
		Y 27263848 27268411 BSR/Beta 1000 .
		Y 27269388 27280315 BSR/Beta 1000 .
		Y 27286226 27288494 BSR/Beta 1000 .
		Y 27289462 27305895 BSR/Beta 1000 .
		Y 27337415 27347656 BSR/Beta 1000 .
		Y 27352996 27375497 BSR/Beta 1000 .
		Y 27813984 27814119 TAR1 1000 .
		Y 28555026 28555353 TAR1 1000 .
		Y 28784129 28819695 Satellite_repeat 1000 .
		Y 58819367 58917648 (CATTC)n 1000 .
		Y 58971913 58997782 (CATTC)n 1000 .
		Y 59361267 59362785 TAR1 1000 .

assets/multiqc_config.yaml

+0 −1

Original line number	Diff line number	Diff line
		@@ -11,7 +11,6 @@ report_section_order:
		export_plots: true

		report_header_info:
		- Contact E-mail: "chris.cheshire@crick.ac.uk"
		- Application Type: "CUT&RUN"

		# Run only these modules

assets/samplesheet.csv

+6 −6

Original line number	Diff line number	Diff line
		group,replicate,control_group,fastq_1,fastq_2
		h3k27me3,1,1,READ1_FASTQ,READ2_FASTQ
		h3k27me3,2,1,READ1_FASTQ,READ2_FASTQC
		h3k4me3,1,2,READ1_FASTQ,READ2_FASTQC
		h3k4me3,2,2,READ1_FASTQ,READ2_FASTQC
		igg,1,1,READ1_FASTQ,READ2_FASTQC
		igg,2,2,READ1_FASTQ,READ2_FASTQC
		h3k27me3,1,1,READ1_FASTQ.gz,READ2_FASTQ.gz
		h3k27me3,2,1,READ1_FASTQ.gz,READ2_FASTQ.gz
		h3k4me3,1,2,READ1_FASTQ.gz,READ2_FASTQ.gz
		h3k4me3,2,2,READ1_FASTQ.gz,READ2_FASTQ.gz
		igg,1,1,READ1_FASTQ.gz,READ2_FASTQ.gz
		igg,2,2,READ1_FASTQ.gz,READ2_FASTQ.gz

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