Updated sample sheet and schema input (940fe412) · Commits · Chaos / Cutandrun

assets/samplesheet.csv

+7 −3

Original line number	Diff line number	Diff line
		sample,fastq_1,fastq_2
		SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz
		SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,
		group,replicate,control_group,fastq_1,fastq_2
		h3k27me3,1,1,READ1_FASTQ,READ2_FASTQC
		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
		No newline at end of file

+19 −14

Original line number	Diff line number	Diff line
		@@ -7,10 +7,20 @@
		"items": {
		"type": "object",
		"properties": {
		"sample": {
		"group": {
		"type": "string",
		"pattern": "^\\S+$",
		"errorMessage": "Sample name must be provided and cannot contain spaces"
		"errorMessage": "Sample group must be provided and cannot contain spaces"
		},
		"replicate": {
		"type": "integer",
		"pattern": "^[0-9]*$",
		"errorMessage": "Biological Replicate number within the group - technical replicates must have the same replicate number"
		},
		"control_group": {
		"type": "integer",
		"pattern": "^[0-9]*$",
		"errorMessage": "Group ID that matches to the IgG control group (if provided) - otherwise set to 0"
		},
		"fastq_1": {
		"type": "string",
		@@ -18,22 +28,17 @@
		"errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
		},
		"fastq_2": {
		"errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
		"anyOf": [
		{
		"type": "string",
		"pattern": "^\\S+\\.f(ast)?q\\.gz$"
		},
		{
		"type": "string",
		"maxLength": 0
		}
		]
		"pattern": "^\\S+\\.f(ast)?q\\.gz$",
		"errorMessage": "FastQ file for reads 2 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
		}
		},
		"required": [
		"sample",
		"fastq_1"
		"replicate",
		"control_group",
		"fastq_1",
		"fastq_2"
		]
		}
		}