Included is_control metadata and additional control column tests (c30b5819) · Commits · Chaos / Cutandrun

bin/check_samplesheet.py

+11 −4

Original line number	Diff line number	Diff line
		@@ -57,6 +57,7 @@ def check_samplesheet(file_in, file_out, igg_control):
		num_fastq_list = []
		sample_names_list = []
		control_names_list = []
		is_control = []
		sample_run_dict = {}
		with open(file_in, "r") as fin:

		@@ -115,6 +116,12 @@ def check_samplesheet(file_in, file_out, igg_control):
		print_error("Replicate id not an integer!", "Line", line)
		replicate = int(replicate)

		## Create control identity
		if control != "":
		is_control = "0"
		else:
		is_control = "1"

		## Check FastQ file extension
		for fastq in [fastq_1, fastq_2]:
		if fastq:
		@@ -132,9 +139,9 @@ def check_samplesheet(file_in, file_out, igg_control):
		## Auto-detect paired-end/single-end
		sample_info = []
		if sample and fastq_1 and fastq_2: ## Paired-end short reads
		sample_info = [sample, str(replicate), control, "0", fastq_1, fastq_2]
		sample_info = [sample, str(replicate), control, "0", fastq_1, fastq_2, is_control]
		elif sample and fastq_1 and not fastq_2: ## Single-end short reads
		sample_info = [sample, str(replicate), control, "1", fastq_1, fastq_2]
		sample_info = [sample, str(replicate), control, "1", fastq_1, fastq_2, is_control]
		else:
		print_error("Invalid combination of columns provided!", "Line", line)
		## Create sample mapping dictionary = {sample: {replicate : [ single_end, fastq_1, fastq_2 ]}}
		@@ -183,7 +190,7 @@ def check_samplesheet(file_in, file_out, igg_control):
		make_dir(out_dir)
		with open(file_out, "w") as fout:

		fout.write(",".join(["id", "group", "replicate", "control", "single_end", "fastq_1", "fastq_2"]) + "\n")
		fout.write(",".join(["id", "group", "replicate", "control", "single_end", "fastq_1", "fastq_2", "is_control"]) + "\n")
		for sample in sorted(sample_run_dict.keys()):

		## Check that replicate ids are in format 1..<NUM_REPS>

Admin message