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update samplesheet specs

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This commit is contained in:
maxibor 2022-02-18 13:11:18 +01:00
parent 1aba3ed01c
commit 54a1a4fd45
1 changed files with 6 additions and 21 deletions
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27
bin/check_samplesheet.py
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@ -47,13 +47,10 @@ def check_samplesheet(file_in, file_out):
This function checks that the samplesheet follows the following structure:
sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta
2611,ERR5766174,ILLUMINA,NA,NA,FA_EXTENSIONSERX5474930_ERR5766174_1.fa.gz
2612,ERR5766176,ILLUMINA,ERX5474932_ERR5766176_1.fastq.gz,ERX5474932_ERR5766176_2.fastq.gz,NA
2612,ERR5766174,ILLUMINA,ERX5474936_ERR5766180_1.fastq.gz,NA,NA
2613,ERR5766181,ILLUMINA,ERX5474930_ERR5766174_1.fa.gz,ERX5474930_ERR5766174_2.fa.gz,NA
For an example see:
https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv
2611,ERR5766174,ILLUMINA,,,ERX5474930_ERR5766174_1.fa.gz
2612,ERR5766176,ILLUMINA,ERX5474932_ERR5766176_1.fastq.gz,ERX5474932_ERR5766176_2.fastq.gz,
2612,ERR5766174,ILLUMINA,ERX5474936_ERR5766180_1.fastq.gz,,
2613,ERR5766181,ILLUMINA,ERX5474937_ERR5766181_1.fastq.gz,ERX5474937_ERR5766181_2.fastq.gz,
"""
FQ_EXTENSIONS = (".fq", ".fq.gz", ".fastq", ".fastq.gz")
@ -216,21 +213,9 @@ def check_samplesheet(file_in, file_out):
with open(file_out, "w") as fout:
fout.write(",".join(HEADER_OUT) + "\n")
for sample in sorted(sample_mapping_dict.keys()):
## Check that multiple runs of the same sample are of the same datatype
if not all(
x[0] == sample_mapping_dict[sample][0][0]
for x in sample_mapping_dict[sample]
):
print_error(
"Multiple runs of a sample must be of the same datatype!",
"Sample: {}".format(sample),
)
for idx, val in enumerate(sample_mapping_dict[sample]):
fout.write(
",".join(["{}_T{}".format(sample, idx + 1)] + val) + "\n"
)
fout.write(f"{sample},{','.join(val)}\n")
# fout.write(f",".join(["{}".format(sample)] + val) + "\n")
else:
print_error("No entries to process!", "Samplesheet: {}".format(file_in))