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