search

cnr-ibba / nf-resequencing-mem

Nextflow resequencing pipeline with bwa-mem and freebayes
MIT License
0 stars 0 forks source link

:bug: check_samplesheet can't detect header in certain conditions #31

Closed bunop closed 1 year ago

bunop commented 1 year ago

check_samplesheet.py can't detect header in certain case, even if it's provided correctly. This could be due to csv.Sniffer.has_header method, which is known to produce both false positive and negatives: for exaple

sample,fastq_1,fastq_2
200-1-5,/home/ngs/freeclimb_resequencing/IGA_2022-01/delivery_20220110/raw_sequences/1_ID2101_200-1-5-H9H05KWZ-H1_S1_L001_R1_001.fastq.gz,/home/ngs/freeclimb_resequencing/IGA_2022-01/delivery_20220110/raw_sequences/1_ID2101_200-1-5-H9H05KWZ-H1_S1_L001_R2_001.fastq.gz
201-1-9,/home/ngs/freeclimb_resequencing/IGA_2022-01/delivery_20220110/raw_sequences/1_ID2101_201-1-9-H9H05KWZ-A2_S1_L001_R1_001.fastq.gz,/home/ngs/freeclimb_resequencing/IGA_2022-01/delivery_20220110/raw_sequences/1_ID2101_201-1-9-H9H05KWZ-A2_S1_L001_R2_001.fastq.gz
202-1-10,/home/ngs/freeclimb_resequencing/IGA_2022-01/delivery_20220110/raw_sequences/1_ID2101_202-1-10-H9H05KWZ-B2_S1_L001_R1_001.fastq.gz,/home/ngs/freeclimb_resequencing/IGA_2022-01/delivery_20220110/raw_sequences/1_ID2101_202-1-10-H9H05KWZ-B2_S1_L001_R2_001.fastq.gz

has issue in detecting header