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heathsc / gemBS

gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (WGBS).
GNU General Public License v3.0
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mapping merge fails if one of the file_id's is equal to the Barcode #94

Open IsmailM opened 2 years ago

IsmailM commented 2 years ago

If I have the following samplesheet:

Barcode,File_id,end_1,end_2
S001,S001,sample1_R1.fq.gz,sample1_R2.fq.gz
S001,S001_1,sample1_1_R1.fq.gz,sample1_1_R2.fq.gz

(i.e. in cases with multiple rows for single barcode, one of the file_id is equal to the barcode):

Then during gembs map, the merging does not work as expected.

Specifically, no index / md5 files are produced, and I suspect that the merging doesn't actually happen.

i.e. During the first step of gembs map, it generates S001.bam + S001_1.bam, which it would normally try to merge into a single file named S001.bam. But because this file already exists, it does not run the merge (and hence the index/md5 files are missing...