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nunofonseca / irap

integrated RNA-seq Analysis Pipeline
GNU General Public License v3.0
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bamToFastq pickup the wrong bam file name #41

Closed byb121 closed 6 years ago

byb121 commented 6 years ago

When input is a bam file (eg: the_sample.bam), bamToFastq is using the_sample.bam.sorted.bam as its input, while samtools sort produces a the_sample.bam.sorted, hence bamToFastq produces empty Fastqs.

bamToFastq should raise an error at this point as well, not to wait till Fastqc complains.

byb121 commented 6 years ago

seems just need to change sorted.bam to sorted on this line: https://github.com/nunofonseca/irap/blob/master/scripts/irap_fastq_qc#L359

nunofonseca commented 6 years ago

It should be fixed in the new version of the script (devel branch). The code now uses samtools to perform the conversion. Please reopen the issue if the problem persists. Cheers.