After launching a process .nf with htseq-count (HTSeq) and failing I realised that the version of htseq in the cluster is anterior to the one I used locally and succeeded to obtain output files for same bam file.
Two flags that were NOT accepted in the /0.11 version, but are available in the latest one :
Moreover, even when running the command without these flags, there is a problem with the decoding of bam or gtf file used , but they are fine since I used them locally and had no error.
The error I got :
Error occured when processing GFF file (line 1 of file /shared/projects/[...]/DM1cl5_1_Aligned.sortedByCoord.out.bam): 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte [Exception type: UnicodeDecodeError, raised in codecs.py:322]
A reproducible script can be found in
The documentation about the error is quite old, and appears to other tools/packages too, but no other solution provided to overcome it.
So, i suggest if possible to provide the latest version of the package in the cluster.
For any other suggestion, please give feedback.
Thanks in advance !