Missing header column in salmon transcript output

[tijeco]

Description of the bug

I've noticed that when running star_salmon the output file salmon.merged.transcript_counts.tsv has one fewer header columns that it needs. This actually appears to be the case in the AWS test data output provided on the nf-co.re/rnaseq website (s3://nf-core-awsmegatests/rnaseq/results-7106bd792b3fb04f9f09b4e737165fa4e736ea81/aligner_star_salmon/salmon/salmon.merged.transcript_counts.tsv)

The header has 10 tab delimited fields, while the data has 11.

Eyeballing it, it seems that the tx column was duplicated, maybe?

Command used and terminal output

No response

Relevant files

No response

System information

No response

[drpatelh]

Thanks for reporting @tijeco ! This appears to be a duplicate of #775 and will be fixed in v3.7 which I will try and get out tomorrow. You can test the pre-release code by using -r dev when running Nextflow.

[tijeco]

Aha! Y'all are on top of it!