SALMON_TXIMPORT process produces two tsv files that are not marked for export

[robsyme]

Description of the bug

The -profile test of nf-core/rnaseq runs the SALMON_TXIMPORT which produces six tsv files which marked for output:

• salmon.merged.gene_counts.tsv
• salmon.merged.gene_counts_length_scaled.tsv
• salmon.merged.gene_counts_scaled.tsv
• salmon.merged.gene_tpm.tsv
• salmon.merged.transcript_counts.tsv
• salmon.merged.transcript_tpm.tsv

... and two tsv files which are not marked for output:

• salmon.merged.gene_tpm_length_scaled.tsv
• salmon.merged.gene_tpm_scaled.tsv

I think that these files include valuable data and should be published alongside the others in the outdir.

Command used and terminal output

$ nextflow run -profile test,docker --outdir results

Relevant files

No response

System information

No response

[dross101]

Another file which would be helpful in the output (STAR-Salmon) would be the *gene_lengths.tsv: effective gene lengths. It is not included in output and would be good base information to have.

[pinin4fjords]

@dross101 the effective lengths have been output since 3.12.2

[pinin4fjords]

Modules has recently moved to nf-core/modules, so addressing this there, will then bump module etc here.

[pinin4fjords]

Solved in #1302