Hi, transdecoder

publishDir

is empty. See results for profile

test_megahit_transdecoder

. The pipeline completes successfully and the files are present in the

work-dir

:

fcef5a3d6fbff8fad9b26220b56e71/
├── megahit_assembly.contigs.fa
├── megahit_assembly.contigs.fa.gz -> /home/user/work/f6/aeed8dd16d5c54c1f031afdc5bbc30/megahit_out/megahit_assembly.contigs.fa.gz
├── megahit.transdecoder
│   ├── megahit_assembly.contigs.fa.transdecoder.bed
│   ├── megahit_assembly.contigs.fa.transdecoder.cds
│   ├── megahit_assembly.contigs.fa.transdecoder_dir
│   ├── megahit_assembly.contigs.fa.transdecoder.gff3
│   └── megahit_assembly.contigs.fa.transdecoder.pep
└── versions.yml

2 directories, 7 files

expected?

I would say no, that's not what we want. I'd say the four normal files in the

megahit.transdecoder

subdirectory should be published. I suppose we need to check the other two ORF callers too. I'd be happy for another PR! :-)

other tests seem to publish the results::

test_megahit_prodigal/results/prodigal/
├── spades.prodigal_all.txt.gz
├── spades.prodigal.faa.gz
├── spades.prodigal.fna.gz
├── spades.prodigal_format.gff.gz
└── spades.prodigal.gff.gz

0 directories, 5 files

test_megahit_prokka/results/prokka/
├── prokka.faa.gz
├── prokka.ffn.gz
└── prokka.gff.gz

0 directories, 3 files

happy to if I find it 😄

OK. At one time we updated the

conf/modules.config

and set

enabled: false

as a default. We've updated this for some modules but obviously not this one. I don't know what's most effective: that you do a PR and I review or the other way around?

as you prefer, do you need an issue on that?

No, no issue needed. Please do the PR. Since I can merge even if there are tests that don't pass, maybe it's better if I review.