CWL unrecognised argument GCA_...fasta

[jjkoehorst]

I am working on a CWL implementation of bakta using the example CWL file provided (after some tweaking).

It starts up nicely but it does not understand the genome file...

INFO [job bakta] /tmp/agl_dkt4$ docker \
    run \
    -i \
    --mount=type=bind,source=/tmp/agl_dkt4,target=/qPdSea \
    --mount=type=bind,source=/tmp/by2e9c77,target=/tmp \
    --mount=type=bind,source=/home/jasperk/GCA_001095185.1.fasta,target=/var/lib/cwl/stg49bfe0f3-b800-47f2-a70d-9e1322abe626/GCA_001095185.1.fasta,readonly \
    --mount=type=bind,source=/unlock/references/databases/bakta/db,target=/var/lib/cwl/stge0793215-c3f8-4df0-9353-7aeb59e7eb7b/db,readonly \
    --workdir=/qPdSea \
    --read-only=true \
    --net=none \
    --user=1001:1001 \
    --rm \
    --cidfile=/tmp/l9h2ywk3/20230712085438-886264.cid \
    --env=TMPDIR=/tmp \
    --env=HOME=/qPdSea \
    oschwengers/bakta \
    bakta \
    --force \
    --output \
    bakta_output \
    --db \
    /var/lib/cwl/stge0793215-c3f8-4df0-9353-7aeb59e7eb7b/db \
    --prefix \
    PREFIX \
    --threads \
    2 \
    /var/lib/cwl/stg49bfe0f3-b800-47f2-a70d-9e1322abe626/GCA_001095185.1.fasta
usage: bakta [--db DB] [--min-contig-length MIN_CONTIG_LENGTH]
             [--prefix PREFIX] [--output OUTPUT] [--force] [--genus GENUS]
             [--species SPECIES] [--strain STRAIN] [--plasmid PLASMID]
             [--complete] [--prodigal-tf PRODIGAL_TF]
             [--translation-table {11,4}] [--gram {+,-,?}] [--locus LOCUS]
             [--locus-tag LOCUS_TAG] [--keep-contig-headers]
             [--replicons REPLICONS] [--compliant] [--proteins PROTEINS]
             [--meta] [--skip-trna] [--skip-tmrna] [--skip-rrna]
             [--skip-ncrna] [--skip-ncrna-region] [--skip-crispr] [--skip-cds]
             [--skip-pseudo] [--skip-sorf] [--skip-gap] [--skip-ori]
             [--skip-plot] [--help] [--verbose] [--debug] [--threads THREADS]
             [--tmp-dir TMP_DIR] [--version]
             <genome>
bakta: error: unrecognized arguments: /var/lib/cwl/stg49bfe0f3-b800-47f2-a70d-9e1322abe626/GCA_001095185.1.fasta
INFO [job bakta] Max memory used: 103MiB
WARNING [job bakta] exited with status: 2
WARNING [job bakta] completed permanentFail

Am I missing something obvious?

bakta: error: unrecognized arguments: /var/lib/cwl/stg9c555c37-fcd6-4c32-a7ce-928db11ab715/GCA_001095185.1.fna

Changing the fasta > fna did not do the trick either.

[oschwengers]

Hey @jjkoehorst , thanks for reaching out and reporting. Unfortunately, I don't have much experience with CWLmyself, but I've very often encounters such an error, whenever either a parameter was misspelled or an argument was missing. However, I cannot spot such a trivial case here. Could you maybe double check, that all parameters/arguments are forwarded to Bakta as expected? File names/suffices don't matter.

Besides this, you mentioned that you have tweaked the CWL file. Is there anything wrong that we could fix for others, as well?

[oschwengers]

Hi @jjkoehorst, Is this still active? is there anything we could help with?

Just in case you've managed to get it working, we'd happily accept a PR with fixed code a working example ;-)

[jjkoehorst]

@oschwengers thanks for the reminder, a colleague @bartns fixed the final issues and created a pull request.

[oschwengers]

Wonderful and thanks a lot! I'll have a look at this ASAP.

[oschwengers]

@jjkoehorst , I've just merged the PR. In addition, I'll amend some parts of the described parameters and close this for now. Please do not hesitate to re-open this, and again, thanks a lot!