error pulling docker image and minor issues

phpeters commented 2 years ago

Hej,

Thanks for developing this pipeline! I tried it but sadly, I ran into some issues, maybe you could have a look into it? I'm using nextflow version 21.10.6 and singularity version 3.7.3

Thanks and best! Philpp

docker pull ontresearch/wf-isoforms which results in Using default tag: latest Error response from daemon: manifest for ontresearch/wf-isoforms:latest not found: manifest unknown: manifest unknown

same holds for wf-isoforms:v0.0.1 and for singularity.

docker pull ontresearch/wf-isoforms:sha4a978c1a works fine though, so I used this image. I'm not sure whether it is our system's settings or is the tag v0.0.1 just not set?

"tuple(sample_id)" in main.nf -> process generate_fq_stats should probably be "tuple val(sample_id)" ?
"--threads n" with n>4 fails with e.g. "Process requirement exceed available CPUs -- req: 16; avail: 4" I fixed this for me by commenting out the local executor in nextflow.config, since it uses all available cores by default ( https://www.nextflow.io/docs/latest/config.html#scope-executor )
csvtk is not included in image sha4a978c1a, which makes process getVersions fail. Since it's not use anywhere I removed it from the process

cjw85 commented 2 years ago

Hi @phpeters,

Sorry about the problems you are having, it looks like something went awry in our release process last week and some of the necessary software didn't get pushed external to our servers, notably the docker container. @nrhorner will get this done this afternoon.

nrhorner commented 2 years ago

Hi @phpeters

I've released the version, v0.1.0, that should have been released previously. Sorry about that. Please try the workflow out now.

phpeters commented 2 years ago

Hej, Thanks for fixing this so quick! Pulling the image works fine now, the issue with the number of threads remains. It's running right now, I'll let you know the outcome. Thanks again and have a nice evening! Philipp

phpeters commented 2 years ago

Hej, The example runs through, thanks a lot! But I get no entries in the "Read mapping summary" table and an error message stating "ESC[31m[ERRO]ESC[0m EOF".

I assume seqkit is missing an input stream, updating line 27 in reference_assembly.nf from

| samtools sort -@ ${params.threads} -o "${sample_id}_reads_aln_sorted.bam" - \ to | samtools sort -@ ${params.threads} - | tee "${sample_id}_reads_aln_sorted.bam" \

is fixing this for me. Besides this the issue can be closed. Thanks and best! Philipp

nrhorner commented 2 years ago

Hi Philip,

Thanks. This is fixed now.

Neil

epi2me-labs / wf-isoforms

error pulling docker image and minor issues #2