rm container option that crashes singularity

[hoelzer]

Removed the container option from

    withLabel: seqkit           { container = 'nanozoo/seqkit:0.13.2--cd66104' ; containerOptions = '--shm-size 2g' }

bc this is a Docker option and if coded like that it crashes Singularity. Also, it is probably not needed anyway.

I am doing some further tests on SLURM/Singularity and will then report here if the PR is ready

[hoelzer]

VS2 fails:

Could not create conda environment from /opt/conda/lib/python3.8/site-packages/virsorter/rules/../envs/vs2.yaml:

>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/conda/exceptions.py", line 1079, in __call__
    return func(*args, **kwargs)
  File "/opt/conda/lib/python3.8/site-packages/conda_env/cli/main.py", line 80, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "/opt/conda/lib/python3.8/site-packages/conda_env/cli/main_create.py", line 119, in execute
    result[installer_type] = installer.install(prefix, pkg_specs, args, env)
  File "/opt/conda/lib/python3.8/site-packages/mamba/mamba_env.py", line 44, in mamba_install
    index = load_channels(
  File "/opt/conda/lib/python3.8/site-packages/mamba/utils.py", line 93, in load_channels
    index = get_index(
  File "/opt/conda/lib/python3.8/site-packages/mamba/utils.py", line 74, in get_index
    is_downloaded = dlist.download(True)
RuntimeError: Download error (7) Couldn't connect to server [https://conda.anaconda.org/bioconda/noarch/repodata.json]
Failed to connect to conda.anaconda.org port 443: Connection refused

$ /opt/conda/bin/mamba create --quiet --file /scratch/hoelzerm/databases/wtp/nextflow-autodownload-databases/virsorter2-db/db/conda_envs/bd7b4199.yaml --prefix /scratch/hoelzerm/databases/wtp/nextflow-autodownload-databases/virsorter2-db/db/conda_envs/bd7b4199

But maybe this is because of the RKI HPC setup... and nothing directly related to how SIngularity is configurred...

I am ignoring VS2 for now

[hoelzer]

The filter steps for virsorter and virsorter_virome failed for me when the output of viruses of cat 1,2,3,4 is empty. I integrated a check now if the file is empty. Will push the code soonish here as well

[mult1fractal]

can you do a testrun ? with the added code? I will merge it then

[hoelzer]

@mult1fractal I am on it.

THe filtering of virsorter (virome) works now for me. But now the test run fails at

[ce/4d99bf] process > phage_tax_classification_wf:sourmash_for_tax (8) [100%] 8 of 8, failed: 8

Looking into it

[hoelzer]

Hm sorry, I dont have time to look into this further. I did some fixes as described above. Please have a look and if it is fine please merge @mult1fractal !