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nf-core / configs

Config files used to define parameters specific to compute environments at different Institutions
https://nf-co.re/configs
MIT License
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Call containerOptionsCreator #691

Closed mahesh-panchal closed 4 months ago

mahesh-panchal commented 4 months ago

Fix to call the containerOptionsCreator rather than assign the closure

pontus commented 4 months ago

I don't mind this change but out of curiosity; did you have issues related to it? I don't see now why it would cause problems.

mahesh-panchal commented 4 months ago

Nextflow wasn't evaluating the closure. Agata reported it to me. Her run scripts looked like:

    nxf_launch() {
        set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} SINGULARITYENV_NXF_DEBUG="${NXF_DEBUG:=0}" singularity exec --no-home --pid -B /cfs/klemming/projects Script8C84027CBF0BFB90846176A9D9C58EDE$_run_closure2@3a53a874 /cfs/klemming/projects/snic/--redacted--/containers/depot.galaxyproject.org-singularity-ubuntu-20.04.img /bin/bash -c "cd $PWD; eval $(nxf_container_env); /bin/bash /cfs/klemming/projects/supr/--redacted--/work/df/5238938689a64af1a2c9f34443b5a6/.command.run nxf_trace"
    }

and then nextflow complained it couldn't find the image Script8C84027CBF0BFB90846176A9D9C58EDE$_run_closure2@3a53a874