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clean_work_dirs bug #263
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I get the same error running with the locally stored CORG fastq.gz files, so that should be easier to replicate:
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It seems the problem is indicated with these lines in the error log: First:
Followed by:
Then by:
I'm not sure where the GEMmaker/bin/clean_work_files.sh Line 15 in 9a880fd
The |
Perhaps, the best solution would probably be to specify a container that this step should run in, that has the correct libraries, and binaries. |
Description of the bug
I am running GEMmaker on the PRP with a human kidney dataset stored locally in split fastq format. Just with the CORG reference for now to test.
Command used:
nextflow -C nextflow.config kuberun systemsgenetics/gemmaker -profile k8s -v pvc-storage-test --pipeline kallisto --kallisto_index_path /workspace/projects/systemsgenetics/gemmaker/assets/demo/references/CORG.transcripts.Kallisto.indexed --input /workspace/data/kidneydata/sra/*.fastq --outdir /workspace/gemmaker/output --max_cpus 8
nextflow.config to add k8s profile:
I get the following error, even after deleting the work dir:
Any idea what the issue may be? I have used a slight variation of this command in the past during the scidas workshop and had no issues.
Command used and terminal output
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