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After consulting the manual I still have difficulty running the pipeline. I would like to run PGAP on a system where I do not have `sudo` access but I can run a singularity container and have full acc…
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There appear to be 2 bugs in `cwltool` handling of `InitialWorkDirRequirement`, in the use of symlinks to optimize and avoid making copies of directories:
- Directories get corrupted with incorrect s…
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## Description
https://github.com/athenarc/whole-exome-seq/blob/main/workflows/Whole_Exome-Seq.cwl fails to visualize
## Expected Behavior
┆fixVersions: Dockstore 2.X
┆friendlyId: DOCK-281
┆sprint: …
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some test cases are not working well with Jenkins
need to make a list of all the troublesome test cases and get them updated cleanly to work with Jenkins better
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Dragen has released new reference genome files and recommends using these for Dragenv3.9 and onwards https://sapac.illumina.com/science/genomics-research/articles/dragen-demystifying-reference-genomes…
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```
(py374) tss1@bio-PowerEdge-T640:~/SJARACNe$ sjaracne local -e ./test_data/inputs/BRCA100.exp -g ./test_data/inputs/tf.txt -n 2 -o ./test_data/outputs/cwl/cwltool/SJARACNE_out.final
INFO:root:tes…
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Hi, I am sorry for bothering you again with the empty output file issue. I really like this method and would like to apply it to my own RNA-seq data.
I actually ran the example command provided in …
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As noted in https://github.com/DataBiosphere/toil/issues/4147#issuecomment-1159085124, when you launch a Toil cluster and connect to it, your `/tmp` is a `tmpfs` in-memory filesystem.
It should be an…