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NAL-i5K / Organism_Onboarding

A workflow to make organism onboarding pipeline easy to handle as an I/O pipeline
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bigwig_symlink-gaps step in createsymlink.cwl needs to be optional #144

Closed mpoelchau closed 1 year ago

mpoelchau commented 1 year ago

Link to @mpoelchau current attempt: https://github.com/NAL-i5K/Organism_Onboarding/blob/05674ac648b96f5c26239266ecfa8d3019c8ae18/CreateSymlink-workflow.cwl#L146

mpoelchau commented 1 year ago

@amcooksey can you test branch issue-144 on the server? @spcspin has pushed an update.

amcooksey commented 1 year ago

@mpoelchau I pulled the updates to the issue-144 branch in my personal copy of Organism_onboadring and re-ran it on vesman (with no gaps file). I've copied all of the output to the attached file. vesman_nogaps_errors.txt

mpoelchau commented 1 year ago

Thanks @amcooksey! @spcspin do you know what's going on?

spcspin commented 1 year ago

@mpoelchau I forgot to remove the conditional line in the CreateSymlink-workflow.cwl file. Sorry about that. The other error was the data type I changed when I tested the script. Both of the errors I have modified it. Thank you so much.

The line that I deleted: when:$($(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_bigwig[0])/$(inputs.genome_fasta_name[0]).gaps.bigwig.gz != "")

mpoelchau commented 1 year ago

Thanks @spcspin ! @amcooksey can you pull and try again?

amcooksey commented 1 year ago

@mpoelchau @spcspin Success! I was able to run the workflow successfully using the updated issue-144 branch in my personal directory.

mpoelchau commented 1 year ago

Excellent @amcooksey !

Can you try using this branch again on stage when you're onboarding an organism that has the gaps file? That way we can test whether this fix works in both situations on our servers. Once you've confirmed that it works, I'll merge the new fix.

amcooksey commented 1 year ago

Successfully tested with ploint (has gaps file).

mpoelchau commented 1 year ago

Great, thanks! Merged.