These are changes necessary to allow our alignment workflow to run end-to-end using cwltool:
Pulled out the rg_string value from the argument block. When left in the argument block, cwltool would not "interpret" the value. So if you hand it ('hello\tworld') it would explicitly pass the double escaped tab ('\t') rather than simply a tab ('\t'). The solution was to split the argument block into things that come before and after it then use inputBinding to put it between them.
No longer rm bams in gatherbamfiles. The bams it tries to delete are typically readonly files in cwltool and users won't have rm permissions.
Rewrote the flatten function in sambamba merge anylist. The old function was only flattening a single level so I rewrote it to recursively flatten. All other changes are just cleaning up the code in that tool.
[x] Bug fix (non-breaking change which fixes an issue)
[x] New feature (non-breaking change which adds functionality)
How Has This Been Tested?
Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration
[x] Ran the tool end to end using cwltool on my personal VM
[x] IPC folks ran it as well and were satisfied with the results
Description
These are changes necessary to allow our alignment workflow to run end-to-end using cwltool:
Resolves https://github.com/d3b-center/bixu-tracker/issues/591
Type of change
Please delete options that are not relevant.
How Has This Been Tested?
Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration
Test Configuration:
Checklist: