Add methylation summary workflow #307
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analyses/methylation-summary/tools/03-methyl-tpm-correlation.cwl
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| - class: InlineJavascriptRequirement | ||
| - class: ResourceRequirement | ||
| ramMin: ${return inputs.ram * 1000} | ||
| coresMin: 4 |
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why 4 and not 1 ? does this script requires 4 cores?
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It probably doesn't need 4. When I run it, I'll try with 1.
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| shellQuote: false | ||
| valueFrom: |- | ||
| ./.git | ||
| mkdir -p ./.git/objects |
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These are created because the scripts in open ped can try to find the data and module dir based on searching the directory tree until it finds the .git directory which is created at the root dir of a git repo. In R, the command just looks for a directory containing a directory called .git however, GitPython checks for a few more directories and files that are also created by git. So the tools are creating these fake git directories so GitPython can find the corret root dir.
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Hey @ewafula and @sickler-alex. Given the state of this project, should we close this PR? |
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Going to close this as MTP-specific and not needed right now |
Purpose/implementation Section
What GitHub issue does your pull request address?
d3b-center/ticket-tracker-OPC#456
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Review workflow and corresponding tools. None of the R or python scripts were changed so this module should still run the same from the shell script and in CI.
Which areas should receive a particularly close look?
Is there anything that you want to discuss further?
Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?
No, will need to run with the full data set.
Results
What types of results are included (e.g., table, figure)?
Cavatica Test
What is your summary of the results?
Reproducibility Checklist
Documentation Checklist
READMEand it is up to date.analyses/README.mdand the entry is up to date.