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Adds possibility to make drop database #147
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I haven't modified the CHANGELOG yet to avoid conflicts with the other this open PR |
I'll give this a go now! Will let you know how it goes. |
A first question. Should it be possible to generate the db without assigning the three DROP annotation parameters? Seems to me that it skipped DROP entirely when running without them. |
It should work, those options are now optional :) |
Looks like it is passing the DROP config building step now, nice! We will see whether it passes the AE and AS steps as well, will let you know. |
Great 🤞 |
Some updates. It initially crashed. I recognize the error from my previous testing (gagneurlab/drop#568). When debugging before, the error came from the columns with Also, I think it needs the After doing the following updates, it is running for me:
After these changes it has been running fine for 15+ minutes. We'll see how it goes. |
Nice! Did you just remove the |
I totally removed it. Haven't tested what happens if leaving it empty (i.e. without the 'NA' strings). |
The aberrant expression run was successful! I now see the I'll try the splicing module next. Caching did not seem to work for the AE process though - it restarted when I did |
Happy to hear that the AE module worked 😄 |
For the splicing, I am running into the same DROP error as I received previously. It seems there is a bug triggered when running with no external counts. Seems to be a silly issue, due to symlink and create a folder in the same location. See issue: gagneurlab/drop#558 Have you managed to get around this somehow? 🤔 |
I have run without external counts but have not encountered this issue 🤔 |
Hmm, strange. Was it a different version of DROP? Yes, I still get it on reruns! |
No, same version |
I think I figured out the issue (see notes in gagneurlab/drop#558). Seems the splicing workflow cannot handle a relative "root" path as it will yield an invalid softlink in one step. I am trying now a run where I have asigned the path in
Before it was:
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Great! Let me know how it goes 😄 |
Now it passed that step! Still crashing though :( In the step The debugging continues ... |
After updating the DROP container to version 1.4.0 the run went through 🎉 |
Great! Thanks for all the help with the debugging! |
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).nextflow run . -profile debug,test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).