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Add module gzrt (#6918) #7052

Merged
merged 7 commits into from
Nov 28, 2024
Merged

Add module gzrt (#6918) #7052

merged 7 commits into from
Nov 28, 2024

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mazzalab
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@mazzalab mazzalab commented Nov 21, 2024 •
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Added a new module

PR checklist

Closes #6918

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda

@mazzalab mazzalab closed this Nov 21, 2024
@mazzalab mazzalab reopened this Nov 21, 2024
@mazzalab mazzalab self-assigned this Nov 23, 2024
@mazzalab mazzalab added the new module Adding a new module label Nov 23, 2024
LouisLeNezet
LouisLeNezet requested changes Nov 26, 2024
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Just a few changes needed before merging it ;)

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@mazzalab
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Just a few changes needed before merging it ;)

I couldn't pipe gzrecover to gzip because the former specifies the output file name with a -o params. At least, I did not know what to do. Thus, I've resorted to a named pipe that should prevent me from allocating temp space.

Now I have got an odd error with conda checks. I'm waiting for feedback and we should be done

LouisLeNezet
LouisLeNezet approved these changes Nov 28, 2024
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Seems good to me 😄

@mazzalab mazzalab added this pull request to the merge queue Nov 28, 2024
Merged via the queue into nf-core:master with commit 60fbc3e Nov 28, 2024
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@mazzalab mazzalab deleted the gzrt branch November 28, 2024 09:13
LouisLeNezet pushed a commit to LouisLeNezet/modules that referenced this pull request Dec 4, 2024
@mazzalab @tm4zza
Add module gzrt (nf-core#6918) (nf-core#7052)
58e7596 
* Add module gzrt (nf-core#6918)

* fixed environment.yml

* Reply to review

* gzrecover and gzip oneliner

* gzrt uses a named pipe to avoid temp files

---------

Co-authored-by: tm4zza <mazza.tommaso@gmail.com>
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new module: gzrt aka gzrecover
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@mazzalab @LouisLeNezet @tm4zza