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Bug fixes #46

Merged
merged 21 commits into from
May 31, 2024
Merged

Bug fixes #46

merged 21 commits into from
May 31, 2024

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itrujnara
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Fixed a few errors caused by nonexistent files
Fixed isoform handling in OMA fetch
Improved large script readability
Added execute permissions to report run script

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).

@itrujnara itrujnara marked this pull request as draft May 29, 2024 11:26
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github-actions bot commented May 29, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 134da3f

+| ✅ 212 tests passed       |+
#| ❔  20 tests were ignored |#
!| ❗  10 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-31 13:40:23

@itrujnara itrujnara marked this pull request as ready for review May 29, 2024 14:45
JoseEspinosa
JoseEspinosa requested changes May 30, 2024
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Just some small comments but very nice! 😄
Maybe we could add to safe_get to requests.get a timeout, this way even if the problem is in the user site as with the new CRG cluster it won't stay idle for ever, something such as:
return requests.get(url, timeout = 300)

bin/fetch_oma_group.py Outdated Show resolved Hide resolved
bin/fetch_panther_group.py
uniprot_id = i["target_gene"].split("|")[-1].split("=")[-1]
print(f"{uniprot_id}")
except KeyError:
pass # yes, I mean this, we just want to return an empty file if nothing is found
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😆 Nice comment! Maybe we could add a warning here? Something as "id not found"?

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Might be tricky, as the module captures stderr from this script to get the database version

modules/local/fetch_eggnog_group_local.nf Outdated Show resolved Hide resolved
modules/local/fetch_oma_group_local.nf
@@ -25,10 +25,11 @@ process FETCH_OMA_GROUP_LOCAL {
prefix = task.ext.prefix ?: meta.id
"""
# Obtain the OMA ID for the given Uniprot ID of the query protein
omaid=\$(uniprot2oma_local.py $uniprot_idmap $uniprot_id)
uniprot2oma_local.py $uniprot_idmap $uniprot_id > oma_id.txt || test -f oma_id.txt
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😍

modules/local/fetch_oma_group_local.nf Outdated Show resolved Hide resolved
modules/local/fetch_oma_group_local.nf Outdated Show resolved Hide resolved
modules/local/fetch_panther_group_local.nf Outdated Show resolved Hide resolved
modules/local/fetch_panther_group_local.nf Outdated Show resolved Hide resolved
itrujnara and others added 6 commits May 31, 2024 14:03
@itrujnara @JoseEspinosa
Update bin/fetch_oma_group.py
38ca63a 
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
@itrujnara @JoseEspinosa
Update modules/local/fetch_eggnog_group_local.nf
19da5de 
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
@itrujnara @JoseEspinosa
Update modules/local/fetch_oma_group_local.nf
ebff50f 
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
@itrujnara @JoseEspinosa
Update modules/local/fetch_oma_group_local.nf
403f616 
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
@itrujnara @JoseEspinosa
Update modules/local/fetch_panther_group_local.nf
ab04193 
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
@itrujnara @JoseEspinosa
Update modules/local/fetch_panther_group_local.nf
6b9d3d0 
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
JoseEspinosa
JoseEspinosa approved these changes May 31, 2024
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Awesome! thanks! 🚀

@itrujnara itrujnara merged commit d33db22 into nf-core:dev May 31, 2024
8 checks passed
@itrujnara itrujnara deleted the bug_fixes branch October 7, 2024 15:39
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@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

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@itrujnara @JoseEspinosa