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New module: SKA/DISTANCE #7437

Merged
merged 46 commits into from
Feb 11, 2025
Merged

New module: SKA/DISTANCE #7437

merged 46 commits into from
Feb 11, 2025

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itrujnara
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@itrujnara itrujnara commented Feb 5, 2025 •
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PR checklist

Add SKA/DISTANCE module
There is no non-stub test for the list input because SKA cannot handle URLs in the list

  • 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

itrujnara and others added 26 commits November 20, 2024 17:24
@itrujnara
Add ska/fasta module
add5383
@itrujnara
Merge branch 'nf-core:master' into master
c44357a
@itrujnara
Merge branch 'master' into master
5d08909
@JoseEspinosa
Merge branch 'master' into master
b280c43
@itrujnara @JoseEspinosa
Update modules/nf-core/ska/fasta/main.nf
03f96d8 
Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
@itrujnara @JoseEspinosa
Update modules/nf-core/ska/fasta/main.nf
d0c0913 
Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
@itrujnara @JoseEspinosa
Update modules/nf-core/ska/fasta/main.nf
e90a4b0 
Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
@itrujnara @JoseEspinosa
Update modules/nf-core/ska/fasta/meta.yml
15fe5d4 
Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
@itrujnara @JoseEspinosa
Update modules/nf-core/ska/fasta/tests/main.nf.test
d53565a 
Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
@itrujnara
Tweak tests for unstable md5
8abf794
@itrujnara
Merge branch 'master' into master
f9702f2
@itrujnara @sateeshperi
Update modules/nf-core/ska/fasta/meta.yml
1c13ec2 
Co-authored-by: Sateesh_Peri <[email protected]>
@itrujnara @sateeshperi
Update modules/nf-core/ska/fasta/meta.yml
fec98ed 
Co-authored-by: Sateesh_Peri <[email protected]>
@itrujnara @sateeshperi
Update modules/nf-core/ska/fasta/meta.yml
4308d89 
Co-authored-by: Sateesh_Peri <[email protected]>
@itrujnara @sateeshperi
Update modules/nf-core/ska/fasta/meta.yml
083c55b 
Co-authored-by: Sateesh_Peri <[email protected]>
@itrujnara
Delete nxf-tmp.xaQb2l
6631375
@itrujnara @sateeshperi
Update modules/nf-core/ska/fasta/main.nf
2d1d11a 
Co-authored-by: Sateesh_Peri <[email protected]>
@itrujnara
Merge branch 'nf-core:master' into master
7373259
@itrujnara
Merge branch 'nf-core:master' into master
4081944
@itrujnara
Add ripgrep module
9286632
@itrujnara
Fix meta
f91dc4b
@itrujnara
Add name safety, add compression to stub
10df560
@itrujnara
Merge branch 'nf-core:master' into master
75c2f7b
@itrujnara
Merge branch 'nf-core:master' into master
991a335
@itrujnara
Add ska/distance module
36f7920
@itrujnara
Remove TODO from test
458a371
famosab
famosab reviewed Feb 6, 2025
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What exactly is the difference between the test with and without list? Would the list contain the URLs then? We could probably chain a setup with wget / curl to get local files?

modules/nf-core/ska/distance/main.nf Outdated
"""
touch ${prefix}.distances.tsv
touch ${prefix}.clusters.tsv
touch ${prefix}.cluster.1.txt
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Can you adjust this stub test to produce a different number of cluster.*.txt files based on the args or the input?

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The number of clusters is not determinable from the size of the input, but I can assume every input file is a separate cluster

modules/nf-core/ska/distance/main.nf Outdated
Comment on lines 42 to 49
stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.distances.tsv
touch ${prefix}.clusters.tsv
touch ${prefix}.cluster.1.txt
touch ${prefix}.dot
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More general: Can the stub be modified so that only the files are produced that are to be expected upon a specific input (because you marked the outputs as optional)?

itrujnara and others added 12 commits February 6, 2025 10:37
@itrujnara @famosab
Update modules/nf-core/ska/distance/meta.yml
1e6511e 
Co-authored-by: Famke Bäuerle <[email protected]>
@itrujnara @famosab
Update modules/nf-core/ska/distance/meta.yml
b02c87f 
Co-authored-by: Famke Bäuerle <[email protected]>
@itrujnara @famosab
Update modules/nf-core/ska/distance/meta.yml
440ed84 
Co-authored-by: Famke Bäuerle <[email protected]>
@itrujnara @famosab
Update modules/nf-core/ska/distance/meta.yml
e6c808e 
Co-authored-by: Famke Bäuerle <[email protected]>
@itrujnara @famosab
Update modules/nf-core/ska/distance/meta.yml
75116f6 
Co-authored-by: Famke Bäuerle <[email protected]>
@itrujnara @famosab
Update modules/nf-core/ska/distance/meta.yml
deded74 
Co-authored-by: Famke Bäuerle <[email protected]>
@itrujnara @famosab
Update modules/nf-core/ska/distance/meta.yml
6fbc7f5 
Co-authored-by: Famke Bäuerle <[email protected]>
@itrujnara @famosab
Update modules/nf-core/ska/distance/meta.yml
0534616 
Co-authored-by: Famke Bäuerle <[email protected]>
@itrujnara @famosab
Update modules/nf-core/ska/distance/meta.yml
031eafc 
Co-authored-by: Famke Bäuerle <[email protected]>
@itrujnara
Apply some code review comments for ska/distance
f3b6aa3
@itrujnara
Apply nf-test suggestions in ska/distance
ca4c914
@itrujnara
Make linter happy
3c17c22
@itrujnara itrujnara requested a review from famosab February 6, 2025 15:04
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Implementing the list test took way too long, but it works now. I hope I haven't added too many evil lines.

famosab
famosab approved these changes Feb 10, 2025
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It loks really good to me. Impressive tests :) There is still one conda based on failing, but I think this is good to go when the test is fixed.

modules/nf-core/ska/distance/tests/main.nf.test Outdated
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maybe the tests need to be rename to sarscov2 - plasmodium - ... but thats just to undertand a little better which kind of data went into the test

famosab
famosab approved these changes Feb 11, 2025
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LGTM 🚀

@itrujnara itrujnara added this pull request to the merge queue Feb 11, 2025
Merged via the queue into nf-core:master with commit 9c1acf9 Feb 11, 2025
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3 participants
@itrujnara @famosab @JoseEspinosa