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Add module seqfu/stats #5275

Merged
merged 10 commits into from Mar 20, 2024
Merged

Add module seqfu/stats #5275

merged 10 commits into from Mar 20, 2024

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telatin
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@telatin telatin commented Mar 19, 2024 •
edited

PR checklist

Closes #5240

Description

added a first sub-program from SeqFu: seqfu stats, which collates a number of sequences, total size, N50, min, max,... from one or more FASTA or FASTQ files (Gzipped or not).

Output files are:

  • A tsv table
  • A MultiQC-ready table

Help wanted

It's my first module and first experience with nf-test. I checked for output channels and even the MD5 of the outputs, but more guidance on good tests is welcome.

Checklist

  • 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 i use nf datasets (sarscov2)
  • 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 (with Docker version 20.10.12, build e91ed57)
      • nf-core modules test <MODULE> --profile singularity (with singularity version 3.8.5)
      • nf-core modules test <MODULE> --profile conda (multiple versions)

@telatin telatin requested a review from a team as a code owner March 19, 2024 15:39
@telatin telatin requested review from vagkaratzas and removed request for a team March 19, 2024 15:39
sateeshperi
sateeshperi approved these changes Mar 19, 2024
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minor suggestions about abt extra spaces and spacing. Rest looks good. Good Job!

modules/nf-core/seqfu/stats/main.nf Outdated Show resolved Hide resolved
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telatin and others added 5 commits March 19, 2024 21:00
@telatin @sateeshperi
Update modules/nf-core/seqfu/stats/main.nf
dd7cc3b 
Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
@telatin @sateeshperi
Update modules/nf-core/seqfu/stats/main.nf
4442190 
Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
@telatin @sateeshperi
Update modules/nf-core/seqfu/stats/tests/main.nf.test
ab08023 
Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
@telatin @sateeshperi
Update modules/nf-core/seqfu/stats/tests/main.nf.test
0e0bacf 
Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
@sateeshperi
Merge branch 'master' into seqfu/stats
e88e279
@sateeshperi sateeshperi added this pull request to the merge queue Mar 20, 2024
Merged via the queue into nf-core:master with commit 383a1fa Mar 20, 2024
11 checks passed
vlebars pushed a commit to vlebars/modules that referenced this pull request Mar 20, 2024
@telatin @sateeshperi
Add module seqfu/stats (nf-core#5275)
0084ac2 
* seqfu/stats

* fix test

* improve-tests

* improve-tests-fixsnap

* Update modules/nf-core/seqfu/stats/main.nf

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/seqfu/stats/main.nf

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/seqfu/stats/tests/main.nf.test

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/seqfu/stats/tests/main.nf.test

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

---------

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
jvfe added a commit to jvfe/modules that referenced this pull request Mar 20, 2024
@jvfe
Merge branch 'master' into nf-test_islandpath
2be1844 
* master:
  Added contrast limited adaptive histogram equalization module (nf-core#5268)
  Leviosam2 index (nf-core#5316)
  Add subworkflow mapAD (nf-core#5239)
  Remove AMRFinderPlus DB update on each invocation (nf-core#5232)
  Revert "add paths in output directive in cellranger cout module" (nf-core#5306)
  Revert "update kallistobustools count output list" (nf-core#5307)
  Igv reports (nf-core#5263)
  Remove unnecessary .view() in subworkflows/nf-core/vcf_phase_shapeit5 & tests/modules/nf-core/shapeit5/ligate/main.nf (nf-core#5280)
  Add wittyer as module (nf-core#5171)
  Bamstats (nf-core#4474)
  gatk4_asereadcounter add updated meta and nf-tests (nf-core#5164)
  4557 new module kaijumergeoutputs + stub Kraken2/Kraken2 (nf-core#5249)
  add cram/index support to bwamem2 (nf-core#5248)
  Add README to modules build with Docker (nf-core#4935)
  update paths for VEP (nf-core#5281)
  nf-test bases2fastq (nf-core#5272)
  Add module seqfu/stats (nf-core#5275)
jvfe added a commit to jvfe/modules that referenced this pull request Mar 20, 2024
@jvfe
Merge branch 'master' into nf-test_phispy
294a9c0 
* master:
  Added contrast limited adaptive histogram equalization module (nf-core#5268)
  Leviosam2 index (nf-core#5316)
  Add subworkflow mapAD (nf-core#5239)
  Remove AMRFinderPlus DB update on each invocation (nf-core#5232)
  Revert "add paths in output directive in cellranger cout module" (nf-core#5306)
  Revert "update kallistobustools count output list" (nf-core#5307)
  Igv reports (nf-core#5263)
  Remove unnecessary .view() in subworkflows/nf-core/vcf_phase_shapeit5 & tests/modules/nf-core/shapeit5/ligate/main.nf (nf-core#5280)
  Add wittyer as module (nf-core#5171)
  Bamstats (nf-core#4474)
  gatk4_asereadcounter add updated meta and nf-tests (nf-core#5164)
  4557 new module kaijumergeoutputs + stub Kraken2/Kraken2 (nf-core#5249)
  add cram/index support to bwamem2 (nf-core#5248)
  Add README to modules build with Docker (nf-core#4935)
  update paths for VEP (nf-core#5281)
  nf-test bases2fastq (nf-core#5272)
  Add module seqfu/stats (nf-core#5275)
  Added gt/gff3validator (nf-core#4718)
  Added liftoff (nf-core#5209)
tucano pushed a commit to tucano/modules that referenced this pull request Mar 20, 2024
@telatin @sateeshperi @tucano
Add module seqfu/stats (nf-core#5275)
aef8675 
* seqfu/stats

* fix test

* improve-tests

* improve-tests-fixsnap

* Update modules/nf-core/seqfu/stats/main.nf

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/seqfu/stats/main.nf

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/seqfu/stats/tests/main.nf.test

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/seqfu/stats/tests/main.nf.test

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

---------

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
jennylsmith pushed a commit to RSC-RP/modules that referenced this pull request Mar 20, 2024
@telatin @sateeshperi @jennylsmith
Add module seqfu/stats (nf-core#5275)
bd52d31 
* seqfu/stats

* fix test

* improve-tests

* improve-tests-fixsnap

* Update modules/nf-core/seqfu/stats/main.nf

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/seqfu/stats/main.nf

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/seqfu/stats/tests/main.nf.test

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/seqfu/stats/tests/main.nf.test

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

---------

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
alexnater pushed a commit to alexnater/nf-core-modules that referenced this pull request Mar 21, 2024
@telatin @sateeshperi
Add module seqfu/stats (nf-core#5275)
b782f95 
* seqfu/stats

* fix test

* improve-tests

* improve-tests-fixsnap

* Update modules/nf-core/seqfu/stats/main.nf

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/seqfu/stats/main.nf

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/seqfu/stats/tests/main.nf.test

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/seqfu/stats/tests/main.nf.test

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

---------

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
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@sateeshperi sateeshperi sateeshperi approved these changes

@vagkaratzas vagkaratzas Awaiting requested review from vagkaratzas vagkaratzas is a code owner automatically assigned from nf-core/nf-test

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new module: seqfu/stats
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@telatin @sateeshperi