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Add samtools cramsize #5743

Merged
merged 86 commits into from
Jun 3, 2024
Merged

Add samtools cramsize #5743

merged 86 commits into from
Jun 3, 2024

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SPPearce
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@SPPearce SPPearce commented Jun 3, 2024

PR checklist

Closes #XXX

  • 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
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

limrp and others added 30 commits June 24, 2023 16:10
@limrp
New module for the cram-size command of samtools.
13c52e9
@limrp
"Adding module for cram-size command of the samtools tool"
9d24d79
@limrp
Merge branch 'master' into master
d64477f
@limrp @nvnieuwk
Update modules/nf-core/samtools/cramsize/main.nf
65b3a9a 
Adding name of the tool

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
@limrp @nvnieuwk
Update modules/nf-core/samtools/cramsize/main.nf
99c3260 
Adding prefix to make the module set up more flexible.

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
@limrp @nvnieuwk
Update modules/nf-core/samtools/cramsize/main.nf
20c1d63 
Changing `.baseName` by `prefix` in output names.

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
@limrp
Stub added to the main.nf script.
43fa886
@limrp
Adding generated test.yml file.
dda123d
@limrp
Merge branch 'master' of https://github.com/nf-core/modules
62af573
@limrp
Updating my master branch with the changes made in cramsize-branch:
7506ff9 
- Stub section added to main.nf script.
- test.yml file added to module samtools/cramsize
@limrp
Adding pytest.
e80fa18
@limrp
Adding a new nf-core module called plasflow.
afda96d
@limrp
Merging branch with new module plasflow
7b0714f
@maxulysse @limrp
Update manta modules (#3615)
e6aebc5 
* Update manta somatic

* Update manta tumoronly
@FriederikeHanssen @maxulysse @limrp
add varlociraptor call subcommand (#3529)
21d77d8 
* add call subcommand

* at calls runs now [skip ci]

* add test files

* linting

* fix tests

* add contains check

* Update tests/modules/nf-core/varlociraptor/callvariants/main.nf

Co-authored-by: Maxime U Garcia <maxime.garcia@scilifelab.se>

---------

Co-authored-by: Maxime U Garcia <maxime.garcia@scilifelab.se>
@CharlotteAnne @limrp
add new module iCount-mini/metagene (#3612)
9f28ebe 
* add module template

* first version

* update testing and linting

* update file naming

* update test

* fix test
@CharlotteAnne @limrp
Newmodule ngmerge (#3626)
9a7a2ec 
* ngmerge first commit

* main module code

* complete module

* remove trailing whitespace

* fix versions.yml

* fix version yml

* versions yml

* vyml

* try vyml again

* touch versions yml

* vyml
@CharlotteAnne @limrp
NEW MODULE: PURECLIP (#3624)
c076b4d 
* initial commit

* module version 1

* full testing

* linting

* fix version yaml

* fix version yaml command

* fix version yml maybe this time please

* fix version yml for real this time

* try again versions yaml

* fix version yml

* vyml

* version yaml

* vyml

* update ref to have meta
@sstrong99 @limrp
fix integer overflow (#3620)
c69b9ca 
Co-authored-by: Steven Strong <steven.strong@adelabio.com>
@prototaxites @limrp
Fix metaeuk_easypredict when using mmseqs database (#3525)
c7e83fa 
Fix metaeuk and add tests
@CharlotteAnne @limrp
3630 add unstitched reads as emitted output of ngmerge (#3632)
40a29ea 
* add -f option

* update tests
@nvnieuwk @limrp
Update vardictjava (#3633)
b971c6a 
* new module picard/scatterintervalsbyns

* update annotsv to 3.3.6

* update installannotations

* update vardictjava
@nvnieuwk @limrp
Adding modules from #scrnaseq for simpleaf (#3619)
10085b1 
* Start adding modules from #scrnaseq for simpleaf

* Fix tests

* t2gene is necessary, simplify tests

* Linteing fixes

* Fix test files

* Test fixes

* prettier

* Address feedback

* Update test string- logs in newer version lack some messages

* Apply suggestions from code review

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

* Post-review index fixes

* Post-review quant fixes

* add stubs

* Add metas, fix meta usage

* Appease eclint

---------

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
@CharlotteAnne @limrp
update icount mini version (#3640)
1e42df3 
module currently fails, i've fixed the error in icount-mini so now by bumping the version here we fix the issue (old matplotlib syntax)
@jfy133 @limrp
Bump taxpasta version (biocontainer not yet available) (#3639)
4fcf729
@aldosr @limrp
Purecn/run (#3140)
8f61632 
* Set up nf-core template for purecn/run module

* Add run script and I/O

* Clean TODOs and set main script

* Fix duplicate entry

* Set up main script

* [ci skip] Format with prettier

* [ci skip] Address review question and set up stub

* [ci skip] Set stub for testing

* Reformat with prettier

* [CI skip] Adjust some typos

* [CI skip] Set up test script using stub

* Set up test yml

* Reformat with prettier

* Set up meta.yml file and fix typos

* Reformat with prettier

* Fix typo

* Remove quay.io from container string

* Remove optional input argument

* Add optional outputs and clean non-mandatory parameters

* Clean non-mandatory outputs

* Reformat outputs

* Fix minor and address reviews
@matthdsm @limrp
new module: samtools/import (#3642)
4592ece 
* new module: samtools/import

* fix versions

* fix versions some more

* Update modules/nf-core/samtools/import/main.nf

* fix meta
@DLBPointon @muffato @limrp
Adding seqkit sliding command (#3637)
e335edf 
* Adding seqkit sliding command

* Linting fix

* Updating for better matching

* reverted to regex using end line markers for better matching other wise fastq gets caught by fa, error in other modules

* Added a test for fastq too

---------

Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
@jianhong @sguizard @limrp
Hicexplorer hicpca (#2933)
60c0ee5 
* create module hicpca

* Update modules/nf-core/hicexplorer/hicpca/main.nf

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>

* Update modules/nf-core/hicexplorer/hicpca/main.nf

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>

* add more keywords.

* remove quay.io.

---------

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
@jasmezz @limrp
Fix bug in pyrodigal module (#3643)
ad367dc 
Add "--force" to pigz
limrp and others added 15 commits July 31, 2023 10:09
@SPPearce
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SPPearce commented Jun 3, 2024

Splitting off the samtools cram-size from #3555

@SPPearce SPPearce marked this pull request as ready for review June 3, 2024 13:42
@SPPearce SPPearce requested a review from a team as a code owner June 3, 2024 13:42
@SPPearce SPPearce requested review from CarsonJM and removed request for a team June 3, 2024 13:42
CarsonJM
CarsonJM approved these changes Jun 3, 2024
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LGTM! Just a teeny change regarding how the test data path is specified.

modules/nf-core/samtools/cramsize/tests/main.nf.test Outdated Show resolved Hide resolved
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SPPearce and others added 3 commits June 3, 2024 20:41
@SPPearce @CarsonJM
Update modules/nf-core/samtools/cramsize/tests/main.nf.test
7aad419 
Co-authored-by: Carson J Miller <68351153+CarsonJM@users.noreply.github.com>
@SPPearce @CarsonJM
Update modules/nf-core/samtools/cramsize/tests/main.nf.test
661f402 
Co-authored-by: Carson J Miller <68351153+CarsonJM@users.noreply.github.com>
@SPPearce
Merge branch 'master' into cramsize
f8b90ed
@SPPearce SPPearce added this pull request to the merge queue Jun 3, 2024
Merged via the queue into master with commit 49cc8dc Jun 3, 2024
12 checks passed
@SPPearce SPPearce deleted the cramsize branch June 3, 2024 19:53
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