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Kma index #1

Merged
merged 28 commits into from
Dec 20, 2024
Merged

Kma index #1

merged 28 commits into from
Dec 20, 2024

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Krannich479
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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

Krannich479 and others added 28 commits December 17, 2024 16:26
@Krannich479
initial commit of kma_index
d9eb239
@Krannich479
trying to fix linting for meta.yml
e82cf63
@Krannich479
fix linting of meta.yml again
f0ff8e1
@Krannich479
fixing DOI for linting
a555a38
@Krannich479
fixing file type for linting
45f194b
@Krannich479
fix output file name for linting
7c613db
@pinin4fjords
Fix fastp merge issue with subworkflow (nf-core#7237)
8a01490 
* Fix fastp merge issue with subworkflow

* Restore file

* Update subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/meta.yml

* Apply suggestions from code review
@maxulysse
split out gunzip from nf-core#7215 (nf-core#7221)
ce35ce9 
* split out gunzip from nf-core#7215

* forgot 1 file

* update snapshots

* add stubs

* fix deepbgc/download tests

* update snapshot for deepbgc/pipeline

* fix snapshot

* update meta data in snap
@maxulysse
Split untar out from nf-core#7215 (nf-core#7222)
3e54887 
* split untar out

* update snapshot rgi_main

* code polish - test + snapshot update but no change

* update snapshot for rgi/cardannotation

* code polish - test + snapshot update but no actual change in the snapshotted files

* code polish - test + snapshot update but no actual change in the snapshotted files

* code polish - test + snapshot update but no actual change in the snapshotted files

* code polish - test + snapshot update but no actual change in the snapshotted files

* code polish - test + snapshot update but no actual change in the snapshotted files

* code polish - test

* code polish

* fix linting
@famosab
update parabricks/fq2bam (nf-core#7227)
8dd5f4c 
* update fq2bam

* harshil
@famosab @maxulysse
Update vcf2maf and add stub tests (nf-core#7202)
538cbd3 
* update and add stubs

* update snap

* make tests work with new vep cache

* fix version and add test

---------

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
@amizeranschi @jasmezz @maxulysse
Update main.nf (nf-core#7120)
41623bc 
* Update main.nf

Should fix nf-core/funcscan#426

* Update snapshot

---------

Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com>
Co-authored-by: jasmezz <jasmin.frangenberg@hki-jena.de>
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
@prototaxites
Bump metamdbg version and update snapshot (nf-core#7234)
88fbcaa
@Krannich479
add snapshot
92fda87
@suzannejin @pinin4fjords
Add propd to abundance_differential_filter subworkflow (nf-core#7220)
fb6b588 
* [differential] add propd

* [differential] add test to run propd

* [differential] update snapshot

* [differential] fix meta

* [differential] add test to run deseq2 + limma-voom + propd

* [differential] update test snapshots

* Apply suggestions from code review

Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>

* [differential] add comments and fix authors

* [differential] correct errata

* [differential] rename PROPR_PROPD to PROPD_DIFFERENTIAL to maitain coherence naming with the rest of differential modules in the subworkflow

* [differential] modify back the naming of propr_propd

---------

Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>
@suzannejin @pinin4fjords
Add module custom_tabulargseatochip (nf-core#7218)
7900e49 
* [tabulartogseachip] Add the TABULAR_TO_GSEA_CHIP
module used in nf-core/differentialabundance.

This module was originally written by:
Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>

* [tabulartogseachip] add test

* [tabulartogseachip] pass test

* [tabulartogseachip] update environment.yml

* [tabulartogseachip] update test snapshot

* [tabuolartogseachip] update meta.yml

* [tabulartogseachip] fix lint in meta.yml

* [tabulartogseachip] fix linting

* [tabulartogseachip] add versions snapshot

* Apply suggestions from code review

Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>

* [tabulartogseachip] fix meta

* [tabulartogseachip] update test

* [tabulartogseachip] fix output meta and update snapshots

* Revert changes to modules/nf-core/propr/propd/meta.yml

* [tabulartogseachip] use gawk version and update snapshot

* [tabulartogseachip] add stub

* Apply suggestions from code review

Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>

* [tabulargseatochip] fix prefix and udpate snapshot

---------

Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>
@mazzalab @tm4zza
@mashehu @SPPearce
Add wipertools module (nf-core#7184) (nf-core#7185)
b31e778 
* Add wipertools module (nf-core#7184)

* Update environment.yml

* Update fastqgather's environment.yml

* Update environment.yml

* Update environment.yml

* fixed linting fastqgather and reportgather

* Reply to @famosab review

* updated meta.yml if fastqscatter

* Fix fastqwiper linting and add snapshots

* Fixed paths in WIPERTOOLS_FASTQGATHER's tests

* Update main.nf.test

* Fixed tests

* Fixed remaining issues

* Reply to @SPPearce review

* Replies to @SPPearce and @famosab reviews

* Fixed default prefix and control in-out names collision

* Fixed prefix and control collisions for stub as well

* Update disambiguation checks to cope with multiple input files

* shortened error msg in case of name clash

* push test restart

* Update main.nf

---------

Co-authored-by: Tommaso Mazza <69600392+tm4zza@users.noreply.github.com>
Co-authored-by: irongraft <mazza.tommaso@gmail.com>
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
@Krannich479
Merge branch 'master' into kma_index
6de9795
@Joon-Klaps
DESeq2 R script make r.version export more readable (nf-core#7243)
c038be5 
make r.version export more readable
@pinin4fjords
bump star build (nf-core#7194)
6a36761 
* bump star build

* bump version in star/align

* update snaps

* update conda envs to fix requirements of star build with required fixes

* Try permission fix

* Revert "Try permission fix"

This reverts commit 173507b.
@charles-plessy
Update LAST aligner to 1595 and fix last/train output file name (nf…
3c7402a 
…-core#7238)

* Run bump-versions on LAST submodules

for mod in $(ls modules/nf-core/last) ; do nf-core modules bump-versions last/$mod ; done

* Refresh snaps

for mod in $(ls modules/nf-core/last) ; do nf-test test --tag last/$mod --profile singularity --update-snapshot; done

* Remove the index name from the output file.

Leaving it was an oversight.  Pipelines know the index name and can
insert it in meta.id if needed.  This is exactly what
nf-core/pairgenomealign does, and adding it again unconditionally causes
file names to be longer, redundant, and irregular when listed with other
last/* submodules output files.
@LouisLeNezet
Nf-test migration CNVKIT/EXPORT (nf-core#7229)
ba47b8c 
* Update cnvkit

* Fix test

* Add all tests

* Remove old file

* Update cnvkit test

* Update cnvkit other tests

* Update bed test

---------

Co-authored-by: LouisLeNezet <louislenezet@gmaio.com>
@LeonHafner
Change flye oras container (nf-core#7252)
ce1a665 
change flye container
@jfy133 @sateeshperi
Update CENTRIFUGE: bump versions, fix missing args, and command forma…
8581a56 
…tting (nf-core#7205)

* bump versions and fix missing args and command formatting

* CI: docker self hosted - userEmulate and dont fixOwnership

* try suggestion from claude

* fix cgroup parent slice

* rm cgroup parent slice

* rm security opts

* userns n security opts

* Update tests/config/nf-test.config

---------

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Sateesh <perisateesh@gmail.com>
@prototaxites
Allow Metabat2 to take uncompressed depths file and bump version (nf-…
cc217b9 
…core#7230)

* Metabat2 takes uncompressed depths file

* Update main.nf.test

* Update main.nf

* Update environment.yml

* update snapshot

* Move shared setup outside of test blocks to facilitate reuse, switch to regex for cleaning depths
@Krannich479
update output format
f52f84b
@Krannich479
Merge branch 'master' into kma_index
a7cf40e
@Krannich479
upgrade latest container build trying to satisfy docker CI
2d0e4ab
@Krannich479 Krannich479 merged commit 53cb113 into kma_kma Dec 20, 2024
@Krannich479 Krannich479 deleted the kma_index branch December 20, 2024 15:55
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