Bulk update meta yml modules #6015

mirpedrol · 2024-07-22T14:19:29Z

Updates the meta.yml of modules to the correct structure by using nf-core/tools after implementing nf-core/tools#3028 and nf-core/tools#3032
The changes were generated by running nf-core modules lint --all --fix

Needs updating the JSON schema which validates meta.yml files: #5837

Same changes should be implemented for subworkflows.

Note

Open as a draft PR to avoid requresting review to code owners.

…l and add stub (nf-core#5849) * Add missing optional input channel to abricate * Update abricate module to include missing optional input path * Update modules/nf-core/abricate/run/tests/main.nf.test Co-authored-by: Carson J Miller <[email protected]> * Fix linting * Update modules/nf-core/abricate/run/main.nf * Get downstream module test --------- Co-authored-by: Carson J Miller <[email protected]>

* Update environment.yml * Update main.nf

* update to samtools 1.20 * keep samtools 1.19.2 for now * update snapshot * [automated] Fix linting with Prettier * keep 1.20 afterall * update snapshot --------- Co-authored-by: nf-core-bot <[email protected]>

* update recipe * update rthreads * update tests * Update meta.yml

….10 (nf-core#5857) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* add unoutput option * trying to fix emit * CI fixed, tests still incorrect * Fixed the checksums * Fixed the syntax * Call this "unselected" rather than "unoutput" * Alignment rocks * bugfix: the variable needs to be visible by the output declaration * bugfix: this was not the regular file name * Updated the test case * fixup! Alignment rocks * Updated the meta.yml --------- Co-authored-by: Matthieu Muffato <[email protected]>

* stubs and test for bbmap_bbsplit * add test for index * add stubs for custom/catadditionalfasta * add stubs for fq/subsample * add stubs for hisat2/extractsplicesites * update fastq_align_hisat2 snapshot * add stubs for hisat2/build * add stubs for hisat2/align * more stubs bbmap/bbsplit * add stubs for preseq/lcextrap * more stubs for fq/subsample * proper stubs for hisat2/align * remove old snaps

This reverts commit 0fa8c1b.

* Bump concoct/cutupfasta version, add stub, add nf-test * Fix linting

* Adding meta to multivcfanalyzer, updating test to nf-test * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <[email protected]> * fix meta.yml * Add sort to vcfs * Add tab to tags * add checks for files due to failing md5 sums across docker,conda,singularity --------- Co-authored-by: James A. Fellows Yates <[email protected]> Co-authored-by: Simon Pearce <[email protected]>

* Bump concoct/cutupfasta version, add stub, add nf-test * Bump conda build, add stub and nf-test for CONCOT/concoctcoveragetable * Remove pytest entry --------- Co-authored-by: Aida Andrades Valtueña <[email protected]>

* Added stub logic and test to fastq_fastqc_umitools_fastp * Now emitting trimmed reads

…output (nf-core#5850) * Enable single fastq.gz-output from spring/decompress by setting meta.single_end or meta.one_strand * Controlling output with value-channel write_one_fastq_gz * Update modules/nf-core/spring/decompress/meta.yml Co-authored-by: Maxime U Garcia <[email protected]> * nf-test for spring/decompress * Trying to please linter * Trying to please linter --------- Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]>

* everything but snapshot * fix gz snap * update testdata paths * Update main.nf.test * update test --------- Co-authored-by: Simon Pearce <[email protected]>

mapAD: fix `version.yml` emission

* add stub and stub test to chromap, change test names * add stub and stub test to chromap, change test names * change setup * move setup out of test * move

…a to v0.28.6 (nf-core#5878) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

update peddy

* Update main.nf VEP html report is missing when publishing results because by default vep html file is `_summary.html` instead of `.summary.html`. This changes just adjust the module to the vep defaults to avoid the issue. * Updated html pattern in VEP to be more generic

bump MQC

* Bump shinyngs modules * Bump versions for snapshot

…e#5869) * Version update, stub, nf-test for concoct/concoct * Bump version, add nf-test, stub to concoct/mergecutupclustering * nf-test, stub, and version conda build version bump for concoct/extrafastabins * Remove a superfluous config and specify a used one * Update modules/nf-core/concoct/extractfastabins/main.nf Co-authored-by: Simon Pearce <[email protected]> * Remove superfluous config file * Clean up code * Repair all stub tests that were empty --------- Co-authored-by: Simon Pearce <[email protected]>

* fix: do not fail on mismatch for samples not binned with concoct * Migrate to pytest * Improved Harshil alignment --------- Co-authored-by: James A. Fellows Yates <[email protected]>

* Generated structure for new module * Implemented module * Added semi-functional tests * Cleaned tests - test don't work yet * fix main, start nf-test * add new test data * fix linting * try to assert folders * fix tests * change output to prefix * change to prefix * update to prefix --------- Co-authored-by: vickylaram <[email protected]>

…uated (nf-core#5887) Fix bug causing output name to be incorrectly evaluated

* nf-test for snpsites * remove old pytest * Delete modules/nf-core/snpsites/tests/nextflow.config * Update modules/nf-core/snpsites/tests/main.nf.test Co-authored-by: Joon Klaps <[email protected]> * Update assert Co-authored-by: Joon Klaps <[email protected]> * renamed test Co-authored-by: Joon Klaps <[email protected]> * reverted the input * updated input...again Co-authored-by: Joon Klaps <[email protected]> * fixed typo Co-authored-by: Joon Klaps <[email protected]> * Regenerate snapshot and fix linting --------- Co-authored-by: Joon Klaps <[email protected]> Co-authored-by: Simon Pearce <[email protected]>

….toString() - '.gz'` (nf-core#5879) * Added prefix to gunzip * Fixed linting issues in fargene and leviosam2/lift * Removed unstable liftoff/conda

…ultiqc) (nf-core#5501) * created new output channel capturing stderr of trimmomatic * updated output channel for trimmomatic * Add stub test and update snapshots * Add stub and update tests * Fix linting and add tee --------- Co-authored-by: John Palmer <[email protected]> Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: James A. Fellows Yates <[email protected]>

* Added agat/spmergeannotations * Added tests with config

* Edit content with subworkflow name * Rename subworkflow folder * Readd subworkflow with old name, with deprecation * remove rogue word * Appease eclint * Remove test suite for deprecated subworkflow

…ore#5823) * Using seqera containers for sentieon * update containers for sentieon modules with quay.io registry --------- Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Adam Talbot <[email protected]> Co-authored-by: maxulysse <[email protected]>

* unzip stub, nf-test, snap * Revert "unzip stub, nf-test, snap" This reverts commit dec35aa. * Reapply "unzip stub, nf-test, snap" This reverts commit e0d708e. * added minimal required tests for process and stub * added snapshot * simplify snapshot input in stub test Co-authored-by: Matthias Hörtenhuber <[email protected]> * remove unneeded stub files * migrate pytest for unzipfiles * add snapshot file for script block * added stub * added stub and stub test * updated stub snapshot for unzip * remove unneeded test config * Update snaps and malt * Update malt for linting * Fix linting for maltextract * Swap test-data paths for malt modules * Update modules/nf-core/maltextract/tests/main.nf.test --------- Co-authored-by: Sateesh <[email protected]> Co-authored-by: Jenny Leopoldina Smith <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]>

…5982) * Improve strandedness devivation * Add missing params to nf-test

…FASTAs, port tests (nf-core#5988) * rrna sequences make more sense as a channel of FASTAs * Also update tests * Add function test to swf * Fix up subworkflow function testing

…ules (nf-core#5989) * add meta2 to input fasta channel * update snapshot; nothing new but timestamp * Update modules/nf-core/lofreq/viterbi/tests/main.nf.test Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/lofreq/viterbi/tests/main.nf.test Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/lofreq/viterbi/tests/main.nf.test Co-authored-by: Felix Lenner <[email protected]> --------- Co-authored-by: Felix Lenner <[email protected]>

* Initial commit * Rerun nf-test * Change assertion for duplex_qc output * Add ggplot2 to version.yml * Update snapshot * Correct conda packages version

* add-usearch-unoise3 * add seqfu/derep * Delete modules/nf-core/usearch/unoise3/environment.yml * Delete modules/nf-core/usearch/unoise3/main.nf * remove files * update metadata * Update modules/nf-core/seqfu/derep/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/seqfu/derep/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/seqfu/derep/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/seqfu/derep/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/seqfu/derep/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/seqfu/derep/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Fix dataset in -stub * Clarify description * Update modules/nf-core/seqfu/derep/meta.yml Co-authored-by: Simon Pearce <[email protected]> * check for pre-existing output file && update test * Update main.nf --------- Co-authored-by: Simon Pearce <[email protected]>

Co-authored-by: Cristina Araiz <[email protected]>

* liftoff: Readded conda environment * Added liftoff to env file * Cleaned up env file

….3 (nf-core#5996) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Fix output naming, add req argument to input * add new input to nf-test * update nf-test due to changes in upstream module inputs * update snapshots * add metas to other input channels * update tests according to changes in module inputs. * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <[email protected]> * rename elongation factor for consistency with other CM module --------- Co-authored-by: James A. Fellows Yates <[email protected]>

* Fix output naming, add req argument to input * add new input to nf-test * update nf-test due to changes in upstream module inputs * update snapshots * add metas to other input channels * update tests according to changes in module inputs. * add meta to elongation factor channel for consistency with other CM module * update nf-test to include new meta * rename metas

* Add stub and test to lofreq/indelqual * Add author * new test setup using --migrate-pytest and PR feedback * Update main.nf.test * Update meta.yml * Update main.nf * add snap; del pytest * Update meta.yml * Update main.nf.test * Update meta.yml * update test * minor fix in stub test

* Update tabix and add threads * fix linting

* refactor: Clean up the logic and let Sentieon figure it out * refactor: Remove Sentieon license server IP check * fix: Add a -n * Try accessing secrets in the module? * fix: Use Nextflow for if statement * update snapshot * update snapshot * extend logic to all main.nf * ci: Add Sentieon logic to pytest-workflow * test(sentieon): Add env section to every config * Revert "ci: Add Sentieon logic to pytest-workflow" This reverts commit 76884d2. * test: Remove pytest_modules for sentieon --------- Co-authored-by: maxulysse <[email protected]>

…f-core#5978) * ltrharvest: Added test to verify graceful handling of no ltr input * Updated test data paths * Fixed test data path * Removed unstable items from snapshot * Updated snapshotting logic

…-core#5979)

nf-core#5980) * ltrretriever/ltrretriever: Added test to verify graceful handling of no ltr input * Removed unstable items from snapshot

* Updated mkfastq module * Combined input channels * Updated main.nf.test and snap --------- Co-authored-by: zxBIB Schcolnicov <[email protected]> Co-authored-by: Anabella Trigila <[email protected]>

…information

jfy133 and others added 30 commits June 19, 2024 19:37

Fix custom/catadditionalfasta (nf-core#5851)

13c7a1b

* Update environment.yml * Update main.nf

update to samtools 1.20 (nf-core#5852)

41a4135

* update to samtools 1.20 * keep samtools 1.19.2 for now * update snapshot * [automated] Fix linting with Prettier * keep 1.20 afterall * update snapshot --------- Co-authored-by: nf-core-bot <[email protected]>

Update input params for bwameme (nf-core#5853)

0aa157a

* update recipe * update rthreads * update tests * Update meta.yml

chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.4…

8ed9774

….10 (nf-core#5857) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

Remove CUTUPFASTA from pytests

0fa8c1b

Revert "Remove CUTUPFASTA from pytests"

f958600

This reverts commit 0fa8c1b.

Bump concoct/cutupfasta version, add stub, add nf-test (nf-core#5864)

73a6d7e

* Bump concoct/cutupfasta version, add stub, add nf-test * Fix linting

Concoct/concoctcoveragetable modules updates (nf-core#5868)

2aee476

* Bump concoct/cutupfasta version, add stub, add nf-test * Bump conda build, add stub and nf-test for CONCOT/concoctcoveragetable * Remove pytest entry --------- Co-authored-by: Aida Andrades Valtueña <[email protected]>

Added stub logic and test to fastq_fastqc_umitools_fastp (nf-core#5858)

db35d26

* Added stub logic and test to fastq_fastqc_umitools_fastp * Now emitting trimmed reads

Update stranger (nf-core#5717)

c48824e

* everything but snapshot * fix gz snap * update testdata paths * Update main.nf.test * update test --------- Co-authored-by: Simon Pearce <[email protected]>

mapAD: fix versions.yml emission (nf-core#5874)

b5198a1

mapAD: fix `version.yml` emission

add stub and stub test to chromap, change test names (nf-core#5872)

4bd9481

* add stub and stub test to chromap, change test names * add stub and stub test to chromap, change test names * change setup * move setup out of test * move

produce stub files (nf-core#5875)

89d1482

chore(deps): update pre-commit hook python-jsonschema/check-jsonschem…

d5b47a2

…a to v0.28.6 (nf-core#5878) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

update peddy tests (nf-core#5880)

bb8c1e0

update peddy

bump MultiQC version (nf-core#5884)

314d742

bump MQC

Bump shinyngs modules (nf-core#5881)

91fc365

* Bump shinyngs modules * Bump versions for snapshot

fasta_binning_concoct subworkflow: do not fail on join (nf-core#5824)

373d3e2

* fix: do not fail on mismatch for samples not binned with concoct * Migrate to pytest * Improved Harshil alignment --------- Co-authored-by: James A. Fellows Yates <[email protected]>

samtools/reheader: Fix bug causing output name to be incorrectly eval…

d5622b0

…uated (nf-core#5887) Fix bug causing output name to be incorrectly evaluated

Added prefix to gunzip and while keeping the default name as `archive…

a7231cb

….toString() - '.gz'` (nf-core#5879) * Added prefix to gunzip * Fixed linting issues in fargene and leviosam2/lift * Removed unstable liftoff/conda

GallVp and others added 25 commits July 15, 2024 22:06

Added agat/spmergeannotations (nf-core#5772)

8e30f5d

* Added agat/spmergeannotations * Added tests with config

Rename preprocess rnaseq (nf-core#5959)

81ed776

* Edit content with subworkflow name * Rename subworkflow folder * Readd subworkflow with old name, with deprecation * remove rogue word * Appease eclint * Remove test suite for deprecated subworkflow

Improve strandedness derivation in rnaseq preprocessing swf (nf-core#…

0a8d335

…5982) * Improve strandedness devivation * Add missing params to nf-test

RNAseq preprocessing: rrna sequences make more sense as a channel of …

b86de50

…FASTAs, port tests (nf-core#5988) * rrna sequences make more sense as a channel of FASTAs * Also update tests * Add function test to swf * Fix up subworkflow function testing

Add module fgbio/collectduplexseqmetrics (nf-core#5960)

af50683

* Initial commit * Rerun nf-test * Change assertion for duplex_qc output * Add ggplot2 to version.yml * Update snapshot * Correct conda packages version

modify valCutoff funtion in propr.R (nf-core#5995)

132fa6c

Co-authored-by: Cristina Araiz <[email protected]>

liftoff: Re-added conda environment (nf-core#5981)

fb8d53f

* liftoff: Readded conda environment * Added liftoff to env file * Cleaned up env file

chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.5…

538474b

….3 (nf-core#5996) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

Update tabix and add threads (nf-core#5999)

964d13e

* Update tabix and add threads * fix linting

Remove problematic ifEmpty() from rnaseq preprocessing (nf-core#6000)

22c8d53

ltrharvest: Added test to verify graceful handling of no ltr input (n…

78575b0

…f-core#5978) * ltrharvest: Added test to verify graceful handling of no ltr input * Updated test data paths * Fixed test data path * Removed unstable items from snapshot * Updated snapshotting logic

ltrfinder: Added test to verify graceful handling of no ltr input (nf…

be4f907

…-core#5979)

ltrretriever/ltrretriever: Added test to verify graceful handling of … (

35787cd

nf-core#5980) * ltrretriever/ltrretriever: Added test to verify graceful handling of no ltr input * Removed unstable items from snapshot

update nf-test t0 0.9.0 (nf-core#6010)

0a774c6

Fix keyword meta (nf-core#6011)

b50aa17

Updated mkfastq module (nf-core#5984)

2bb941b

* Updated mkfastq module * Combined input channels * Updated main.nf.test and snap --------- Co-authored-by: zxBIB Schcolnicov <[email protected]> Co-authored-by: Anabella Trigila <[email protected]>

bulk update of meta.yml modules structure

9922d22

mirpedrol mentioned this pull request Aug 5, 2024

xx is present as an output in meta.yml but not in main.nf nf-core/tools#3097

Closed

mirpedrol added 2 commits September 18, 2024 09:42

merge branch batch_update_staging accepting their changes

07e9a6b

update meta.yml files automatically with manual curation for missing …

6ae6305

…information

mirpedrol mentioned this pull request Sep 18, 2024

POC of new meta.yml structure and ontologies #5867

Closed

FriederikeHanssen approved these changes Sep 19, 2024

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Bulk update meta yml modules #6015

Bulk update meta yml modules #6015

mirpedrol commented Jul 22, 2024

Bulk update meta yml modules #6015

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Bulk update meta yml modules #6015

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mirpedrol commented Jul 22, 2024