…en staging

* Code refactoring for mitohifi input

* Fix md5sum

* Fix md5sum for versions

* Bring back md5sum value

* Update md5sum again

* Remove md5sum

* Bring back versions.yml

* It looks like $HOME needs be writable in the container. Trying mounting it

* Add test for reads

* Update modules/nf-core/mitohifi/mitohifi/main.nf

Refactor the mitohifi command line

Co-authored-by: Solenne Correard <[email protected]>

* Fix md5sums

---------

Co-authored-by: Ksenia Krasheninnikova <[email protected]>
Co-authored-by: Matthieu Muffato <[email protected]>
Co-authored-by: Solenne Correard <[email protected]>

* Adding module sentieon/tnfilter

* WIP: CI-tests for sentieon/tnfilter. (test-data just local for now.)

* Skipping conda-based test of sentieon/tnfilter

* Remove avail_mem stuff.

* Fix description of output vcf

* Using test-data from nf-core test-datasets repo

* add tests for sentieon/tnfilter

* nf-test for pycoqc. snapshots for versions and json['All reads']

* tags.yml

* test naming conventions. Fix indentation. Add test for html output

---------

Co-authored-by: Jose Espinosa-Carrasco <[email protected]>

* update bclconvert to 4.2.4

* regenerate snapshot

* ci(renovate): Change schedule to monthly and pinDigests

https://emmer.dev/blog/keep-docker-base-images-updated-with-renovate/#default-renovate-config

* ci(renovate): Add security PRs immediately

https://emmer.dev/blog/keep-docker-base-images-updated-with-renovate/#custom-renovate-config

* ci(renovate): Just use best-practices

https://docs.renovatebot.com/presets-config/#configbest-practices

* ci(renovate): Set PR hourly limit to 3

* ci(renovate): Add conda support

Ulthran/ShotgunUnifrac#22

* ci(renovate): Add pre-commit

* ci(renovate): Request modules instead of maintainers

* ci(renovate): Don't scan the meta.ymls

…a to v0.27.0 (nf-core#4256)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

…nf-core#4257)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* new module picard/scatterintervalsbyns

* update annotsv to 3.3.6

* update installannotations

* fix all modules conda declaration

chore(config): migrate config .github/renovate.json5

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

nf-core#4220)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

…f-core#4231)

* new module picard/scatterintervalsbyns

* update annotsv to 3.3.6

* update installannotations

* try to fix linting with nf-test

* small change to trigger tests

* fix if statement

* also test pytest

* remove nf-test exclude from linting

* try for a conda fix

* revert last commit

* Update .github/workflows/test.yml

Co-authored-by: Adam Talbot <[email protected]>

* temporarily reactivate pytest for vardictjava

* run fastp test

* revert test triggers

---------

Co-authored-by: Adam Talbot <[email protected]>

* new module picard/scatterintervalsbyns

* update annotsv to 3.3.6

* update installannotations

* nf-test rtgtools rocplot

* remove pytest tag

* update according to comments

* Update modules/nf-core/rtgtools/rocplot/tests/main.nf.test

Co-authored-by: Adrien Coulier <[email protected]>

* Update modules/nf-core/rtgtools/rocplot/tests/main.nf.test

* update conda declaration

---------

Co-authored-by: Adrien Coulier <[email protected]>

Emit crai file for CRAM file

…re#4214)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* We should use "error" rather than "exit 1"

* Fixed the syntax

* Removed the quay.io prefix since it is the default registry

…4259)

* chore(deps): update biocontainers/goat docker tag to v0.2.5

* Version bump (across all 3 package systems)

* Fixed the type of the "taxon" parameter

* Updated the test md5

* Added me as a maintainer since GoaT is (partly) in my team

---------

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: Matthieu Muffato <[email protected]>

…se (nf-core#4245)

change ndb to nin

Co-authored-by: Damon-Lee Pointon <[email protected]>

* add nf-tests and snapshots for kallisto index & quant

* rm kallisto tags from pytest_modules.yml

* Update modules/nf-core/kallisto/index/tests/main.nf.test

Co-authored-by: Adam Talbot <[email protected]>

* Update modules/nf-core/kallisto/quant/tests/main.nf.test

Co-authored-by: Adam Talbot <[email protected]>

* Update modules/nf-core/kallisto/quant/tests/main.nf.test

Co-authored-by: Adam Talbot <[email protected]>

* update kallisto quant

* Update modules/nf-core/kallisto/index/tests/main.nf.test

Co-authored-by: Adam Talbot <[email protected]>

* Update modules/nf-core/kallisto/quant/tests/main.nf.test

Co-authored-by: Adam Talbot <[email protected]>

* Update modules/nf-core/kallisto/quant/tests/main.nf.test

Co-authored-by: Adam Talbot <[email protected]>

* Update modules/nf-core/kallisto/quant/tests/main.nf.test

Co-authored-by: Adam Talbot <[email protected]>

* remove superfluous quote marks

* fix linting

---------

Co-authored-by: Adam Talbot <[email protected]>
Co-authored-by: mashehu <[email protected]>

* Add Kmer coverage to module output

* Update test.yml

* Update modules/nf-core/genescopefk/meta.yml

Co-authored-by: Matthieu Muffato <[email protected]>

* Add bash directive

* Fix whitespace

---------

Co-authored-by: Matthieu Muffato <[email protected]>

* Move mandatory busco arg to input:

* bump busco version

* Update test.yml

…re#4212)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

…f-core#4213)

* chore(deps): update biocontainers/checkm-genome docker tag to v1.2.2

* Fix meta.yml and update singularity container

---------

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: Mahesh Binzer-Panchal <[email protected]>

* Main changes

* Add check for correct input parameters

* Code clean-up

* Conda is not supported

* Dropping the hyphen, as per @mahesh-panchal suggestion

---------

Co-authored-by: Ksenia Krasheninnikova <[email protected]>
Co-authored-by: Matthieu Muffato <[email protected]>

Follow up to nf-core#4213

Co-authored-by: Mahesh Binzer-Panchal <[email protected]>

…#4266)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Try to fix up kallisto quant for real usage

* More kallisto fixes

* appease eclint

* Fix tests

* Add single-end config specifically

* try to fix kallisto nf-test

* Fix snapshot testing

* Tidy up config

* Just check the tsv

* syntax fix

* Revert "syntax fix"

This reverts commit 1becc26.

* Revert "Just check the tsv"

This reverts commit 7a9d272.

* Poor nf-test attempt

* [skip ci] Apply suggestions from code review

Co-authored-by: Sateesh_Peri <[email protected]>

* Last fix-up to tests, re-add paired

* Bump indexing to match quant in kallisto

* Bump kallisto index snapshot

---------

Co-authored-by: Sateesh_Peri <[email protected]>

* fix gatk4 version

* rename and update all gatk4_<module>spark to gatk4spark_<module>

* update pytest_modules.yml

* fix meta.yml

* fix typo

* remove now useless exclude statements

* fix output path

* update multiqc to 1.17

* update snapshot

* update snapshot

* Rename utility subworkflows

Changes:
 - nextflow_pipeline_utils -> utils_nextflow_pipeline
 - nfcore_pipeline_utils -> utils_nf_core_pipeline
 - nfvalidation_plugin_utils -> utils_nf_validatation_plugin

Names by @drpatelh

Not 100% on the names, I think it would be better if it said what they
_did_ rather than what they _are_. However, this is usable right now.
Better answers here please.

* Correct utility subworkflow tags

* Fixup comments

* config fix

* fix linting by faking pytest tests

* rename files

* update pytest_modules.yml

* fix fake pytest tests

---------

Co-authored-by: maxulysse <[email protected]>

* add nf-test and snapshot for umitools/extract

* remove pytest tag and add nf-test tag

* add nftest and snapshot for ucsc/bedgraphtobigwig

* Update modules/nf-core/ucsc/bedgraphtobigwig/tests/tags.yml

Co-authored-by: Adam Talbot <[email protected]>

* Update modules/nf-core/umitools/extract/tests/main.nf.test

Co-authored-by: Adam Talbot <[email protected]>

* [automated] Fix linting with Prettier

* Feat/fastp nf-test (nf-core#4028)

* init nf-test fastp

* add initial test fastp

* init html test fastp

* all tests fastp

* unequal files reads.fastq.gz

* finishing tests (finally)

* removing fastp from pytest

* fixing tag fastp

* adding the s

* adding relative path

---------

Co-authored-by: Maxime U Garcia <[email protected]>

* Rasusa nf test (nf-core#4081)

* Initial main.nf.test

* Full nf-test suite for module rasusa

* add "modules" tag to nf-test

Co-authored-by: Sateesh_Peri <[email protected]>

* Remove tags from tests/config/pytest_modules.yml

---------

Co-authored-by: Sateesh_Peri <[email protected]>

* Glimpse ligate nftest (nf-core#4048)

* Restart as new

* Delete pytest from config

* Update main.nf.test

* Glimpse chunk nftest (nf-core#4034)

* Add nf-test for glimpse_chunk

* Delete pytest for glimpse 1 not glimpse 2

* Update main.nf.test

* Added fq nf-tests (nf-core#4084)

* Added fq nf-tests

* Removed from pytest suite

* Test fix

---------

Co-authored-by: Maxime U Garcia <[email protected]>

* Feat/gunzip nf tests (nf-core#4103)

* add nf-test and snapshot for gunzip

* add modules/nf-core/gunzip/tests/tags.yml

* remove gunzip from tests/config/pytest_modules.yml for switch to nf-test

---------

Co-authored-by: Sateesh_Peri <[email protected]>

* added nf-test files for art/illumina (nf-core#4038)

* added nf-test files

- two tests (single- and paired-end)
- including two nextflow.configs for `ext.args`

* change tests topass on conda/mamba and singularity/docker

- due to gzip the fastq files will have different md5sums with different engines

* added art/illumina

- should trigger the nf-test CI

* extended tag to art/illumina

* fixed typos -.-

* fixed typo again

- missing quote

* renamed test.yml to tags.yml

* removed art/illumina

* added <tool> tag

* added nf-tests for -stub-run

---------

Co-authored-by: Sateesh_Peri <[email protected]>

* nf-test for module sourmash/sketch (nf-core#4104)

* nf-test for module sourmash/sketch

* add "sourmash" and "sourmash/sketch" tags

Co-authored-by: Sateesh_Peri <[email protected]>

---------

Co-authored-by: Sateesh_Peri <[email protected]>

* Renovate migrate (nf-core#4114)

* chore: Migrate renovate config

https://github.com/renovatebot/renovate/blob/main/docs/usage/config-validation.md
renovate-config-validator

* style: Add renovate to prettier ignore list

* Feat/picard_markduplicates nf-test  (nf-core#4096)

* picard nf-test init

* created first (failing)test

* tests succeeding

---------

Co-authored-by: Sateesh_Peri <[email protected]>

* Rename test.yml in getchromsizes (nf-core#4118)

* Rename test.yml and trigger pytest

* Update main.nf

* Feat/trimgalore nf-test (nf-core#4110)

* trimgalore nf-test init

* relative paths

* Update modules/nf-core/trimgalore/tests/main.nf.test

Co-authored-by: Sateesh_Peri <[email protected]>

---------

Co-authored-by: Sateesh_Peri <[email protected]>

* nf-test migration (nf-core#4113)

* nf-test for module fastqscan (nf-core#4097)

Co-authored-by: Sateesh_Peri <[email protected]>

* Mlst nf test and version bump to 2.23 (nf-core#4061)

* add nf-test to module mlst

* fix ownership for nf-test

* add "modules" tag to nf-test

Co-authored-by: Adam Talbot <[email protected]>

* Add module keywords to meta.yml

* Lint meta.yml

* Update to mlst version 2.23

* Update snap with new versions.yml after bump to v2.23

* Remove mlst from pytest_modules

---------

Co-authored-by: Maxime U Garcia <[email protected]>
Co-authored-by: Adam Talbot <[email protected]>
Co-authored-by: Sateesh_Peri <[email protected]>

* remove umitools/extract files

* Apply suggestions from code review

* remove umitools tests

* Apply suggestions from code review

* Update tests/config/pytest_modules.yml

---------

Co-authored-by: Maxime U Garcia <[email protected]>
Co-authored-by: Adam Talbot <[email protected]>
Co-authored-by: nf-core-bot <[email protected]>
Co-authored-by: Joon Klaps <[email protected]>
Co-authored-by: Koen Bossers <[email protected]>
Co-authored-by: Sateesh_Peri <[email protected]>
Co-authored-by: Louis LE NEZET <[email protected]>
Co-authored-by: KamilMaliszArdigen <[email protected]>
Co-authored-by: Kevin Ryan <[email protected]>
Co-authored-by: MarieLataretu <[email protected]>
Co-authored-by: Edmund Miller <[email protected]>
Co-authored-by: Simon Pearce <[email protected]>
Co-authored-by: Maxime U Garcia <[email protected]>

* chore(deps): Bump htseq conda env

* chore(deps): Update bowtie2 conda env

* ci(renovate): Assign CodeOwners to PRs

* ci(renovate): Move gitAuthor to main config

* ci(renovate): Try to add a header to stop the merge

* ci(renovate): Remove docker hub

* ci(renovate): Update environment.yml regex

* ci(renovate): Copy regex from anaconda

https://github.com/anaconda/renovate-config/blob/176696853379d878a87575ba03b1b12fd29d24ac/default.json#L64-L71

* ci(renovate): Toss in pypi while we're here

* chore: Try adding :'s

* ci(renovate): Finally figured it out

https://github.com/anaconda/renovate-config/blob/176696853379d878a87575ba03b1b12fd29d24ac/docs/conda-environment.md?plain=1#L24
https://github.com/search?q=renovate%3A+datasource%3Dconda&type=code

* ci(renovate): Add pre-commit hook

* ci: Add a pre-commit workflow

* ci: Validate GitHub Workflows with pre-commit

* ci: Run pre-commit on only changed files

* initial commit

* add full module details and run tests

* fix linting

* fix linting and version number

* Update modules/nf-core/arriba/download/meta.yml

Co-authored-by: Annick Renevey <[email protected]>

---------

Co-authored-by: Annick Renevey <[email protected]>

* add agat/convertspgff2tsv module

* correct output path

* update getting the version

* reverse other agat modules as not updated software

* correct md5sum

* adding bam bai

* Fix typo

* md5sum not text

* use correct tag name in tags.yml

* add missing tag

* add subworkflow tag

* copy pasta typo

---------

Co-authored-by: Maxime U Garcia <[email protected]>
Co-authored-by: Matthias Hörtenhuber <[email protected]>

* new module gridss GeneratePonBedpe

* Update main.nf

quay.io removed

* Update modules/nf-core/gridss/gridssgenerateponbedpe/main.nf

Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

* Update modules/nf-core/gridss/gridssgenerateponbedpe/main.nf

Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

* Update main.nf

fix input and output names
change meta names

* Update meta.yml

add meta 3 and meta 4 information

* Update main.nf

---------

Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

* initial commit

* new module: gridss_somatic_filter

* Update main.nf

quay.io removed

* Update modules/nf-core/gridss/gridsssomaticfilter/main.nf

Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

* Update modules/nf-core/gridss/gridsssomaticfilter/meta.yml

Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

---------

Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

* Added a meta map for the reference genome of minimap2

* Added a meta map for the reference genome of minimap2

* Skip the Conda test since it produces a slightly different BAM file

…ded, gz input support, megan makedb test updated (nf-core#4194)

* diamond/makedb container, stub, meta, gz updated

* diamond/blastp container, stub, prefix, gz updated

* diamond/blastx container, stub, gz, megan module test upgraded

* nf-test diamond/makedb

* nf-test diamond/blastp

* nf-test diamond/blastx

* diamond blastp and blastx daa md5sums removed

* db input fix for blastp and blastx

* megan test makedb updated

* updated conda version in environment.yml

* correct conda paths per tool

* nf-tests with new conda envs and zipped tests for diamond tools

* diamond tools revision points

* db to tuple with meta

* blastp daa snapshot added

* revert snapshot

* revisions + debugging snapshots - conda failing

* daa check for existence instead of snapshot due to conda error

nf-core#4197)

* blastp added choice for xml or tsv outputs other than the existing csv

* rerun skipped jobs

* nf-tests with new conda env + zipped file tests added for blast modules

* meta updated

* testing snapshots

* updated snapshots to work properly where possible

Co-authored-by: Sateesh_Peri <[email protected]>

Co-authored-by: Mahesh Binzer-Panchal <[email protected]>
Co-authored-by: Matthias Hörtenhuber <[email protected]>

Co-authored-by: Mahesh Binzer-Panchal <[email protected]>

Co-authored-by: Mahesh Binzer-Panchal <[email protected]>

disable in nf-test not in pytest