…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 <68351153+CarsonJM@users.noreply.github.com>

* Fix linting

* Update modules/nf-core/abricate/run/main.nf

* Get downstream module test

---------

Co-authored-by: Carson J Miller <68351153+CarsonJM@users.noreply.github.com>

* 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 <core@nf-co.re>

* 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 <mm49@sanger.ac.uk>

* 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 <jfy133@gmail.com>

* 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 <jfy133@gmail.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

* 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 <aida.andrades@gmail.com>

* 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 <maxime.garcia@seqera.io>

* nf-test for spring/decompress

* Trying to please linter

* Trying to please linter

---------

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>

* everything but snapshot

* fix gz snap

* update testdata paths

* Update main.nf.test

* update test

---------

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

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 <24893913+SPPearce@users.noreply.github.com>

* Remove superfluous config file

* Clean up code

* Repair all stub tests that were empty

---------

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

* 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 <jfy133@gmail.com>

* 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

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* change output to prefix

* change to prefix

* update to prefix

---------

Co-authored-by: vickylaram <mielczarekv@rki.de>

…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 <61584065+Joon-Klaps@users.noreply.github.com>

* Update assert

Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com>

* renamed test

Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com>

* reverted the input

* updated input...again

Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com>

* fixed typo

Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com>

* Regenerate snapshot and fix linting

---------

Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

….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 <john.palmer@bccdc.ca>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

)

* port to nf-test, add meta to tuple and stub

* modify meta and fix tags

* change from each to tuple

* Pass annotation files to last-dotplot

The annotation of the target (plotted horizontally) genome is passed as
a new channel.

The annotation of the query (plotted vertically) genome is passed as a
new component of the first channel.

This is because this module typically loops on a list of alignments of
various query genomes (from samplesheet) to a single target genome.

The annotation files are called `annot_a` and `annot_b` because they are
passed to the `-a` and `-b` arguments of `last-dotplot`.

* Put arguments on separate lines.

* Add meta map and reorder channels.

* Test with dummy annotation files.

Thanks @SPPearce for the hint.

* Add meta to bowtie build

* Swap fastq ngscheckmate tests

* Swap to nf-test

* Remove spurious changes to bowtie2

* Actually revert bowtie2

* Add the rest of bowtie2

* Again

* Revert bowtie2 changes

* Swap to meta.id as prefix

* Swap bowtie align to nftest

* Update tests

* Use nft-bam

* Update modules/nf-core/bowtie/build/tests/main.nf.test

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>

* Swap to testdata path

* Update modules/nf-core/ngscheckmate/patterngenerator/main.nf

* Swap index finding to $

* Fix vafncm test

* Update meta

* Remove bam header md5sum

* Update fastq test

* Update paired bam test

* Delete modules/nf-core/bowtie/align/tests/nextflow.config

---------

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>

* nf-test for pilon

* linting for license

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* Add missing END_VERSIONS and alignment

* Add optional outputs to stub

---------

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

* Add stub section

* Update yml

* Add nf-test

* Get rid of pytest

* Make lint happy

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* Update tests to make lint happy

* update tests

* Make lint happy

* Using the same version as CI of nf-test locally might be a good idea

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---------

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

* Added variant filtering to matrix filter

* Corrected indentation

* Simplified function in single conditional block

* fixed line indentation

* Fixed whitespace

* Fixed logic

* line wrapping change

* added whitespace around comments

* [automated] Fix linting with Prettier

* remove trailing whitespace

* Update matrixfilter.R

* Remove whitespace

---------

Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io>
Co-authored-by: nf-core-bot <core@nf-co.re>
Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

* Fix version string spurious text in singularity tests

* Add config for subworkflow

* Update md5sum module to work with multiple files

* linting

* Fix stub

* Add option to generate single file

* Update modules/nf-core/md5sum/main.nf

Co-authored-by: Matthieu Muffato <cortexspam-github@yahoo.fr>

* Simplify versions processing

---------

Co-authored-by: Matthieu Muffato <cortexspam-github@yahoo.fr>

* build: Bump deepvariant to 1.6.1

* interim dir not allowed to be a dot in 1.6

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

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>

* hack: Hard code version

google/deepvariant#830

---------

Co-authored-by: Felix Lenner <felix.lenner@igp.uu.se>
Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>

* bump version

* nf-test migratino

* revert ancestry

* fix linting

* Update snap

* fix unicode space

---------

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

* Added evigene/tr2aacds

* Sorted file list and added activation script

* Fixed issues raised by feedback

* correct president stub

* Large update to module

* Update prefix and meta

---------

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

Fix EClint

* Add the new module nanoq

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

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

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

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

* define the output_format

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

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

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

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

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

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

* update the stub run with gzip

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

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

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

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

---------

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

…s added (nf-core#5906)

* foldseek/createdb version bump, added stub nf-test

* foldseek/easysearch version bump, stub nf-test added

* test.snap for createdb added

* sourmash/compare stub, nf-test, snapshot

* Add sort

* Add a sort

* Update snap

* Try sort inside the module

* Add meta to output and change formatting on test

---------

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

* adding chewbbaca/createschema module

* updated for handling a mix of uncompressed and compressed files

* update the formatting

* update the formatting

* updated module to emit meta

* updated test.yml

* update pytest

* clean the meta.yml

* clean the meta.yml

* clean the meta.yml

* replaced conda package with environment.yml file

* py-test to nf-test migration

* add stub and update tests, snapshot

* updated stub

* update stub test

* update stub test

* bump the version

* update

* updating container version

* updated test snapshot

* updated nf-test snapshot

* added libmamba to environment file

* Fix tests and linting

* Update modules/nf-core/chewbbaca/createschema/main.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Apply suggestions from code review

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

---------

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
Co-authored-by: Sateesh <perisateesh@gmail.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* add stubs for rsem

* add stubs for rseqc

* add stubs for subread/featurecounts

* add stubs for trimgalore

* add stubs for ucsc/bedclip

* add stubs and more tests for umitools/extract

* update snap

* update snapshot for umitools/extract

* fix umitools/extract tests

* Apply suggestions from code review

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

---------

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

* affy/justrma add stub, nf-test and snapshot

* Update snapshot and environment

* Update snap

* Update modules/nf-core/affy/justrma/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Swap test data file paths, fix config, update snaps and stub

---------

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Convert callduplex and callmolecular to nftest and update version

* Convert zipperbams

* Convert groupreadsbyumi

* Convert sortbam and add stubs

* Convert filterconsensusreads

* Update snapshot

* Update modules/nf-core/fgbio/callmolecularconsensusreads/main.nf

* Add collision checks, swap test data paths

* Fix conda version and linting

* Apply suggestions from code review

Co-authored-by: Nils Homer <nh13@users.noreply.github.com>

* Update modules/nf-core/fgbio/callmolecularconsensusreads/meta.yml

Co-authored-by: Nils Homer <nh13@users.noreply.github.com>

* Update duplex snap

---------

Co-authored-by: Nils Homer <nh13@users.noreply.github.com>
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>

* Added pbtk/pbindex

* Removed prefix

* Added agat/spfilterfeaturefromkilllist

* Added AGAT config

* Included test with agat config

bump stranger

* fix stub and add tests + single snapshot

* add stub

* fix stub

* snapshot versions + better snap for stub

* add versions to snapshot + add tests for stub

* Add stub tests + single snapshot

* Add stub tests + single snapshot

* maxime sorted

* Add stub tests + single snapshot

* Add stub tests

* Add stub tests + single snapshot

* code polish + update snap

* update snapshot using nft-bam

* Add stub tests + single snapshot

* Add stub tests + single snapshot

* fix stub and update tests for kallisto modules

* Add stub tests + single snapshot

* Add stub tests + single snapshot

)

* bcftools isec input can be bcf or bcf.gz as well as vcf.gz

* Add stub and stub test

* Update tests

* Update meta.yml

* Add stub to name of stub test

* Update meta

* Update tests

Changes:
- exclude .tbi files from snapshot due to failing conda tests
- update main.nf.test.snap
- specificy path type of the  output

* Update tests again

Changes:
- include versions
- sort file name list for consistent order
- update snapshot

---------

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Co-authored-by: Theresa Störiko <theresa.stoeriko@gmx.de>
Co-authored-by: Theresa Störiko <73145457+tstoeriko@users.noreply.github.com>

* do not snapshot input

* do not snapshot input

do not snapshot input with stub

* vardict-java bgzip mulled container

* update bioconda env

* code polishing

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

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

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

* args3 for bgzip

* args3

* Update snap

* removed whitespace

---------

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

)

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

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

* all_files_update

* Update environment.yml

* update_meta.yml

* input==input_bam

* update_snapshot

* meta.yml,tags.yml update

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

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>

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

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>

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

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>

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

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>

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

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>

* update_author

---------

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>

* ADD argnorm module

* ENH correct pattern for 'hamronized' input

* ENH specify hamronization command in script

* ENH don't pass 'hamronized' as val

* Fixed trailing whitespace

* "single_end" is not relevant in this module

* alignment

* "db_args" to avoid any confusion with the input channel

* Added a test to check $tool is provided

* Implemented the stub mode

* Added a test for the missing database

* Reordered the arguments to match the script

---------

Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>

* test it out

* ci: Add license_message script

nf-core/sarek#1380
https://github.com/DonFreed/docker-actions-test?tab=readme-ov-file

* test: Add tests for sentieon bwamem

Because the pytest-workflow tests are taking so long

* Add scratch from meeting

* Clean up sentieon secrets

* ci: Fix Nextflow secrets setup

* fix(sentieon): Remove encryption key because it won't get used

* fix #

* ci: Fix when to setup secrets

* feat: Add sentieon auth mech secret

* chore(sentieon): Remove bwamem pytest-workflow tests

* fix: Spike in with environment variables

* fix: Add SENTIEON_AUTH_DATA in env file

The reason for this is because when we require it in the module it
fails. That doesn't make sense for normal Sentieon users. They don't
care, this is more of a GitHub actions thing.

* docs(sentieon): Make this a README

* test: Add local testing setup

* test: Remove publishDir

* style: Remove sentieon/bwamem

* fix: Change comments to prints for debugging and better reporting

* fix: Add a quote?

* chore: Remove unnecessary variable

* debug: Print variables

* Fix typo

Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com>

* chore: Clean up code

* docs: Write up all the learnings from Sentieon

* style: Run prettier

* style: Add tags for nf-core lint

* docs: Clean up notes

Co-authored-by: maxulysse <maxulysse@users.noreply.github.com>

* chore: Add @DonFreed as maintainer

---------

Co-authored-by: Edmund Miller <git@edmundmiller.dev>
Co-authored-by: Edmund Miller <20095261+edmundmiller@users.noreply.github.com>
Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com>
Co-authored-by: maxulysse <maxulysse@users.noreply.github.com>

* ci: Remove setting secrets in pytest-workflow

* ci: Add a longer note about conditionals

https://docs.github.com/en/actions/security-guides/using-secrets-in-github-actions#using-secrets-in-a-workflow
Secrets cannot be directly referenced in if: conditionals.
Instead, consider setting secrets as job-level environment variables, then referencing the environment variables to conditionally run steps in the job.
For more information, see "Contexts" and jobs.<job_id>.steps[*].if.

* ci: Check for secrets in env

Because if this is coming from a fork it will fail

* improve bbmap_split stub

* update stub tests

* improve stub

* single snapshot

* fix stub + add stub tests

* fix stub + add stub tests

* fix stub

* restore tags

* fix stub + better stub tests

* fix snapshot

* test(narfmap): Add segfault test

* fix(narfmap): Clean up log error

* test(narfmap): Should segfault

* chore(narfmap): Bump to 1.4.2

* test(narfmap): Mark test as passing

bioinformaticsorphanage/NARFMAP#10

* style: Add extra tag for nf-core/lint

* test: Update all the snapshot declarations

* chore: Add a TODO for poddar's test

* chore: Add Note about issue

* test: Remove bam name

Co-authored-by: maxulysse <maxulysse@users.noreply.github.com>

---------

Co-authored-by: maxulysse <maxulysse@users.noreply.github.com>

* feat: Add cram/index support to narfmap

* chore: Remove singularity image comment

* test: Update tests for CRAM

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

* bump bclconvert

* fix snapshots

* bump multiqc

* update snapshot

* bump picard

* fix hsmetrics test

* fix markduplicates

* fix extractfingerprints

* fix addorreplacereadgroups

* fix crosscheckfingerprints

* Add prefix to output file

* Update barrnap to nf-test

* Update tags.yml

* Add missing bracket and run test

* Correct format of license

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

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

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

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

* Review suggestions

* Prettier

* Update meta.yml

* Update tests

---------

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

)

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

* last train modified to output multiqc

* Report alignment length and percent similarity, for MultiQC.

* Update snapshot file.

* Document the new channels

* Fix indentation

* Update test results.

* Give a longer suffix for better MultiQC search patterns.

---------

Co-authored-by: Mohammed Mahdi <mohammed.mahdi@oist.jp>

* update lofreq callparallel and somatic ssh

* [automated] Fix linting with Prettier

* suggestions

* remove files tests

* label lofreq somatic

* Update modules/nf-core/lofreq/callparallel/main.nf

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>

* port lofreq/callparallel to nf-test

* Swap to nftest

* update paths

* add meta

* Update main.nf

* modify main

* update paths

* fix small errors

* Update modules/nf-core/lofreq/somatic/tests/main.nf.test

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

* Update main.nf.test.snap

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Co-authored-by: AitorOP <aitor.pesetaop@gmail.com>
Co-authored-by: nf-core-bot <core@nf-co.re>
Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
Co-authored-by: Francisco Martínez <f.martinezpico@gmail.com>
Co-authored-by: Famke Bäuerle <famke.baeuerle@gmail.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

…f-core#5943)

Update dupradar.r according to new MultiQC config values.

Co-authored-by: Matthias Zepper <MatthiasZepper@users.noreply.github.com>

* update nanoq module

* update nf-test

* Update Glimpse2 phase

* Fix label

* Update snapshot

* Update modules/nf-core/glimpse2/phase/main.nf

Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>

* Update meta.yml

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Co-authored-by: LouisLeNezet <louislenezet@gmaio.com>
Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>

* Update dupradar test snapshot

* Dummy commit to try and trigger nf-test in ci

* Revert "Dummy commit to try and trigger nf-test in ci"

This reverts commit 130f998.

* fix stubs and add stub tests

* fix linting

* fix some linting

* fix linting

* better comment

* change container

* update snapshots

* improve untar stubs

* update snapshots

* update snapshots

* update env

* better

* use seqera containers

* quay.io

* proper usage

* update snapshots

* keep ubuntu for now

* update tests and snap

* update test and snapshot

* update test and snapshot

…e#5973)

* Add new input to multiqc module for use with --rename_samples

* Update tests

* update meta.yml

* Add provision for sample_names

* port

* remove pytest files

* fix meta

* Update meta.yml

* fix indentation

* update test with bam plugin

* fix indents, try other test

* remove --assembly flag for now

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Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>

….2 (nf-core#5975)

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

* fix: emit all fastqs, remove global log file

* fix: remove rg parseing

* fix(subworkflow/bcl_demultiplex): remove rg parsing, output empty fastqs, remove log file

* test: update snaps

* lint: traill\ing whitespace

* feat: include read group parsing and empty file check in single closure

* test: update snapshot

* fix: lint final new line

* fix: lint trailing whitespace

* fix: add branch and emit empty fastq channel

* tests: update snaps

* lint: trailing whitespace

* fix: filter bool and add test

* test: update snaps

* test: assert empty file exist

* test: assert empty file exist

* test: check file exists, update snap

* Update test.yml

* Update test.yml

* ci: debug nf-test failure

* ci: debug nf-test failure

* ci: debug nf-test failure

* ci: debug nf-test failure

* ci: debug nf-test failure

* ci: debug nf-test failure

* ci: debug nf-test failure

* ci: debug nf-test failure

* ci: debug nf-test failure

* ci: debug nf-test failure

* ci: debug nf-test failure

* ci: debug nf-test failure

* ci: debug nf-test failure

* ci: debug nf-test failure

* ci: debug nf-test failure

* ci: debug nf-test failure

* ci: debug nf-test failure

* ci: debug nf-test failure

* ci: debug nf-test failure

* ci: debug nf-test failure

* ci: debug nf-test failure

* lint: fix lint

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Co-authored-by: khazen@clearnotehealth.com <--unset>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

* Add basic gtffilter implementation

* Add gtffilter stub

* Add gtffilter meta map

* Update gtffilter meta.yml

* Fix gtffilter formatting

* Add first gtffilter tests

* Fix problems in gtffilter module defintion

* Add gtffilter nf-test snapshot

* Add support for gzipped inputs to gtffilter

* Add gtffilter gzip stub

* Update nf-test definition for gtffilter

* Add meta2 to fasta input

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

* Add fasta meta map to gtffilter test definitions

* Add gtffilter MIT license text

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

* Added agat/spmergeannotations

* Added tests with config