* Update LAST to version 1453.

* update lastdb version to 1453

* update last mafconvert to 1453

* update last mafswap to 1453

* update postmask to last v1453

* update last split to v1453

* last update train to v1453

* Update meta.yml

Change output value type to string

* Update meta.yml

Change output value type to string

---------

Co-authored-by: Charles Plessy <charles.plessy@oist.jp>
Co-authored-by: Charlotte Capitanchik <charlotte.capitanchik@crick.ac.uk>
Co-authored-by: Johannes Nicolaus Wibisana <johannes.nicolaus@oist.jp>
Co-authored-by: Charlotte Capitanchik <CharlotteAnne@users.noreply.github.com>

* Update LAST to version 1453.

* update lastdb version to 1453

* update last mafconvert to 1453

* update last mafswap to 1453

* update postmask to last v1453

* update last split to v1453

* last update train to v1453

* Update meta.yml

Change output value type to string

* Update meta.yml

Change output value type to string

---------

Co-authored-by: Charles Plessy <charles.plessy@oist.jp>
Co-authored-by: Charlotte Capitanchik <charlotte.capitanchik@crick.ac.uk>
Co-authored-by: Johannes Nicolaus Wibisana <johannes.nicolaus@oist.jp>
Co-authored-by: Charlotte Capitanchik <CharlotteAnne@users.noreply.github.com>

* use id as index name

* prettier yml

* Update modules/nf-core/fastqscreen/buildfromindex/main.nf

Co-authored-by: Adrien Coulier <adrien.coulier@medsci.uu.se>

* remove comment

* Update tests/modules/nf-core/fastqscreen/buildfromindex/main.nf

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

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

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

* Update tests/modules/nf-core/fastqscreen/buildfromindex/main.nf

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

* change genome to database

* rename input

* remove meta2

* update md5sum

* correct container

* Update main.nf

* Update meta.yml

* remove inplace in sed to work on macos and linux

* Gem2/gem2bedmappability (#3572)

* new module picard/scatterintervalsbyns

* update annotsv to 3.3.6

* update installannotations

* new module gem2/gem2bedmappability

* add sizes output

* update meta

* review comments

* Update genmap modules (#3579)

* new module picard/scatterintervalsbyns

* update annotsv to 3.3.6

* update installannotations

* update genmap modules

* revert label changes index

* Gcnvcaller modules (#3581)

* update modules

* update uri

* review suggestions

* update germlinecnvcaller

* Update germlinecnvcaller (#3584)

* update modules

* update uri

* review suggestions

* update germlinecnvcaller

* update params

* Add singularity.registry = 'quay.io' for tests (#3499)

* Add singularity.registry = 'quay.io' for tests

* Bump min NF version to 23.04.0

* Move registry definitions to top-level config scope

---------

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>

* Automatically rename input files in cellranger module (#3537)

* add README

* Implement cellranger autorename

* Fix container paths

* Various fixes

* Revert "Fix container paths"

This reverts commit 4163e2b52c584571352e2f1ac6d4080b84ae592c.

* Update modules/nf-core/cellranger/count/templates/cellranger_count.py

Co-authored-by: Kevin L. Keys <klkeys@users.noreply.github.com>

* Apply suggestions from code review

Co-authored-by: Kevin L. Keys <klkeys@users.noreply.github.com>

* Include container registry

* Update modules/nf-core/cellranger/count/main.nf

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

* Update documentation

---------

Co-authored-by: Kevin L. Keys <klkeys@users.noreply.github.com>
Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>

* Bump taxpasta version (#3586)

* Bump taxpasta version

* Update modules/nf-core/taxpasta/merge/main.nf

Co-authored-by: Moritz E. Beber <midnighter@posteo.net>

* Update modules/nf-core/taxpasta/standardise/main.nf

Co-authored-by: Moritz E. Beber <midnighter@posteo.net>

* Update modules/nf-core/taxpasta/merge/main.nf

Co-authored-by: Moritz E. Beber <midnighter@posteo.net>

---------

Co-authored-by: Moritz E. Beber <midnighter@posteo.net>

* change authorship (#3580)

* change authorship

* prettier

* trailing whitespace

* prettier

* sub-tool names must be one word - msisensorpro/msisomatic (#3590)

* sub-tool names must be one word

* No md5 checksum needed for versions.yml

* License on sentieon script (#3594)

* Adding info on using file-based sentieon license

* Adding BSD 2-Clause license

* New module: emboss/cons  (#3583)

* init emboss cons

* completing tests

* Implementing suggetions

* Ucsc update (#3588)

* Updated the container to samtools 1.17 and so that container and bioconda pretext versions match

* Updates to version

* Updates to yaml

* Update yaml

* Update version

* Update version and yaml values

* Update incorrect value

* Updated md5sums

* Updated md5sum for versions

* Updated md5sums

* Prettier linting

* Update to version

* Updating md5sums

* Updated version

* Updated version

* Version update + md5sum update

* Version update + md5sum update

* Added Stub

* Version updates, stub addition, remove unnecessary stub testing, md5sum updates

* Version updates, stub addition, remove unnecessary stub testing, md5sum updates

* Linting Fixes

* Linting Fixes

* Incorrect version output

* Apply suggestions from code review

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

* Updating md5sums due to changes in review

* Adding versions, removing md5sum

* Adding versions, removing md5sum

* Adding versions, removing md5sum

* stuff

* Removing changes to liftover

---------

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

* Windowmasker update (#3587)

* Updated the container to samtools 1.17 and so that container and bioconda pretext versions match

* Updates to version

* Updates to yaml

* Update yaml

* Update version

* Update version and yaml values

* Update incorrect value

* Updated md5sums

* Updated md5sum for versions

* Updated md5sums

* Prettier linting

* Update to version

* Updating md5sums

* Updated env

* Updated env

* Updated fix fix versions and directory name

* Apply suggestions from code review

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

* Updating pytest

* Removing old files

* Removing old files

---------

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

* Use `gzip -cd` because `gunzip` preserves the group ownership (#3593)

* Use `gzip -cd` because `gunzip` preserves the group ownership

* Added a comment to explain why we're doing it this way

* update postprocessgermlinecnvcalls (#3596)

* update modules

* update uri

* review suggestions

* update germlinecnvcaller

* update params

* update input definition

* update tests

* update eklipse (#3598)

add bai

* new module:  mmseqs2/createdb (#3601)

* init mmseqs/createdb

* remove todo

* Implementing suggestions

* add peka module (#3402)

* add peka module

* linting

* update stub test

* update peka test

* update test

* update checksum is variable

* add versions to test

* salmon/quant update to handle multiple pairs of fastqs (#3438)

* added handling for multiple single-end fastqs and multiple pairs of fastqs

* Empty-Commit

* remove stageAs option from inputs

* Fix pytests

* fix linting errors with prettier

---------

Co-authored-by: Anne Marie Noronha <anoronh4@users.noreply.github.com>

* Metaphlan4 update: add --index (#3604)

* Add --index to metaphlan

* correct --input_type

* Update bcftools query (#3605)

* new module picard/scatterintervalsbyns

* update annotsv to 3.3.6

* update installannotations

* update output of bcftools query

* New module:  mmseqs/search (#3595)

* init mmseqs2/search

* setup .nf file

* prefix is null in path

* remove _h

* I've no idea why it's not working

* Fixing linting and pipeline run

* Successfull docker test

* naming conventions & need fix for db identify

* Fixing test by creating own database

* updated method for extracting db basename

* alignment output

* removing head

* find depth 1

* maxdepth 1

* typo name

* Adding args2,3 to search for specific db files

* avoid args injection

* New module: mmseqs/cluster (#3600)

* prefilter step died

* Succesful test mmseqs cluster

* include args2 for specific database within folder

* document the extraction

* avoid args injection

* New module:  mmseqs/createtsv (#3603)

* Initialise mmseqs createtsv

* container fix mmseqs_createtsv

* optional db_target mmseqs/createtsv

* finishing tests succesfully

* Update tests/modules/nf-core/mmseqs/createtsv/main.nf

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

* Update tests/modules/nf-core/mmseqs/createtsv/main.nf

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

---------

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

* Add geoquery/getgeo (#3585)

* Add geoquery/getgeo

* fix meta

* Tidy up R

* Fix test prefix

* Remove quay.io

* Remove r object checksums

* bam_markduplicates_samtools (#3606)

* FASTQ_ALIGN_BWAALN: Fixes bwa_aln subworkflow inconsistency with reads and the references they map against when multiple references supplied (#3479)

* Start trying to fix bwa_aln subworkflow

* Fix support for multi-references

* Additional comment

* Debugging: the id_index is not being inserted into the file names resultsing in overwriting

* Add test for multiref

* Apply suggestions from code review

Co-authored-by: Thiseas C. Lamnidis <thisseass@gmail.com>

* Document `meta.id_index`

---------

Co-authored-by: Thiseas C. Lamnidis <thisseass@gmail.com>

* Add mapAD/map (#3609)

* Add mapad/map

* Extend keyword list

* Improve description of IO channels

* Mark file inputs as mandatory

* State that only SE or merged PE data are supported

* Update modules/nf-core/mapad/map/meta.yml

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

* Update modules/nf-core/mapad/map/meta.yml

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

* Update meta.yml

---------

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

* Add proteus module (#3578)

* trying to get the tests to run

* Module seems to work, will test some additional params after this commit

* This should fix prettier and the conda fail

* Removed md5sums for plots because of inconsistency

* Added final newline, removed duplicate org_path

* Sorted yml, removed delete_me

* Added authors, reordered output

* Added licence

* Update manta modules (#3615)

* Update manta somatic

* Update manta tumoronly

* add varlociraptor call subcommand (#3529)

* 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>

* add new module iCount-mini/metagene (#3612)

* add module template

* first version

* update testing and linting

* update file naming

* update test

* fix test

* Newmodule ngmerge (#3626)

* 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

* NEW MODULE: PURECLIP (#3624)

* 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

* fix integer overflow (#3620)

Co-authored-by: Steven Strong <steven.strong@adelabio.com>

* Fix metaeuk_easypredict when using mmseqs database (#3525)

Fix metaeuk and add tests

* 3630 add unstitched reads as emitted output of ngmerge (#3632)

* add -f option

* update tests

* Update vardictjava (#3633)

* new module picard/scatterintervalsbyns

* update annotsv to 3.3.6

* update installannotations

* update vardictjava

* Adding modules from #scrnaseq for simpleaf (#3619)

* 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>

* update icount mini version (#3640)

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)

* Bump taxpasta version (biocontainer not yet available) (#3639)

* Purecn/run (#3140)

* 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

* new module: samtools/import (#3642)

* new module: samtools/import

* fix versions

* fix versions some more

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

* fix meta

* Adding seqkit sliding command (#3637)

* 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>

* Hicexplorer hicpca (#2933)

* 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>

* Fix bug in pyrodigal module (#3643)

Add "--force" to pigz

* Update gecco/run (#3652)

Version bump to 0.9.8

* New module: instrain/compare (#3623)

* Started instrain compare tests

* instrain compare

* Update modules/nf-core/instrain/compare/main.nf

* Update modules/nf-core/instrain/compare/main.nf

* Update modules/nf-core/instrain/compare/main.nf

* Updated test.yml and added stub

* Update modules/nf-core/instrain/compare/main.nf

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

* Update meta.yml to include meta2

* Updated test.yml output files

* Changed md5 to content for several test.yml files

* changed content to contains

* Added another contains option in test.yml

* shortened contains string to pass prettier check

---------

Co-authored-by: Margot Lavitt <margotl9@n3065.hyak.local>
Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

* Update LAST modules to v1453 (#3303)

* Update LAST to version 1453.

* update lastdb version to 1453

* update last mafconvert to 1453

* update last mafswap to 1453

* update postmask to last v1453

* update last split to v1453

* last update train to v1453

* Update meta.yml

Change output value type to string

* Update meta.yml

Change output value type to string

---------

Co-authored-by: Charles Plessy <charles.plessy@oist.jp>
Co-authored-by: Charlotte Capitanchik <charlotte.capitanchik@crick.ac.uk>
Co-authored-by: Johannes Nicolaus Wibisana <johannes.nicolaus@oist.jp>
Co-authored-by: Charlotte Capitanchik <CharlotteAnne@users.noreply.github.com>

* Hisat2-build: index construction w/ truly optional inputs  (#3649)

* index construction mode dependent on optional inputs rather than memory availability

* added tests for new functionality

* updated tests to use appropriate test data

* cleaned up test.yml to only contain BUILD outputs

* removed unnecessary extract ss call

* added : to empty metamaps. Reverted to sarscov2 test files

---------

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

* update metaphlan module (#3661)

* CNVKit 0.9.10 update (#3651)

* upgrade CNVkit to 0.9.10

* homogenise keywords of all CNVkit modules

* Add samtools dependency to bam2seqz module of sequenzautils

Without specifying the dependency to a more or less current version of samtools, conda solves the environment for sequenza by using a very old samtools version that can cause problems when processing subsampled files (automated tests)

* Update cnvkit to 0.9.10

Changes:
 - Update cnvkit to 0.9.10
 - Update samtools in cnvkit modules to 1.17

Based on #3545 authored by @priesgo.

* cnvkit 0.9.10 test update

* update checksums of output files in tests for CNVkit batch

* Update cnvkit/export VCF test

* Additional tags for sequenzautils

---------

Co-authored-by: Pablo Riesgo-Ferreiro <priesgoferreiro@gmail.com>
Co-authored-by: Julian Mohr <81371922+JulianMohr@users.noreply.github.com>

* Update gatk3 modules (#3660)

* update mapdage2 module

* Add meta for all files in gatk modules

* Update tiddit to v3.6.1 (#3663)

* Update stubs for samtools flagstat (#3657)

Update stubs

Co-authored-by: Ram Nanduri <ram@MTLUCMDS1.lund.skane.se>

* R differential modules control over output prefixes (#3664)

* R differential modules control over output prefixes

* Set differential module prefixes

* Actually we need to do prefix handling within the template

* Set differential module prefixes

* Fix test files for new prefix specification

* Add meta to limma test

* Fix DESeq2 tests

* fix remaining tests for limma

* Update grep to fix broken solve

* Try bumping affy

* Use new build

* update md5sum for annotation

* Update stubs for samtools idxstats (#3665)

* Update stubs

* Update stubs for samtools idxstats

---------

Co-authored-by: Ram Nanduri <ram@MTLUCMDS1.lund.skane.se>

* Bump ensembl-vep modules to 110.0 (#3658)

* bump ensembl-vep to 110.0

* update tests

* put conda tests back

* update config for ENSEMBLVEP_DOWNLOAD

* update tests for related subworkflows

* fix path to module

* enable conda tests back

* better tests

* fix tests

* nicer channels

* fix channel queue to value

* fix syntax

* Remove containers with cache with snpEff too (#3670)

* update tests for snpeff

* remove containers in config

* fix cache version in tests

* update meta.yml

* fix meta.yml

* fix meta data

* fix md5sum

* re-enable conda tests

* Update stubs for bwa mem (#3671)

Co-authored-by: Ram Nanduri <ram@MTLUCMDS1.lund.skane.se>

* Additional optional output to homer/annotatepeaks  (#3667)

* add optional stats output for use with the -annStats parameter (to be provided with ext.args)

* Update meta.yml

* add additional stats output to annotatepeaks test

---------

Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>

* Hisat2 align splicesitesoptional (#3656)

* added align tests for splicesitesoptional

* changes to homo sap

* updated splice sites to be optional with tests

* Fix invalid GATK container (#3673)

Fix GATK container which was invalid

Fixes #3668

* Update: bamtools, gstama, ultra (#3655)

* Update Bamtools [2.5.1 -> 2.5.2]

* Update gstama/merge [1.0.2 -> 1.0.3]

* Update ultra [0.0.4.2 -> 0.1]

* Update ultra/index|align|pipeline tests

replace gffread by gnu/sort

* Irregular md5sum for database.db

* Update bamtools/convert test.yml

* Fix centrifuge: reduce number of input channels (#3674)

* Bump taxpasta version (biocontainer not yet available)

* Remove unnecessary (and sometimes problematic) input channel

* Improve output glob for optional alignments

* Remove now unnecessary variable from command

* linting

* Add missing args

* Github Actions uses fixed job names for branch protection rules (#3677)

* Add wait-for-status workflow

* Rename and tidy all GHA workflows for branch protection

* Changing some stuff to kick off real CI/CD

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update .github/workflows/nf-core-linting.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update .github/workflows/code-linting.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update nf-core-linting.yml

* Update nf-core-linting.yml

* Update nf-core-linting.yml

* Add FASTQC fake test

* Revert "Changing some stuff to kick off real CI/CD"

This reverts commit f8e5c941ef2120fd646643a88fd9b51074a02f01.

* Change to fix-linting for consistency

* Remove fake nf-test change

* Delete main.nf.test

* Bump setup-python version to v4

---------

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* changed to version 0.4.0 (#3676)

* changed to version 0.4.0

* Update main.nf

* Update main.nf remove tailing space

* Update main.nf

* Update modules/nf-core/fcs/fcsgx/main.nf

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

---------

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

* Update kmcp modules (#3680)

* Update kmcp profile

* Update kmcp modules

* Remove one line

* Update test.yml for kmcp/profile

* test.yml

* Fix linting

* Update to kmcp:0.9.3

* kmcp=0.9.3

* Version 0.9.1

* Update test.yml for kmcp/search

* Prettier

* Fix linting

* Update test.yml for kmcp/profile

* Update test.yml

* Test without stub

* Prettier

* Add stub to test.yml

* Test gzip in search

* Try to fix gzip

* Try to fix gzip

* Test gzip

* Move conda-checks (first batch) (#3686)

* Moving conda-check and replacing exit 1 with error-cmd

* Adding conda-check in stub-section

* Adding conda-check in stub-section

* Updating certain md5sums. Ok by Emiller88. Related to https://github.com/nf-core/modules/pull/3558

* Switching from exit 1 to error-cmd and correcting error-msg

* Hierarchy of tests applied in order  (#3679)

* Add wait-for-status workflow

* Rename and tidy all GHA workflows for branch protection

* Changing some stuff to kick off real CI/CD

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update .github/workflows/code-linting.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Should reduce concurrent burden at the expense of time. Code is required to lint before running. This will help us during hackathons etc when there is a high burden on the GHA runners, but will be slower in general use.

Changes:
 - linting and testing in one GHA file
 - Linting is required to pass before pytest or nf-test runs
 - Check for changes only happens once

* Fix dependencies in GHA

* Remove files again

* More dependency fixes

* Correct nf-test filtering yaml

* Change to fix-linting for consistency

* Bump setup-python version to v4

* bump eWaterCycle/setup-singularity to v7

* Add final job to test for pass status of all previous jobs

* Add checking for changes to test requirement

* Revert module changes

* Add fake change to FASTQC

* Test in parallel

* Revert "Add fake change to FASTQC"

This reverts commit f050865cd6260c2e6278bdeaef2cb62f14a91a7e.

* Change logic to allow skipped processes

* Format changes

* Change logic again

* Change logic again

* Change logic again

* Add debug step to help work it out

* Caught pytest-changes bug

* Reintroduce change to FASTQC module

* Remove debug statements

* Revert "Reintroduce change to FASTQC module"

This reverts commit 197ffeb0efdba72ab6c14c6d05dba583874790dd.

* Mess up FASTQC deliberately to test failures

* Revert "Mess up FASTQC deliberately to test failures"

This reverts commit c28fef48f041da12116d008463394c97080c2568.

* Changed to all lower case

---------

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Add seqkit/fx2tab module (#3650)

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* Move conda-checks (third batch) (#3692)

Moving conda-check and replacing exit 1 with error-cmd

* Move conda-checks (second batch) (#3690)

Moving conda-check and replacing exit 1 with error-cmd

Ignoring linting errors due to GHCR - will be fixed later.

* Add snakemake module (#3682)

* snakemake: Add module

* snakemake: Updates to testing and modules.

* Add Snakemake nf-test

* Add tag to snakemake nf-test

* Bump snakemake version

* Update snakemake nf-test with snap

* Select only relevant output channel in snakemake nf-test

* Prettier on nf_test_modules.yml

* Apply suggestions from code review

Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* Apply suggestions from code review

Co-authored-by: Jonathan Manning <jonathan.manning@deeplife.co>

---------

Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: Jonathan Manning <jonathan.manning@deeplife.co>

* ADD MODULE: Famsa guidetree  (#3691)

* famsa_guidetree module: add

* famsa_guidetree module: add

* Modify meta.yaml -> family to id

* Remove white space

* Fix report of famsa version

* Remove trailing whitespace

* Updating multiqc to v1.15 (#3701)

* add stub tests for two stubborn modules (#3702)

* Modify subworkflows to pass new nf-core linting (#3672)

* update subworkflows yaml-schema.json field  to

* fix subworkflows linting

* change all 'modules' section in meta.yml to 'components'

* modify yaml-schema.json to require section 'components' instead of 'modules'

* use nf-core/tools dev version for linting

* Add module mmseqs easysearch (#3699)

* Add module mmseqs easysearch

* Fix trailing whitespace

* Update tests/modules/nf-core/mmseqs/easysearch/nextflow.config

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

* Update modules/nf-core/mmseqs/easysearch/main.nf

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

* Update modules/nf-core/mmseqs/easysearch/main.nf

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

* Update modules/nf-core/mmseqs/easysearch/main.nf

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

* Update modules/nf-core/mmseqs/easysearch/main.nf

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

* Add new line

* Update test

* Update modules/nf-core/mmseqs/easysearch/main.nf

---------

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

* New module: galah (#3666)

* Add galah

* NO DOI

* fix versions

* fix dashing version in conda

* fix inputs/outputs

* fix dashing version

* Update model inputs, add tests

* Update error message.

* Update main.nf

* Update test.yml

* Update main.nf

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

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* Update main.nf

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

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* Update main.nf

* Update test

* Update main.nf

* Update main.nf

* fix tests

---------

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* Move conda-checks (fourth batch) (#3694)

Moving conda-check and replacing exit 1 with error-cmd

Forcing merge because these are existing errors that can't really be fixed in the scope of this PR (@adamrtalbot will take the blame).

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* Update shinyngs, remove na.omit() from proteus (#3707)

* Added log_assays param to shinyngs tests, updated shinyngs containers, removed na.omit() from proteus

* Updated shinyngs containers, added test for plot_exploratory
--log_assays param

* added --log2_assays flag back into nextflow.config

* removed redundant process definition

* prettier, updated proteus tests

* Updating output-prefix for sentieon-bwaindex (#3708)

Updating output-prefix

* Extra parenthesis removed and added stub (#3710)

* Extra parenthesis removed

I noticed while running the module that it produces an extra parenthesis in the version output. This is the cause.

* Added stub

* Add GATK's CreateReadCountPanelOfNormals and DenoiseReadCounts (#3709)

* pon

* denoisereadcounts

* add stub

* update version string

* review suggestions

* Update modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf [skip ci]

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

* Update modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf [skip ci]

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

* Update modules/nf-core/gatk4/denoisereadcounts/main.nf [skip ci]

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

* Update modules/nf-core/gatk4/denoisereadcounts/main.nf

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

---------

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

* Move conda-checks (fifth batch) (#3704)

* Moving conda-check and replacing exit 1 with error-cmd

* Adding keywords to meta-file for katgc

* Adding keywords to meta-file for merquryfk

* test-data was seemingly moved to new subdir

* Fixing outdir of unzipped test-data

* Disabling conda-based test of hlala/preparegraph as that module does not support conda

* Adding extra meta-fields for sentieon/applyvarcal (#3716)

* Adding extra meta-fields for fasta and fai in input section of sentieon/applyvarcal

* Fix typo

* Adding more meta-fields to input

* Adding extra meta-fields for fasta and fai

* Update bclconvert readme (#3646)

Update README.md

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* Add sentieon datametrics (#3715)

* datametrics

* review suggestion

* Add module famsa_align (#3697)

* Add module famsa_align

* remove trailing white space

* Adding extra meta-fields for sentieon/bwamem (#3717)

Adding extra meta-fields for fasta and fai

* Update CONCOCT_CONCOCT process label (#3669)

* change process label

* Fix sklearn conda package

* Update main.nf

* Update containers

---------

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Adding extra meta-fields for sentieon/dedup (#3718)

* Adding extra meta-fields for fasta and fai

* fix copy-paste error

* Update other concoct containers (#3719)

* Add seqkit/tab2fx module (#3712)

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* Add sentieon readwriter (#3721)

* readwriter

* update meta

* Update meta.yml

* Apply suggestions from code review

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

---------

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

* Move conda-checks (sixth batch) (#3713)

* Moving conda-check and replacing exit 1 with error-cmd

* Disabling conda-based pytests for parabricks modules

* Add sentieon dnascope (#3722)

* dnascope

* Update main.nf [skip ci]

* Update meta.yml [skip ci]

* Update modules/nf-core/sentieon/dnascope/main.nf

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

* Update main.nf

---------

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

* Update bcftools stats (#3703)

* Add metas. Add exon and reference input channels

* Add tests

* gzipped exons

* update meta.yml

* Use remote

* Update test.yml

* Update test.yml

* Linting

* fixup: Snakemake meta.yml was incorrect (#3728)

* Move conda-checks (seventh batch) (#3723)

* Moving conda-check and replacing exit 1 with error-cmd

* Adding keywords

* METABAT2: reduced number of mv operations (#3732)

* METABAT2: reduced number of mv operations

- mv operations were causing problems on certain filesystems.
- This commit removes some of the mv operations in favour of using the existing files directly.

* METABAT2: Remove false FASTA files from output channels

* code tidy

* METABAT2: Removed subfolder

* METABAT2: code tidy

---------

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

* update sentieon recipes (#3733)

updates

* Add module: Clustalo guidetree (#3730)

* Add clustalo guidetree module

* Add final new line

* Update modules/nf-core/clustalo/guidetree/main.nf

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>

---------

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>

* Add sentieon dnamodelapply (#3726)

* dnamodelapply

* review suggestion

* update tests

* Update tests/modules/nf-core/sentieon/dnamodelapply/main.nf

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

---------

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

* Add module: Clustalo align (#3734)

* Add modules - test and linting to be fied when guidetree gets merged to main

* Fix tests

* Remove trailing whitespace

* Update modules/nf-core/clustalo/align/main.nf

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/clustalo/align/meta.yml

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Add options tree directly in args

---------

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* GHA use shared singularity cache (#3738)

* Add Singularity cachedir for reducing storage footprint

* Use runner temp directory for reducing storage footprint

* Add default NXF directories for reducing memory footprint

* Replace variable with env because GHA scoping

* Add some fake stuff for triggering tests

* Remove working dir stuff.

* Create singularity dirs

* fixup

* Add more fake testing criteria

* Replace parabricks weird cp stuff with stageInMode directive

* parabricks/fq2bam: Replace copy in parabricks with stageInMode

The parabricks/fq2bam module had hard copies from the previous working dir to the local working directory to remove the affect of symlinks. However, this will fail on a number of cases therefore this commit replaces them with the stageInDirective of Nextflow.

* Revert deepvariant to nf-core image

* Revert "parabricks/fq2bam: Replace copy in parabricks with stageInMode"

This reverts commit f94d97193fd6015de12045358e8ab96647d19f7f.

* Revert "Replace parabricks weird cp stuff with stageInMode directive"

This reverts commit 44ed12ac9a1c6c21241759f8b455798f470fca1f.

* Remove fake stuff from parabricks/fq2bam

* Ignore Singularity cache for uploading output(s)

* Fixup

* Add sentieon wgsmetrics (#3727)

* wgsmetrics

* fix lint error

* typo

* Update modules/nf-core/sentieon/wgsmetrics/main.nf

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

---------

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

* FastK has got a -M option to control the memory usage (#3742)

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* Ashlar (#3551)

* working on ashlar nextflow module outside nf-core template.  Input and output working.

* added default output filename.

* changed output parameter to match ashlar param name and changed output path to allow for both output file types

* added optional input parameter channel

* added most input paramters. working code

* clean-up

* added output-channels parameter

* added support for multiple input files

* added ffp input parameter

* bug fix: should not have had multiple channels

* most of meta.yml filled out. still need the case for *.tif output

* ah, also need to add defaults and optional args to meta.yml

* minimal set of input parameters added to meta.yml for testing; need to set defaults for them

* runs simple test with hard-coded paths

* simple test works with input parameter and no hard-coded paths

* added ashlar main module file

* added test image path to test workflow so you can run with default test command

* added ext.args

* added meta map

* passed test with wildcarded input files

* added test config file

* added functionality to handle optional arguments

* added meta map args

* supposed to output meta map if you input one

* clean-up

* changed test input to a channel

* not running, but close I think

* added some missing files

* basic samplesheet working

* clean-up post testing

* enabled multiple input images

* bug fix: sheet meta arg not an it var

* clean-up

* added samplesheet validation

* samplesheet output to subdirs with sample name; needs clean-up

* cleaned up meta.yml and passed test

* clean-up; passed tests

* moved publishDir to test config as suggested by lint

* removed initOptions; lint says deprecated; tests pass

* multi-file row of test_1 failing, but others work

* passes 3 tests with stable md5 sums

* clean-up and changed back to uuid block zero out instead of while loop; added exception check

* removed test publishDir for sample sheets

* clean-up

* added Dockerfile

* clean-up

* updated to correct DOI

* added zero_uuid.nf

* removed test sample sheet

* changed input type to *.tif to match output type

* removed old test ashlar nextflow module

* Update .nf-core.yml

removed added line from mistaken commit.

* restored formatting in pytest_modules.yml

* added more accurate input pattern

* works with new test images

* added test.yml

* removed unsupported output test and updated input and output patterns in meta; tests pass

* refactored zero_uuid.nf to use input parameter offset; passed test

* added tile size test as discussed in PR

* bug fix: off by one error for second test offset

* clean-up

* simplified zero_uuid.nf

* changed to built-in test files

+ use built-in test files
+ changed input parameter to path from val
+ removed input parameter from nextflow.confg

* removed conda command so runs locally

Sorry, didn't mean to push the last commit.
This one has the changes and runs fine locally.  The previous commit fails because of 'conda "bioconda::ashlar=1.17.0"' in main.nf.  Seems that it fails to build the local conda environment.

* added commented code that causes break

* works in linux with conda so uncommented that section

* added containers and tested all 3 ways of running; all working

* ran prettier

* updated docker container URL

* testing container URL with hash

* switched container to docker.io

* fixed meta.yaml lint errors

* trying CI again with both container hashes

* trying with default container registry

* bug fix: removed extra char output in version.yml

* changed container URL syntax and it works locally; testing with CI

* added conda again to test with CI

* trying container URL without quay.io again

* testing URL with quay.io again

* added singularity; passes local tests

* cleaned-up unused files

* removed meta args

* removed unnecessary Channel.toList from test main

* restored tile test using withName technique for param

* simplified input arg name

* updated module output path and emit

* updated module usage command

* updated licence in meta

* cleaned-up meta.yml

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

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

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

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

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

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

* changed dfp and ffp to optional input channels and tested with no input files

* added dfp ffp test with hard-coded files

* added validation for dfp and ffp

* changed validation for dfp/ffp and added test

* now pulling dfp/ffp from test_data repo

* test_data formatting change

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

moved dfp/ffp validation into script block

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* corrected dfp/ffp error message

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

corrected input name

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

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

made file description more informative

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* finished input name change

* Apply suggestions from code review

nice, I didn't realize it could be referenced like that. Thanks!

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* Update tests/modules/nf-core/ashlar/main.nf

Ah, sure, that makes sense.  I was trying to abstract it away, but I see how it's nice to see it all at once. Thanks!

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* broken change for discussion

* Update tests/modules/nf-core/ashlar/main.nf

Oh! sorry, I see. I missed the `tuple` before `val(meta), path(tif)` when I was testing the change.  I should have realized that!

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* fixed zero_uuid output bug

* Use sed to remove UUID inside main module

* Fixed sed

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

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* proposed change to sed command

* adding modified test.yml file

* reverted to in-place sed

---------

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* Mafft version update (#3745)

* Mafft version bump

* Extra keyword to make `nf-core modules lint` happy

* Updated the tags to match the actual steps of the sub-workflow

* Added the missing config file

* Parabricks use stageInMode to prevent unpredictable file operations while running (#3740)

Replace parabricks weird cp stuff with stageInMode directive

* This MD5 differs between Conda and Singularity (#3746)

* Mmseqs: Documentation fix  #3739 (#3743)

* chore: Documenation fix #3739

* Fixing other mmseqs yml db_outputs

* fix doc tsv2exprofiledb

---------

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

* add bedtools groupby (#3751)

* add bedtools groupby

fixes #3749

* remove unnecessary config parameter

* Add filter_vep (#3750)

* filtervep

* fix lint error

* prettier fix

* Fixed bug raised in issue #3747 (#3748)

* Fix Snakemake output channel (#3754)

* Fix Snakemake test typo

* Remove variable snakemake log

* Fix Snakemake output channels which were a bit messed up

* snakemake: tidy

* CICD: Create Singularity cache dir for nf-test

* snakemake: Add assertAll to nf-test

* Module quast update to meet guidelines again (#3753)

* refactor quast, stub incomplete

* stub complete & succesfull tests

* update meta.yml quast

* include tag

* fix outputs

* (harshil) alignment

* fixing output yml

* spelling in quast yml fix

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

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* implementing suggestions and removing symlinks

* Revert "implementing suggestions and removing symlinks"
but keep suggestions

---------

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* Update test_data.config (#3761)

* Update test_data.config

* Update test_data.config

* update gfaffix to 0.1.5 (#3767)

* update gfaffix 0.1.5

* update MD5SUM

* wrong test file LUL

* whoopsi

* update dumpsoftwareversions (#3768)

update versions

* Add sentieon tnscope (#3760)

* add tnscope

* update config

* update path

* update tuple

* update tuple

* update tuple

* fix cardinality error

* add readgroup

* update test.yml

* update meta

* Update modules/nf-core/sentieon/tnscope/main.nf

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* Update modules/nf-core/sentieon/tnscope/meta.yml [skip ci]

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* add contains to test.yml

* fix error

---------

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* Adding stubs to three Sentieon modules (#3776)

* update smoothxg to v0.7.1 (#3775)

* new module: Pairtools stats (#3631)

* [pairtools/stats] new module

* [pairtools/stats] new module

* [pairtools/stats] update test

* [pairtools/stats] lint

* typo in main file

---------

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* [pairtools/sort] Update memory usage (#3627)

* [pairtools/sort] Update memory usage

* [pairtools/sort] Update memory usage

* update authors' name

* run prettier

---------

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* kallisto: add meta information for references (#3777)

* add meta information for references

* adapt md5sum

* Fix filename check for cellranger count (#3780)

* Fix filename check for cellranger count

* fix editorconfig

* Escape regex for nextflow

* Stitch (#3766)

* stitch module yaml

* stitch

* status

* test path

* test path

* stitch seed

* stitch seed

* stitch seed

* stitch seed

* stitch seed

* stitch seed

* stitch test refactoring

* more tests

* more tests

* more tests

* more tests

* more tests

* more tests

* more tests

* more tests

* more tests

* more tests

* more tests

* more tests

* more tests

* more tests

* more tests

* more tests

* more tests

* more tests

* check if bam

* check if bam

* check if bam

* check if bam

* check if bam

* label to medium

* plot hashes removed

* STAR: update (#3771)

* add meta information for references

* prettier

* update containers

* add meta information in output

* update md5sums

* first fixes to FASTQ_ALIGN_STAR

* remove maps from tests

* adapt md5sum

* fix tests

* fix tests

* fix tests

* update containers

* fix tests

* wait for updating star until biocontainer is updated with 2.7.11

* adapt md5sum

* remove moot file

* restore versions printout for samtools and gawk

* Update modules/nf-core/star/align/meta.yml

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>

---------

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>

* update arriba to 2.4.0 and add meta info to references (#3770)

* update arriba to 2.4.0 and add meta info to references

* add extra keyworkd

* change test channels

* add missing bracket

* add meta in empty reference test

* adapt md5sums

* qualimap/rnaseq: add meta information for references (#3779)

* add meta information for references

* add test

* rename test bamqc to bamqccram

* use homo_sapiens instead of sars-cov2 data for rnaseq test

* fixes to tests

* fix include path

* fix path to star modules

* update args

* adapt test files check

* add fake md5sums

* correct md5sum

* fix naming

* remove md5sums

* Update taxpasta 0.5.0 (#3782)

* New module: star/starsolo (#3772)

* Adding STARSolo module

* Correcting test

* Fix linting

* Gzping matrix output

* Removing TODO

* Adding info meta for inputs

* Adding index meta for test

* Fix tuple call

* Fix input call

* Changing to switch logic

* Try ; and remove adding string

* Remove helper function

* Fix whitelist call

* Update modules/nf-core/star/starsolo/meta.yml

Co-authored-by: Jonathan Manning <jonathan.manning@healx.io>

* Fix test since genomegenerate was changed

* Fix indes call

---------

Co-authored-by: Ubuntu <ubuntu@ip-172-31-21-139.ec2.internal>
Co-authored-by: Jonathan Manning <jonathan.manning@healx.io>

* Update bakta to v1.8.2 (#3784)

* New module: umitools/group (#3765)

* init umitools/group

* remove todo's umitools/group

* fix prettier

* remove redundant variables stub

* Update amrfinderplus (#3787)

Update amrfinderplus to 3.11.18

* ci: Switch to setup-nextflow (#3795)

* Update SAMTOOLS_DEPTH (#3801)

* Add intervals input channel for SAMTOOLS_DEPTH
Now intervals can be passed to this module.

* Change test data and minor changes

* Add workflow test_samtools_depth (with no intervals file provided)

* BUSCO: additional outputs (#3289)

* additional outputs

* Updated the patterns to be just the filenames

* Complete list of output directories

* Updated the module documentation

* [lint] must be "directory"

---------

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

* Added support for multiple regions and added per-site r^2 optional output (#3793)

* Added support for multiple regions and added per-site r^2 optional output

I added the optional output that is produced when using the flag --out_r2_per_site and modified the code for producing input.txt so that it can also be run in multiple chromosomes by providing a list of regions as input in val(region). This still allows for a single input.

Running on multiple regions is important to calculate aggregated MAF bin metrics for the whole genome for example.

* reflect changes in meta.yml

* added tests

* Removed space in excess

---------

Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com>

* Update sentieon dnascope (#3790)

* Updating Sentieon Dnascope module to facilitate both vcf and gvcf output from one invocation

* Remove nonconformant tags

* Updating meta.yml for SENTIEON_DNASCOPE

* Update modules/nf-core/sentieon/dnascope/main.nf

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>

* Update modules/nf-core/sentieon/dnascope/main.nf

---------

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>

* bump wfmash to v0.10.5 (#3806)

* bump odgi modules to v0.8.3 (#3805)

* bump odgi modules v0.8.3

* fix linting error

* fix galaxy container

* Re-structure nf-test test files (#3807)

* Re-structure nf-test test files

Changes:
 - Move nf-test files to the same directory as the tool (modules/nf-core/tool/subtool/main.nf.test{,.snap})
 - Will reduce need for separate test folder
 - Automatically imported with module into pipeline by nf-core/tools

* nf-test reduce testing surface

* Add subfolder tests/ to nf-test modules

* sentieon/dnascope : Handling args  (#3811)

Adding space characters around args string

* Update lofreq call & lofreq callparallel modules (#3812)

* Update lofreq call module & tests.
Now it takes intervals input.

* Update lofreq callparallel module.
Now it takes intervals as input. Also updated tests.

* Fix linting where entry for keywords was too short in meta.yml.

* Add mitohifi/mitohifi module (#3573)

* Add mitohifi module

* Lint and add a note in pytest_modules

* Fix prettier checks

* Fix spelling

* Fix data references

* Make a note not to use conda

* Change md5 values

* Remove extra file

* Fix code according to code review

* ECLint check fix

* Extend description of the output

* Fix md5 hash for output

* Fix prettier

* Fix conda checks

* Undo changes before merge

* Skip conda test on gihub

* Update md5sums

---------

Co-authored-by: Ksenia Krasheninnikova <kk16@sanger.ac.uk>
Co-authored-by: Priyanka Surana <ps22@sanger.ac.uk>

* Added new module csvtk/join (#3706)

* Added new module csvtk/join

* removed in_format and out_format input channels for process csvtk/join and replaced logic for specifying delimiters and output extension

* Add out_extension for stub mode

---------

Co-authored-by: Anne Marie Noronha <anoronh4@users.noreply.github.com>

* update GATK's annotateintervals and filterintervals, and CNVkit's batch with extra meta fields (#3813)

* update annotateintervals

* update filterintervals

* update batch

* Update meta.yml

* Update meta.yml

* update GTDB-tk to 2.3.2 (#3791)

* update GTDB-tk to 2.3.2

* update db version in stub

* update prefix

* chore: prettified

* emit meta map

* Update modules/nf-core/gtdbtk/classifywf/main.nf

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

* Update tests/modules/nf-core/gtdbtk/classifywf/main.nf

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

* Update tests/modules/nf-core/gtdbtk/classifywf/main.nf

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

* Update modules/nf-core/gtdbtk/classifywf/meta.yml

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

* Update modules/nf-core/gtdbtk/classifywf/meta.yml

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

* Update tests/modules/nf-core/gtdbtk/classifywf/main.nf

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

---------

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

* Make fasta_align_bwa explicitly note that the fasta channel requires a meta (#3818)

* Fix version string spurious text in singularity tests

* Explicitly state that the fasta channel must have a meta

* Update bamcmp (#3803)

* Fix version string spurious text in singularity tests

* Change input/output names and warn about collisions

* Fix tests

* Change to prefix and prefix2

* Update main.nf

Add stub

* Update main.nf

Line commas up

* update germlinecnvcaller (#3820)

update gcnvcaller

* add kalign (#3825)

* add kalign

* Fix linting check

* fix small prettier/linting issues

* fix small prettier/linting issues

* Update modules/nf-core/kalign/align/meta.yml

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/kalign/align/main.nf

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

---------

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Update stub and relevant tests for gatk's germlinecnvcaller (#3824)

* update gcnvcaller

* add stub

* Update NGSCheckMate/ncm (#3827)

* Update NGSCheckMate/ncm

* Add stub and prettier

* Remove tests for pdf files

* Fix using meta2 as the combined vcf meta

* Update default output prefix

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

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

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

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

* Update tests

* Update module tests too

---------

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

* Update taxpasta version to 0.6.0 (#3830)

Update taxpasta into version 0.6.0

* Setting temp-dir for BCFTOOLS_SORT (#3832)

* Setting temp-dir

* Updating md5sum on sorted output vcf

* Picard modules: Include check input-ouput naming convention  (#3823)

* Adding error and prefixes

* Passing tests

* fix picard/markdupl

* adding stub runs and stub tests

* adorreplace groups stub naming check

* pass tests

---------

Co-authored-by: Joon-Klaps <joon.klaps@gmail.com>

* Add prefix to bwa/index (#3835)

* new module picard/scatterintervalsbyns

* update annotsv to 3.3.6

* update installannotations

* add prefix to bwa/index

* add prefix to bwamem2/index

* revert bwa output change

* Update the biocontainer link (#3836)

update the biocontain link

* fix empty channel assignment in FASTQ_TRIM_FASTP_FASTQC subworkflow (#3815)

fix empty channel assignment

* bump shinyngs (#3834)

* update version controlfreec (#3842)

update version

* FIX: Disable JVM hotspot in gatk4 modules (#3844)

* FIX: disable JVM hotspot in gatk4 modules

* improve gatk4/*/meta.yml

* fix typos

\\ not //
:facepalm:

Co-authored-by: Pontus Freyhult <pontus_github@soua.net>

* fix ling

* fix channels

* fix tests

* fix checksums

---------

Co-authored-by: Pontus Freyhult <pontus_github@soua.net>

* Expansionhunter 5.0.0 (#3845)

* new module picard/scatterintervalsbyns

* update annotsv to 3.3.6

* update installannotations

* Update expansionhunter to v5.0.0

* Seqtk seq 1.4 (#3846)

* Upgrade seqtk container to 1.4

* Add 'filter' as keyword to seqtk/seq

* Add 'transformation' to meta.yml

* Ngscheckmate fastq (#3838)

* Fix version string spurious text in singularity tests

* Initial pass

* Working ngscheckmate fastq with v1.0.1 container

* start on including pattern generation too

* Add pattern generator

* v1.0.1

* Start of vaffastq

* Sync to ncm from master

* vaffastq

* Lint and update meta.ymls

* Update tests

* Remove pt file

* Change vcffastq to vcfncm to match the command

* Add subworkflow

* Update tests

* Rename to vcfncm

* Update modules/nf-core/ngscheckmate/vafncm/meta.yml

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* Update subworkflows/nf-core/fastq_ngscheckmate/main.nf

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* Update subworkflows/nf-core/fastq_ngscheckmate/main.nf

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* Apply code review comments

* Finish the swap to meta from meta1

* Remove md5sum for pt file

* Stop using single_end

* Test size of reads is 2

---------

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* Learnmsa align (#3849)

* Add module LearnMSA

* Fix test

* Fix versioning

* Change test set

* Fix test

* fix test

* Pretty fixes

* fix version

* fix test

* Fix testing

* fix test

* Update modules/modules/nf-core/learnmsa/align/main.nf

Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* Update modules/modules/nf-core/learnmsa/align/main.nf

Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* Remove extra files

* Update modules/nf-core/learnmsa/align/main.nf

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

* Remove extra meta

---------

Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>

* Add INITIALISE subworkflow for starting nf-core pipelines (#3847)

* Add INITIALISE subworkflow for starting nf-core pipelines

* Add test for --version and --help

* Add parameter validation to INITIALISE subworkflow

* [automated] Fix linting with Prettier

* Check for stdout contents to confirm pipeline works. Adds test manifest for better checking

* Move version above other command options

* Remove containerEngine from basic initialise run

---------

Co-authored-by: nf-core-bot <core@nf-co.re>

* Flip order of operations in intialise so --help doesn't error if --input isn't provided (#3850)

* Flip order of operations in intialise so --help doesn't error if --input isn't provided

* Add citation before help again

* INITIALISE uses take and emit (#3852)

* INTIALISE suboworkflow uses take and emit for better modularity

Changes:
 - INTIALISE subworkflow now uses a take to determine what to do
 - Use of take makes it work more portable (i.e. use your own params values!)
 - Emits the parameter summary map

* prettier

* INITIALISE meta.yml updated

* eclint

* BRACKEN_BRACKEN: add extra missing output file (#3853)

* Bump taxpasta version (biocontainer not yet available)

* Add extra output to bracken

* New module: GEM3 (#3837)

* Initial files for gem3-indexer

* Fill template files

* Tests ok

* Lint tests ok

* Update main.nf

* Update modules/nf-core/gem3/gem3indexer/main.nf

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

* Update modules/nf-core/gem3/gem3indexer/main.nf

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

* Update modules/nf-core/gem3/gem3indexer/meta.yml

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

* Update modules/nf-core/gem3/gem3indexer/meta.yml

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

* Update main.nf

---------

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

* Fix initialise linting (#3860)

* allow empty component arrays

* fix linting errors

* add linting for subworkflows to ci (#3861)

* remove 'subworkflows/' prefix in linting command (#3863)

* Add license to cellranger count renaming script.  (#3862)

* Update cellranger_count.py

* Update cellranger_count.py

* Fix output for bcl2fastq & bclconvert (#3796)

* Fix output for bcl2fastq & bclconvert

Fixes #3794

* Add todo about using new test dataset when available

---------

Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>

* fix variable name (#3866)

* add linting for subworkflows to ci

* fix variable name

* add new module for conifer (#3763)

* add new module for conifer

* fixing CI

* fix test

* Update main.nf

---------

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>

* Add samtools reheader (#3869)

* Add samtools reheader

* Update test

* Add yml header

* Update version emission

* Add build number to conda

* Change config and delete md5sum

* Correct test name in yml

* FIX: remove spaces in controlfreec modules (#3870)

remove unnecessary/wrong spaces in controlfreec modules containers declaration

* update KrakenUniq version to the latest (#3873)

* update the version from 1.0.2 to 1.0.4

* change ram_chunk_size type into string

* Add missing output to linting CI (#3877)

* add linting for subworkflows to ci

* fix variable name

* fix output

* Tcoffee align (#3855)

* Add tcoffee align module

* Add tcoffee align

* Linting fixes

* Fix linting issues

* Add right tests

* fixes

* test version

* change test

* Update tests

* update tests

* Update md5 tests

* Update test

* Prettier fixes

* add usage of tree and external information if passed

* Fix flags for input tree and template

---------

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

* Add linting ci (#3878)

* add linting for subworkflows to ci

* fix variable name

* fix output

* try underscore

* undo accidental deletion

* Fix linting ci (#3882)

* add linting for subworkflows to ci

* fix variable name

* fix output

* try underscore

* undo accidental deletion

* use echo

* Fix typo (#3880)

* New module: quilt/quilt (#3804)

* first commit

* fix tests

* add doi

* fix alignment and case convention

* update module with cli

* add warning

* remove warning

* remove md5sum for png

* update to v1.0.5

* reorder inputs to match main.nf, remove some to ext.args

* reorder inputs, remove ngen buffer seed to ext.args

* add commands for optional files

* add default seed if not provided

* buffer and ngen back to val channels

* Add NONPAREIL (#3885)

* Bump taxpasta version (biocontainer not yet available)

* Add nonpareil

* Remove TODO

* Fix version

* Fix Version

* Fix indent

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

Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

---------

Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* Blastp (#3888)

* init blastp

* blastp versions output fix

* removed custom blastp extension

* Blast (#3889)

* blast suite container version update + stubs

* tests updated and reformatted

* CUSTOM/MATRIXFILTER - NA handling (#3868)

* Added log_assays param to shinyngs tests, updated shinyngs containers, removed na.omit() from proteus

* Updated shinyngs containers, added test for plot_exploratory
--log_assays param

* added --log2_assays flag back into nextflow.config

* removed redundant process definition

* prettier, updated proteus tests

* Added na.rm to matrixfilter

* Made params more uniform, updated meta.yml and main.nf

* Bugfix, added tests

* linting

* Combined rejection files into one file

* Updated test file path

* Propose more generic framework for matrixfilter

* Update output definitition

* Fix bool output

* Update tests

* appease eclint

---------

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

* Add config option to manta modules (#3890)

* new module picard/scatterintervalsbyns

* update annotsv to 3.3.6

* update installannotations

* add config to manta modules

* fix mv somatic

* add config tests

* Update main.nf to include stub (#3876)

* Update main.nf to include stub

Adding the stub for SeqKit Sliding

* Review fix

* add GITHUB_TOKEN and use it for paths-filter instead of the default github.token (#3891)

* Fix variable typo in amrfinderplus/run (#3892)

Fix variable typo in amrfinderplus

* Bamcmp sw (#3802)

* Fix version string spurious text in singularity tests

* Add Subworkflow for bwa followed by bamcmp

* Update test.yml

Remove tests for bwa index files

* Update subworkflows/nf-core/fastq_align_bamcmp_bwa/main.nf

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

* Remove sort_bam and add meta

* Add prefix to subworkflow test

* Remove todo

* Remove md5sums for bam files for conda

* Update main.nf

* fix variable resolution

---------

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Co-authored-by: Simon Pearce <{ID}+{username}@users.noreply.github.com>
Co-authored-by: mashehu <mashehu3@gmail.com>
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

* Vcf impute glimpse multiple input bug correction (#3875)

* Correct bug from vcf_impute_glimpse. Correctly use the meta map to aggregate channels

* Test for multiple sample, regions and reference panel

* Simplify version mixing

* Update test vcf_impute_glimpse and channel usage

* Modules stub (#3883)

* Add bcftools index stub

* Add glimpse chunk stub

* Add glimpse concordance stub

* Add glimpse ligate stub

* Add glimpse phase stub

* Add glimpse sample stub

* Add glimpse2 chunk stub

* Add glimpse2 concordance and ligatestub

* Add glimpse2 phase stub

* Add glimpse2 split_reference stub

* Add shapeit5 ligate stub

* Add shapeit5 phase_common stub

* Add shapeit5 phase_rare stub

* Add shapeit5 switch stub

* Add keywords shapeit5 switch

* Remove md5sum from glimpse concordance

* Change output name without :

* Delete all intermediary files from stub section

* Change vcf phase shapit5 test

* Remove md5sum from bcftools index testing

* Remove md5sum from vcf phasing shapeit5 testing

---------

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.c…

* New module for the cram-size command of samtools.

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

Adding name of the tool

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

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

Adding prefix to make the module set up more flexible.

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

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

Changing `.baseName` by `prefix` in output names.

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

* Stub added to the main.nf script.

* Adding generated test.yml file.

* Adding pytest.

* Adding a new nf-core module called plasflow.

* Update manta modules (#3615)

* Update manta somatic

* Update manta tumoronly

* add varlociraptor call subcommand (#3529)

* 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>

* add new module iCount-mini/metagene (#3612)

* add module template

* first version

* update testing and linting

* update file naming

* update test

* fix test

* Newmodule ngmerge (#3626)

* 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

* NEW MODULE: PURECLIP (#3624)

* 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

* fix integer overflow (#3620)

Co-authored-by: Steven Strong <steven.strong@adelabio.com>

* Fix metaeuk_easypredict when using mmseqs database (#3525)

Fix metaeuk and add tests

* 3630 add unstitched reads as emitted output of ngmerge (#3632)

* add -f option

* update tests

* Update vardictjava (#3633)

* new module picard/scatterintervalsbyns

* update annotsv to 3.3.6

* update installannotations

* update vardictjava

* Adding modules from #scrnaseq for simpleaf (#3619)

* 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>

* update icount mini version (#3640)

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)

* Bump taxpasta version (biocontainer not yet available) (#3639)

* Purecn/run (#3140)

* 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

* new module: samtools/import (#3642)

* new module: samtools/import

* fix versions

* fix versions some more

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

* fix meta

* Adding seqkit sliding command (#3637)

* 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>

* Hicexplorer hicpca (#2933)

* 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>

* Fix bug in pyrodigal module (#3643)

Add "--force" to pigz

* Update gecco/run (#3652)

Version bump to 0.9.8

* New module: instrain/compare (#3623)

* Started instrain compare tests

* instrain compare

* Update modules/nf-core/instrain/compare/main.nf

* Update modules/nf-core/instrain/compare/main.nf

* Update modules/nf-core/instrain/compare/main.nf

* Updated test.yml and added stub

* Update modules/nf-core/instrain/compare/main.nf

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

* Update meta.yml to include meta2

* Updated test.yml output files

* Changed md5 to content for several test.yml files

* changed content to contains

* Added another contains option in test.yml

* shortened contains string to pass prettier check

---------

Co-authored-by: Margot Lavitt <margotl9@n3065.hyak.local>
Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

* Update LAST modules to v1453 (#3303)

* Update LAST to version 1453.

* update lastdb version to 1453

* update last mafconvert to 1453

* update last mafswap to 1453

* update postmask to last v1453

* update last split to v1453

* last update train to v1453

* Update meta.yml

Change output value type to string

* Update meta.yml

Change output value type to string

---------

Co-authored-by: Charles Plessy <charles.plessy@oist.jp>
Co-authored-by: Charlotte Capitanchik <charlotte.capitanchik@crick.ac.uk>
Co-authored-by: Johannes Nicolaus Wibisana <johannes.nicolaus@oist.jp>
Co-authored-by: Charlotte Capitanchik <CharlotteAnne@users.noreply.github.com>

* Hisat2-build: index construction w/ truly optional inputs  (#3649)

* index construction mode dependent on optional inputs rather than memory availability

* added tests for new functionality

* updated tests to use appropriate test data

* cleaned up test.yml to only contain BUILD outputs

* removed unnecessary extract ss call

* added : to empty metamaps. Reverted to sarscov2 test files

---------

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

* update metaphlan module (#3661)

* CNVKit 0.9.10 update (#3651)

* upgrade CNVkit to 0.9.10

* homogenise keywords of all CNVkit modules

* Add samtools dependency to bam2seqz module of sequenzautils

Without specifying the dependency to a more or less current version of samtools, conda solves the environment for sequenza by using a very old samtools version that can cause problems when processing subsampled files (automated tests)

* Update cnvkit to 0.9.10

Changes:
 - Update cnvkit to 0.9.10
 - Update samtools in cnvkit modules to 1.17

Based on #3545 authored by @priesgo.

* cnvkit 0.9.10 test update

* update checksums of output files in tests for CNVkit batch

* Update cnvkit/export VCF test

* Additional tags for sequenzautils

---------

Co-authored-by: Pablo Riesgo-Ferreiro <priesgoferreiro@gmail.com>
Co-authored-by: Julian Mohr <81371922+JulianMohr@users.noreply.github.com>

* Update gatk3 modules (#3660)

* update mapdage2 module

* Add meta for all files in gatk modules

* Update tiddit to v3.6.1 (#3663)

* Update stubs for samtools flagstat (#3657)

Update stubs

Co-authored-by: Ram Nanduri <ram@MTLUCMDS1.lund.skane.se>

* R differential modules control over output prefixes (#3664)

* R differential modules control over output prefixes

* Set differential module prefixes

* Actually we need to do prefix handling within the template

* Set differential module prefixes

* Fix test files for new prefix specification

* Add meta to limma test

* Fix DESeq2 tests

* fix remaining tests for limma

* Update grep to fix broken solve

* Try bumping affy

* Use new build

* update md5sum for annotation

* Update stubs for samtools idxstats (#3665)

* Update stubs

* Update stubs for samtools idxstats

---------

Co-authored-by: Ram Nanduri <ram@MTLUCMDS1.lund.skane.se>

* Bump ensembl-vep modules to 110.0 (#3658)

* bump ensembl-vep to 110.0

* update tests

* put conda tests back

* update config for ENSEMBLVEP_DOWNLOAD

* update tests for related subworkflows

* fix path to module

* enable conda tests back

* better tests

* fix tests

* nicer channels

* fix channel queue to value

* fix syntax

* Remove containers with cache with snpEff too (#3670)

* update tests for snpeff

* remove containers in config

* fix cache version in tests

* update meta.yml

* fix meta.yml

* fix meta data

* fix md5sum

* re-enable conda tests

* Update stubs for bwa mem (#3671)

Co-authored-by: Ram Nanduri <ram@MTLUCMDS1.lund.skane.se>

* Additional optional output to homer/annotatepeaks  (#3667)

* add optional stats output for use with the -annStats parameter (to be provided with ext.args)

* Update meta.yml

* add additional stats output to annotatepeaks test

---------

Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>

* Hisat2 align splicesitesoptional (#3656)

* added align tests for splicesitesoptional

* changes to homo sap

* updated splice sites to be optional with tests

* Fix invalid GATK container (#3673)

Fix GATK container which was invalid

Fixes #3668

* Update: bamtools, gstama, ultra (#3655)

* Update Bamtools [2.5.1 -> 2.5.2]

* Update gstama/merge [1.0.2 -> 1.0.3]

* Update ultra [0.0.4.2 -> 0.1]

* Update ultra/index|align|pipeline tests

replace gffread by gnu/sort

* Irregular md5sum for database.db

* Update bamtools/convert test.yml

* Fix centrifuge: reduce number of input channels (#3674)

* Bump taxpasta version (biocontainer not yet available)

* Remove unnecessary (and sometimes problematic) input channel

* Improve output glob for optional alignments

* Remove now unnecessary variable from command

* linting

* Add missing args

* Remove unused ublast module

* Checking tests that were failing from the samtools/cramsize module.

* Writing some errors.

* Checking failed test of the samtools/cram-size module.

* Checking failed test on yml file.

* Fixing test.yml file.

* Fixing test.yml from plasflow module.

* Removing trailing whitespaces from files.

* Fixing test.yml from plasflow module.

* Removing Plasflow from conda. It doesn't work.

* Running prettier on test.yml from plasflow.

* Details of the conda environment.

* Adding specific Tensorflow version for Plasflow.

* Adding channel for python 3.5

* Fixing the channel for python 3.5 for plasflow module.

* Changing the channel for python 3.5 (to conda-forge) for plasflow module.

* Update cramsize

* Excluse cramsize from pytest

* Remove plasflow

* Update and fix linting

* Update modules/nf-core/samtools/cramsize/tests/main.nf.test

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

* Update modules/nf-core/samtools/cramsize/tests/main.nf.test

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

---------

Co-authored-by: limrp <limrod.15@gmail.com>
Co-authored-by: limrp <119093929+limrp@users.noreply.github.com>
Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: Maxime U Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Charlotte Capitanchik <CharlotteAnne@users.noreply.github.com>
Co-authored-by: Steven Strong <sstrong99@users.noreply.github.com>
Co-authored-by: Steven Strong <steven.strong@adelabio.com>
Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com>
Co-authored-by: Jonathan Manning <jonathan.manning@healx.io>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Aldo Sergi <50989854+aldosr@users.noreply.github.com>
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Co-authored-by: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com>
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
Co-authored-by: JIANHONG OU <jianhong@users.noreply.github.com>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com>
Co-authored-by: Carson J Miller <68351153+CarsonJM@users.noreply.github.com>
Co-authored-by: Margot Lavitt <margotl9@n3065.hyak.local>
Co-authored-by: Johannes Nicolaus Wibisana <johannes.nicolaus@gmail.com>
Co-authored-by: Charles Plessy <charles.plessy@oist.jp>
Co-authored-by: Charlotte Capitanchik <charlotte.capitanchik@crick.ac.uk>
Co-authored-by: Johannes Nicolaus Wibisana <johannes.nicolaus@oist.jp>
Co-authored-by: Jack Tierney <43453737+JackCurragh@users.noreply.github.com>
Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>
Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Co-authored-by: Pablo Riesgo-Ferreiro <priesgoferreiro@gmail.com>
Co-authored-by: Julian Mohr <81371922+JulianMohr@users.noreply.github.com>
Co-authored-by: Thiseas C. Lamnidis <thisseass@gmail.com>
Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com>
Co-authored-by: Ram Sai Nanduri <sai.rama7412@gmail.com>
Co-authored-by: Ram Nanduri <ram@MTLUCMDS1.lund.skane.se>
Co-authored-by: Laura Blum <laura.blum.n@gmail.com>
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>