Commit graph

3213 commits

Author SHA1 Message Date
Harshil Patel
589f39c39e
Add manual version definition for artic modules (#1867) 2022-07-12 11:33:51 +01:00
Erik Danielsson
49366ef275
Add CITATION.cff file for the nf-core publication (#1865)
* Add CITATION.cff file for nf-core publication

* Update .editorconfig .cff files
2022-07-12 10:15:32 +02:00
WackerO
b2a8464e3e
This updates the fgbio container version (#1863)
* This updates the fgbio container version

* Also updated conda install command
2022-07-11 16:17:54 +02:00
Björn Langer
b5facb2db2
Ataqv mkarv (#1857)
* first draft

* fix test run

* Apply suggestions from code review

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

* Update tests/modules/ataqv/mkarv/test.yml

* Update tests/modules/ataqv/mkarv/test.yml

* Update tests/modules/ataqv/mkarv/test.yml

* Update tests/modules/ataqv/mkarv/test.yml

* Update tests/modules/ataqv/mkarv/test.yml

* Update modules/ataqv/mkarv/nextflow.config

* Delete nextflow.config

* Update tests/modules/ataqv/mkarv/test.yml

* fix linting

* fix linting

Co-authored-by: bjlang <>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2022-07-07 22:40:31 +02:00
Jose Espinosa-Carrasco
0825fff505
Bump ataqv version (#1860)
* Bump ataqv version

* Remove check for empty file
2022-07-07 16:39:54 +01:00
Harshil Patel
682f789f93
Bump tool versions for modules required in viralrecon (#1859)
* Bump tool versions for modules required in viralrecon

* Fix all the tests

* Fix Prettier lint

* Remove empty md5sums
2022-07-07 14:48:04 +01:00
Sébastien Guizard
2f1eca7467
Adjust requested ressources for gstama/merge, isoseq3/refine, lima, ultra/align (#1858)
Reduce requested resources
2022-07-07 11:10:18 +01:00
James A. Fellows Yates
b02e648c22
Add MOTUS/MERGE (#1734)
* Add motus/merge module, missing test yml

* Fix prefix

* Fix polymersase

* Update test meta.yml

* Try new version system

* Typo fix

* Clairfy docs for the version file

* Switch to directory auto detection

* Now with the change and not just meta

* Remove now unneeded input parameter from test

* Fix input type check

* Try adding db requirement to fix docker issue

* Update modules/motus/merge/main.nf

* Fix input

* Apply suggestions from code review

* Fix md5sums

* Replace debugging db location with actual

* Fix contains due to further varialbility

* Indenting
2022-07-07 09:47:41 +02:00
Adam Talbot
43d05d5482
fix (1852): picard/collectmultiplemetrics supports CRAM (#1853)
* fix (1852): picard/collectmultiplemetrics supports CRAM

Changes:
 - Add .fai input to Picard CollectMultipleMetrics
 - Now supports CRAM effectively.
 - Will break existing pipelines!

Fixes #1852

* 1852 Update meta.yml to include .fai
2022-07-06 19:05:53 +02:00
Aleksei Korzhenkov
848ee9a215
Improve descriptions for modules with missing
Description and keywords

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-07-06 12:03:08 +02:00
Alexander Peltzer
5138acca09
Fix MultiQC conda (#1856) 2022-07-06 10:16:34 +02:00
Sima Rahimi
16536b6936
removed extra ) in the version strings (#1850) 2022-07-05 15:24:08 +02:00
Alexander Peltzer
ed5594bee3
Bump version of kallistobustools/count (#1834)
* Bump version of kallistobustools/count

* Trying to update the entire call of kbtools for scrnaseq

* Improved tests for kallistobustools/count

* Add memory, remove workflow as this is passed as args now

* Update modules/kallistobustools/count/main.nf

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

* adding missing value

* workflow properly chained together

* changing --workflow to ext.args

* fix intron channel

* fixed checking whether filename is empty or not

* bump indentation

* fixed if else

* Fix linting

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Felipe Marques de Almeida <almeidafmarques@gmail.com>
2022-07-05 13:28:57 +02:00
James A. Fellows Yates
aed45dd766
Add MultiVCFAnalyzer (#1845)
* Add MultiVCFAnalyzer

* Fix versions

* Fix tests due to md5sum var

* Apply suggestions from code review

* Linting

* Apply suggestions from code review

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

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-07-05 09:47:10 +02:00
James A. Fellows Yates
6702d2e145
Add MEGAN/DAA2INFO (#1848)
* Add daa2info

* Add right flag in the config

* Fix config

* Apply suggestions from code review

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

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2022-07-05 09:36:22 +02:00
Jose Espinosa-Carrasco
fa37e06626
Add stub run to gunzip module (#1849) 2022-07-04 17:33:55 +02:00
Jasmin F
92c420e7d0
Prokka: Fix typo in variable name (#1846)
Fix typo in variable name
2022-07-04 15:04:59 +02:00
Sébastien Guizard
60c65fb386
New modules: ultra/index and ultra/align (#1830)
* Add ultra/index and ultra/align modules

* Correct tag and prefix

* Fix typos

* Remove SAMTOOLS SORT from test

* Update: Convert sam to bam

* Add tag to docker image

* Fix typo

* Add args2 for samtools
2022-07-04 07:46:49 +01:00
James A. Fellows Yates
0e9fd9370a
Fix Krona ktimporttaxonomy to allow multiple input files and simplifies database input (#1841)
* Remove quotes around input reports variable for ktImportTaxonomy as prevents supplying multiple files

* Add using prefix for output files

* Tweak meta reflecting more flexible input database specification

* Linting

* Fix finding the correct directory

* Update main.nf

* Fix database inport

* Prettier
2022-07-01 15:18:29 +02:00
James A. Fellows Yates
7d0ddbc8ab
Add atlas/call (#1809)
* Add atlas/call

* Apply suggestions from code review

* Update modules/atlas/call/main.nf

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

* Apply suggestions from code review

Co-authored-by: Thiseas C. Lamnidis <thisseass@gmail.com>
2022-07-01 15:06:07 +02:00
louperelo
057a889d3b
new module hamronization/rgi (#1844)
* new module hamronization/rgi

* remove comments

* Update modules/hamronization/rgi/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-07-01 12:03:08 +02:00
Jasmin F
b3acfc54f5
antismashlite: Support GBK input (#1840)
* Support non-GFF input

* Apply suggestions from code review

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

* Fix linting error

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-07-01 09:29:53 +02:00
Harshil Patel
b96066565a
Add ffq module (#1842) 2022-07-01 08:59:13 +02:00
Júlia Mir Pedrol
bd0fa881f6
Add new module: Flye (#1164)
* changing mv by gzip

* changing mv by gzip

* first module creation

* add test.yml

* add flye to pyestes_modules.yml

* update flye module

* delete functions.nf

* generate test.yml

* fix contains from test.yml

* test file assembly_info.txt with regex

* check that file contains at least contig_1

* fix typo in contains

* update version

* split fastq file for raw runs

* use asm-coverage to reduce memory usage

* fix module name error

* add genome-size

* decrease coverage

* change test data for raw runs

* add coverage and genome size

* Apply comments from code review

Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com>

* after many trys, add a stub run

* remove md5sum for stub run

* Apply suggestions from code review

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

* fix review comments

* Apply suggestions from code review

Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com>

* no hardcoded version in stub run

* Update modules/flye/main.nf

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

Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
2022-06-30 22:45:55 +02:00
Matt Olm
031fbd37aa
Instrain profile (#1822)
* add instrain profile

* module instrain/profile

* add instrain profile

* module instrain/profile

* instrain profile

* Update modules/instrain/profile/main.nf

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

* Update modules/instrain/profile/meta.yml

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

* Update modules/instrain/profile/meta.yml

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

* Update modules/instrain/profile/meta.yml

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

* Update modules/instrain/profile/main.nf

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

* Update modules/instrain/profile/main.nf

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

* Update modules/instrain/profile/main.nf

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

* update

* linting

* Apply suggestions from code review

* Update modules/instrain/profile/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-06-30 18:44:41 +02:00
Simon Pearce
d6102dab6d
NGSCheckMate doesn't generate a pdf for only one sample, made optional output (#1839)
NGSCheckMate doesn't generate a pdf if only one sample is included, made optional

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-06-30 17:43:34 +01:00
Simon Pearce
a363c12d71
Set randomseed for UMI tools if not otherwise set (#1837)
Set randomseed if not otherwise set

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
2022-06-30 16:30:38 +01:00
Jose Espinosa-Carrasco
82fdff4fb4
Add khmer unique-kmers.py module (#1838) 2022-06-30 16:23:30 +01:00
Matthias De Smet
44baf85bcc
snapaligner: improve index detection (#1836)
* improve index detection

* fix escaping
2022-06-30 12:19:46 +02:00
Matthias De Smet
253f8c1b0e
snapaligner: fix quotes (#1835)
Fix quotes
2022-06-30 11:15:15 +02:00
James A. Fellows Yates
486eebfd29
Update RGI: add database version reporting to module (#1824)
* Add rgi database version to module as fixed within the container/environment

* Remove check of the version file

* Or rather check for existance of the versions file not contents

* Delete main.nf

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-06-29 16:30:51 -06:00
Mahesh Binzer-Panchal
b67556e29f
Add FastK/Merge (#1828)
* Add FastK/Merge

* Update modules/fastk/merge/main.nf

* Update modules/fastk/merge/meta.yml

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
2022-06-29 18:04:36 +02:00
Annick Renevey
80746895e2
Update Arriba to 2.3.0 (#1827)
* update test files md5sum

* update test files md5sum, again
2022-06-29 14:39:13 +02:00
Matthias De Smet
e2755cb039
add extra output from snap aligner (#1826) 2022-06-29 12:37:38 +02:00
Zhe Wang
0f1e736212
update kb-python version (#1823)
Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
2022-06-29 11:19:34 +02:00
Alexander Peltzer
08376da684
Bump MultiQC to v1.13a (dev) (#1814)
* Bump MultiQC to v1.13a (dev)

* Update main.nf

Predicted new container names ;-)
2022-06-29 08:40:42 +02:00
nvnieuwk
d596571a03
added an optional vcf index to bcftools/norm (#1821)
* added an optional vcf index to bcftools/norm

* updated test.yml for failing conda tests
2022-06-28 16:18:12 +02:00
SusiJo
98ffb09002
Added output files to ASCAT (#1820)
* add unzip alleles + loci

* fix the partial absolute prefix path

* exchanged deprecated function + added metrics

* updated meta

* tested logRCorrection + cram input

* added BED for WES

* added outputs + alleleCounter version

* test samtools chr operations, fixed cancerit conda

* ch formatting, fasta, bed input

* comment out local tests

* added metrics, bed, ref_fasta

* rm print statement

* added stub outputs

* rm versions.yml

* fix linting

* rm fictitious md5sums for stub-run

* try fixing top-level of stub versions.yml

* ordered inputs alphabetically, ref_fasta -> fasta

* rm R system command, adjust meta.yml

* prettier yml

* added outputs + prefix to outputs

* added test-yml outputs

* change underscores to dots
2022-06-28 14:45:57 +02:00
Matthias De Smet
a9521de5ac
bclconvert: Update Dockerfile (#1819)
* Update Dockerfile

* Output only top level InterOp files

* Update tag
2022-06-28 11:11:16 +01:00
Adam Talbot
009f7c691c
Add module: gatk4/leftalignandtrimvariants (#1808)
* Added: gatk4/leftalignandtrimvariants

Additions:
 - GATK4/LeftAlignAndTrimVariants module
 - Use sars-ncov2 test data as this normalises a larger INDEL correctly.

Fixes #1801

* fixup: Added index to output spec

* fixup: Pattern of tbi output corrected to 'tbi'

* gatk4/leftalignandtrimvariants: Added intervals

Changes:
 - gatk4/leftalignandtrimvariants now supports optional interval as BED
 file
 - Tests added with and without interval. Not test BED file excludes all
 variants so no variants are actually normalised.

Fixes #1801

* fixup: leftalignandtrimvariants vcf->tbi fix

* fixup: gatk4/leftalignandtrimvariants Intervals added to meta.yml
2022-06-28 10:44:08 +02:00
Alexander Peltzer
b573ff053e
Bugfix for CellRanger Dockerfile (#1812)
Bugfix to enable Singularity support
2022-06-27 11:07:33 +02:00
Mahesh Binzer-Panchal
233fa70811
Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
Merlin Szymanski
b6fe5d2643
Add Atlas/PMD (#1810)
* add atlas/pmd
* update atlas/pmd tests
* Add atlas/PMD module
* Remove comment
* Run Prettier
* Incorporate Review by @jfy133

Co-authored-by: maxibor <maxime.borry@gmail.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-06-24 16:53:51 +02:00
FriederikeHanssen
9b51362a53
Proposal: Rename output from fastp module (#1802)
* Rename output from fastp module

* UPdate tests

* fix alignment

* prettier

* Update modules/fastp/main.nf

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>

* apply review suggestion -sf

* typo

* update md5

* update md5

* try with human data

* revert, human data also doesn't work

* use contains instead

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
2022-06-24 10:01:14 +02:00
nvnieuwk
1363130410
small changes to vcfanno (#1804)
removed a redundant input field from vcfanno

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
2022-06-24 08:58:26 +02:00
Matthias De Smet
5e2325956c
bump bclconvert version (#1806) 2022-06-24 07:14:42 +02:00
Mahesh Binzer-Panchal
a7193dc628
Add MerquryFK KatGC (#1798)
* Add KAT GC

* Add additional container warning
2022-06-23 20:57:15 +02:00
2f0b192404
Add KAIJU2KRONA module (#1800)
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-06-23 16:38:50 +00:00
SusiJo
7daba6a13f
Update ASCAT module (#1805)
* add unzip alleles + loci

* fix the partial absolute prefix path

* exchanged deprecated function + added metrics

* updated meta

* tested logRCorrection + cram input

* added BED for WES

* added outputs + alleleCounter version

* test samtools chr operations, fixed cancerit conda

* ch formatting, fasta, bed input

* comment out local tests

* added metrics, bed, ref_fasta

* rm print statement

* added stub outputs

* rm versions.yml

* fix linting

* rm fictitious md5sums for stub-run

* try fixing top-level of stub versions.yml

* ordered inputs alphabetically, ref_fasta -> fasta

* rm R system command, adjust meta.yml

* prettier yml
2022-06-23 17:06:00 +02:00
Felipe Marques de Almeida
e1a3ae6bf5
make module output meta map (#1803) 2022-06-23 12:43:06 +02:00