Commit graph

3393 commits

Author SHA1 Message Date
Matthias De Smet
b5aa12ad3b
new module: samtools/getrg (#2123)
* new module: samtools/getrg

* add output file to stub

* add missing config

* Intentionally break prettier linting

* [automated] Fix linting with Prettier

Co-authored-by: Phil Ewels <phil@seqera.io>
Co-authored-by: nf-core-bot <core@nf-co.re>
2022-09-28 14:00:10 +02:00
Phil Ewels
33d9ce79c1
Remove jinja tags from workflow (#2124)
Workflow was copied from the pipeline template but the jinja2 template tags were still there
2022-09-28 12:42:09 +02:00
Aida Andrades Valtueña
0bdd589163
New Module: endorspy (#1916)
* added module endorspy and test

* added endorspy

* Fixed spaces and remove unnecessary lines from test

* added extra new line to test.yml

* added a prefix to to avoid name collision

* Update modules/endorspy/main.nf

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

* Update modules/endorspy/meta.yml

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

* Update modules/endorspy/meta.yml

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

* Update modules/endorspy/meta.yml

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

* Update modules/endorspy/meta.yml

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

* Update modules/endorspy/meta.yml

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

* Update modules/endorspy/meta.yml

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

* Update modules/endorspy/meta.yml

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

* Apply suggestions from code review

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

* Apply suggestions from code review

* Update modules/endorspy/main.nf

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-09-28 11:28:11 +02:00
Michael L Heuer
ee5f59705f
Adding new module gfaffix (#1149)
* Adding new module gfaffix.

* add missing entry to pytest_modules.yml

* update to 0.1.4--hec16e2b_0

* fixup after prettier

* add when section

* update md5sum

* Change to process_single as discussed

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Co-authored-by: Simon Heumos <simon.heumos@qbic.uni-tuebingen.de>
2022-09-28 10:23:18 +02:00
Lucpen
f434d0c671
Adding stubs to PicardLiftovervcf, GATK4_mergevcfs and filterMutectCalls (#1621)
* feat added stubs to picard_liftovervcf

* feat adding stubs to gatk4_mergevcfs

* feat adding stubs to gatk4_filtermutectcalls

* fix tests

* fix output name filtermutectcalls

* fix test

* fix added missing [

* Update tests/modules/gatk4/mergevcfs/test.yml

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

* Update tests/modules/gatk4/filtermutectcalls/test.yml

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

* Update tests/modules/picard/liftovervcf/test.yml

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

* Update modules/gatk4/filtermutectcalls/main.nf

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

* Update modules/gatk4/filtermutectcalls/main.nf

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

* Update modules/gatk4/mergevcfs/main.nf

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

* Update modules/gatk4/mergevcfs/main.nf

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

* Update modules/picard/liftovervcf/main.nf

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

* Trying something on picard_liftovervcf

* fix adding test data for stubs

* fix added bracket and unindented workflow

* fix picard 2.27.1 -> 2.27.0 to solve PaddingError

* Update main.nf

fix added tbi to stub

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
2022-09-28 09:50:11 +02:00
Robert A. Petit III
ec22f9a907
[bug] pin bioperl version in Prokka module (#1307)
* [bug]  pin bioperl version in Prokka module

* Update main.nf

* Update main.nf

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
2022-09-28 01:34:23 +01:00
Chase Mateusiak
786279b473
New Module: NextGenMap (#1938)
adding nextgenmap module

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
2022-09-27 20:44:47 +01:00
James A. Fellows Yates
a0443e2c54
Fixes incorrectly quoted tags (#2113)
* Update main.nf

* Update meta.yml

* Re-add logos as not staged in a way that works with MultiQC config files

* Update main.nf

* Remove now unnecessary input channel

* Remove unused channel from tests

* Update hAMRonization to 1.1.1 and add hAMRonization farGene

* Fix hamronizatio ntests

* Prettier

* Fix fargene linting

* Correct file

* Fix fargene output

* Apply suggestions from code review

Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>

* Fix summarise tests

* Prettier

* Fix incorrect quotes in tags

Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
2022-09-27 20:37:56 +01:00
Simon Pearce
5da2c37458
Teach nf-core bot to fix lint (#2109)
* Teach nf-core bot to lint

* Correct file

* Add empty line at end of file

* Ran prettier

Co-authored-by: SPearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-09-27 18:34:58 +02:00
Maxime U. Garcia
eb15df8036
Deepvariant - Update main.nf (#2110)
Update main.nf

simplify deepvariant container call
2022-09-27 15:34:10 +02:00
James A. Fellows Yates
daab0a77dd
Add HAMRONIZATION/FARGENE and updates all HARMONIZATION tools to 1.1.1 (#2107)
* Update main.nf

* Update meta.yml

* Re-add logos as not staged in a way that works with MultiQC config files

* Update main.nf

* Remove now unnecessary input channel

* Remove unused channel from tests

* Update hAMRonization to 1.1.1 and add hAMRonization farGene

* Fix hamronizatio ntests

* Prettier

* Fix fargene linting

* Correct file

* Fix fargene output

* Apply suggestions from code review

Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>

* Fix summarise tests

* Prettier

Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
2022-09-27 15:32:18 +02:00
James A. Fellows Yates
1780cf9bcf
Add: ANGSD_DOCOUNTS (#2044)
* Update main.nf

* Update meta.yml

* Re-add logos as not staged in a way that works with MultiQC config files

* Add ANGSD doCounts

* Prettier

* Update main.nf

* Apply suggestions from code review

* Apply suggestions from code review

* Apply suggestions from code review

* Try loosening test due to conda

* Remove md5 for binary file

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
2022-09-27 13:21:44 +02:00
Harshil Patel
82501fe6d0
Fix broken Quast module and bump MultiQC version in dumpsoftwareversions (#2108) 2022-09-27 09:35:52 +01:00
nvnieuwk
2a9a8763f9
updated the version of delly (#2105) 2022-09-27 08:57:36 +02:00
nvnieuwk
5d8edefb26
new module gatk4/printsvevidence (#2103)
* new module gatk4/printsvevidence

* linting

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
2022-09-27 08:30:16 +02:00
Francesco Lescai
77d5dd60eb
Adding module bamtools stats (#2104)
* added bamtools stats module and tested

* added bamtools stats module and tested

* fixing prettier complaints

* changed process tag to single
2022-09-27 06:24:43 +01:00
Matthieu Muffato
07e2868920
Added an output channel for the gzi index (#2036)
* When the `-i` option of bgzip is given, an index is created and needs to be considered an output

* It is not necessary to use a subfolder

* Updated meta.yml too

* Also check that an index name hasn't been requested

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-09-26 21:47:41 +02:00
Matthieu Muffato
de7b50fdd0
Updated dumpsoftwareversions.py to match the pipeline template (#2045)
* Updated dumpsoftwareversions.py to match the pipeline template

* Fixed the test

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-09-26 18:45:07 +01:00
Matthieu Muffato
f0a86eaf5b
Multithreaded samtools commands (#2080)
* Multithreaded samtools commands

* Updated the checksums since the BAM files include the actual command line

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
2022-09-26 17:44:36 +01:00
Simon Heumos
1d668eefa2
Bump seqwish/induce to v0.7.6 (#2083)
* Update seqwish to version 0.7.2

* seqwish can work with a comma-separated list of PAFs

* level with nf-core/modules master branch

* update seqwish/induce to v0.7.6

* add pangenome test data

* test seqwish/induce v0.7.6 with pangenomics test data

* we already have pointed to the pangenomics test data sets

* update paths to test data

* add path to bgzipped fa, gzi, fai

* remove one tab

* remove one tab

* actually execute the 2nd test

* try to fix versions.yml

* pangenomic tests can be run in their own subworkflow

* maybe the csv input is the problem

* remove space as suggested by Rike

* csv input was not the problem

* update test.yml

* typo

* enable pangenome tests

* add md5sum for pangenomic test

* Update tests/modules/seqwish/induce/test.yml

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>

* PAF input is a list of files

* beautify comment

Co-authored-by: Michael L Heuer <heuermh@acm.org>
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
2022-09-26 17:01:21 +01:00
Guoying Qi
8e21005d53
Add blast/tblastn module (#2092)
* cherry pick the module files from sanger-tol branch and update the test data from official nf-core test datasets

* Update modules/blast/tblastn/main.nf, align the emit

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

Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
2022-09-26 17:43:41 +02:00
JIANHONG OU
d1c8bddaaa
fix typo in tag of genmap_mappability (#1527)
fix tyop in tag of genmap_mappability
2022-09-26 16:21:45 +01:00
Robert A. Petit III
e3e61068c1
add module for seroba (#1816)
* add module for seroba

* fix lint

* Update modules/seroba/run/meta.yml

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

* Update modules/seroba/run/main.nf

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
2022-09-26 16:06:08 +01:00
Petros
0a59baf293
Add args to mlst (#1962)
Update main.nf

Add args in main command to allow for parsing of arguments from config file

Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
2022-09-26 15:48:35 +01:00
Robert A. Petit III
6d6e3a018f
add module for mykrobe predict and genotyphi parse (#1818)
* add module for mykrobe predict and genotyphi parse

* Update meta.yml

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
2022-09-26 15:18:04 +01:00
Rafal Stepien
876bb807af
Update container version (#2060)
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-09-26 15:10:49 +01:00
Jeanette Tångrot
32ad1746d1
New module: Vsearch sintax (#2094)
* Add vsearch sintax process

* Add tests for vsearch sintax

* Add vsearch sintax process

* Add tests for vsearch sintax

* Update format with prettier

* Remove trailing whitespace

Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
2022-09-26 14:45:01 +01:00
Benedetto Polimeni
29568f72ca
Make stringtie/merge arguments configurable (#2049)
Added $args to command line and made using a reference annotation optional.

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
2022-09-26 14:26:53 +01:00
Michael L Heuer
72adfbff72
Update dsh-bio to 2.1 (#2100)
Update dsh-bio to 2.1.
2022-09-26 10:41:33 +01:00
Alexander Ramos Díaz
9d5ad1894b
2012 bug related to species input in goattaxonsearch module (#2099)
* updated input for taxon

* updated test_single_species

* updated test file

* run prettier on test.yml

* updated label process_low

* restored lable process_single

Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
2022-09-23 10:58:40 -06:00
Priyanka Surana
09159edc9e
Update samtools view (#2098)
* samtools view update

* remove csi output

* prettier

* update meta

* add index functionality

* prettier

* fixed test checks
2022-09-23 16:52:01 +02:00
Priyanka Surana
402631fdaa
Update samtools view (#2096)
* samtools view update

* remove csi output

* prettier

* update meta
2022-09-23 13:03:59 +01:00
Daniel Lundin
0857e6c60f
Adding gappa/examineheattree (#2084)
* Adding gappa/examineheattree

* Update modules/gappa/examineheattree/meta.yml

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

* Check versions.yml for md5 sum instead

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
2022-09-22 15:51:25 +02:00
Daniel Lundin
58ee946ca6
gappa/examineassign: Explicitly output two optional files (#2086)
* gappa/examineassign: Explicitly output two optional files

* Check versions.yml for md5 sum instead
2022-09-22 15:04:32 +02:00
Priyanka Surana
22e144dc63
samtools markdup module (#2087) 2022-09-21 15:39:10 +01:00
SusiJo
41dfa13929
Fix bcftools/stats module (#1953)
* test verified commit bcftools

* adjust tests

* add suggestions

* test for actual file content
2022-09-21 16:10:38 +02:00
Priyanka Surana
ab4c2e440d
samtools collate module (#2078)
* samtools collate module

* prettier fix

* prettier fix

* added cram functionality
2022-09-21 14:12:59 +01:00
Benedetto Polimeni
d5d785b3d8
[samtools] add optional csi output (#2064)
* [samtools] add optional csi output, when applicable

* Remove empty line

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
2022-09-20 21:08:29 +01:00
Matthias De Smet
c13f2274fb
cat/fastq: update conditional (#2085)
update conditional
2022-09-20 14:46:01 +02:00
Ashot Margaryan
d8ba32c6b5
Somalier relate (#2001)
* Working version of somalier relate

* few changes

* new changes

* corrected test.yml

* updated container paths and file paths

* changed container and inputFile paths

* changed left padding

* requested changes

* Update modules/somalier/relate/main.nf

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

* Update modules/somalier/relate/main.nf

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

* Update modules/somalier/relate/main.nf

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

* Update modules/somalier/relate/main.nf

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

* Update modules/somalier/relate/meta.yml

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

* Update modules/somalier/relate/meta.yml

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

* Update modules/somalier/relate/meta.yml

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

* requested changes

* requested changes

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-09-19 13:22:24 +02:00
James A. Fellows Yates
90aef30f43
Set process label to process_single for modules with no task.cpus usage (#2076)
* Set process label to `process_single` for modules with no `task.cpus` usage

* Fix tests of 'borked' modules

* prettier

* More modules are single-threaded and can use process_single

* Adding process_single to hmmer/esl* modules

* Fix failing tests

* Prettier

Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
2022-09-19 11:54:47 +02:00
Daniel Lundin
46ad627a73
Add gappa/examineassign (#2079)
* Created gappa/examineassign from template

* Test passing

* Run only when taxonomy is set

* Revert adding taxonomy to when

* Add period after prefix

* Fix test

* Add some keywords

* Add one more keyword
2022-09-19 11:49:42 +02:00
Daniel Lundin
b6f18f8733
eslreformat: descriptive suffix (#2081) 2022-09-19 09:49:00 +02:00
Ashot Margaryan
f62e4cf5f0
Added Somalier extract module (#1986)
* Added Somalier extract module

* changed somalier_dbg4 to somalier for versions.yml

* added  and minor changes in meta.yml

* Apply suggestions from code review

* Update main.nf

* Typo in quay.io rl

* updated the input

* new updates

* linting

* linting

* changed the test.yml

* Update modules/somalier/extract/main.nf

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

* Update modules/somalier/extract/main.nf

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

* Update modules/somalier/extract/meta.yml

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

* Update modules/somalier/extract/main.nf

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

* Update tests/modules/somalier/extract/main.nf

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

* Update modules/somalier/extract/main.nf

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

* Update tests/modules/somalier/extract/test.yml

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

* last changes

* Update modules/somalier/extract/meta.yml

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

* Update modules/somalier/extract/meta.yml

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

* Update modules/somalier/extract/main.nf

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-09-19 08:58:17 +02:00
Rafal Stepien
38383cfaef
Update eido/validate module (#2071)
* Update eido/validate module

* Update modules/eido/validate/meta.yml

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-09-16 09:00:03 -04:00
Rafal Stepien
9764eef361
Update eido/convert module (#2072)
* Update eido/validate module

* Update modules/eido/convert/meta.yml

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-09-16 08:54:40 -04:00
Matthias De Smet
b98f1b77d1
Bump bcl-convert version (#2077)
* Update main.nf

* update test.yml

* prettier
2022-09-16 14:34:52 +02:00
James A. Fellows Yates
54ff289487
Update mOTUs to remove now unused channel (#2075)
* Update main.nf

* Update meta.yml

* Re-add logos as not staged in a way that works with MultiQC config files

* Update main.nf

* Remove now unnecessary input channel

* Remove unused channel from tests
2022-09-16 10:23:21 +02:00
Daniel Lundin
b121596ae0
Make epang output meta with the jplace channel (#2073) 2022-09-16 10:22:50 +02:00
Jasmin F
e55012ff92
DeepBGC: tiny revisiosn (#2070)
* Fix variable prodigal_tf

* Remove tag in main.nf + tiny suggestions in ymls

Co-authored-by: louperelo <44900284+louperelo@users.noreply.github.com>
2022-09-15 22:57:33 +02:00