Commit graph

3401 commits

Author SHA1 Message Date
Mahesh Binzer-Panchal
96602d03fa
Update Merqury version and sha (#2132) 2022-09-29 15:23:58 +02:00
Priyanka Surana
504028346b
samtools fasta module (#2128) 2022-09-29 08:10:44 +01:00
Harshil Patel
b3e322064e
[POC] Get subworkflows working again - bam_stats_samtools (#2097)
* [POC] Get subworkflows working again - bam_stats_samtools

* Comment out aliased anchors

* Add explicit anchor to pytest_modules.yml

* test(subworkflows): Remove anchors

There are two options to get the tests to trigger:

1. Add the module anchors to the subworkflows (less things to update and maintain because we only have to update the module triggers)

2. Add the tags to the pytest workflow spec.

This is option 2.

Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
2022-09-28 19:20:20 +01:00
Harshil Patel
bfbdc4f79b
Update cores specification in TrimGalore module (#2127)
Update main.nf
2022-09-28 15:47:27 +02:00
James A. Fellows Yates
0ab15c5ee9
Update checkM version and add support for pre-defined database (#2125)
Bump checkM version and add support for pre-defined database

Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
2022-09-28 14:48:18 +02:00
Ramprasad Neethiraj
3d7ce93630
add stub and the option to compress output for vep (#2111)
* add stub

* create tab and json files

* add option to get compressed outputs
2022-09-28 14:34:41 +02:00
Matthieu Muffato
e9bc33485e
bugfix: when there is a single input file, stageAs("?/*) returns the path directly, not in a list (#2114)
* bugfix: when there is a single input file, stageAs("?/*) returns the path directly, not in a list

* Added a test

* Added a test

* Added MD5 checksum

Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
2022-09-28 13:28:52 +01:00
Priyanka Surana
83b05a8dc0
add qname feature to samtools/view (#2115)
* add qname feature to samtools_view

* update tests

* Update modules/samtools/view/meta.yml

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

* Update modules/samtools/view/meta.yml

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

* added filter tests

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-09-28 13:04:41 +01:00
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