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Author SHA1 Message Date
Maxime U. Garcia
d8bef6057b
update snpeff to 5.1 and cache up to 105 (#1877) 
* update snpeff to 5.1 and cache up to 105

* update dm5checksum
 2022-07-13 15:16:21 +02:00
Maxime U. Garcia
973151e9ea
update ensemblvep to 106.1 and cache to 106 (#1876) 2022-07-13 13:43:03 +02:00
James A. Fellows Yates
b6ed584443
Update MOTUS/PROFILE module to output log file (#1871) 
* Add saving of stderr output as a log file as it contains summary statistics

* Apply suggestions from code review
 2022-07-13 11:26:27 +02:00
Sofia Stamouli
957cb9b836
Update filtlong module to output log file (#1873) 
Redirect logging information to log file in filtlong module
 2022-07-12 17:05:31 +02:00
James A. Fellows Yates
b78e19b9da
Update PORECHOP module to output log file (#1870) 
Update porechop to output log file
 2022-07-12 16:07:31 +02:00
Felipe Marques de Almeida
ec806cebf1
diminish memory demand (#1872) 
* diminish memory demand

Kallisto was being told to ask for the same amount of memory as it was said for nextflow to limit.

So, when kallisto tried to use it, nextflow was killing it. Thus, diminishing it per 1 GB solved the issue.

* fix prettier

* removing TODOs
 2022-07-12 15:53:02 +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
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
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
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
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
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
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
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
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
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
Thomas A. Christensen II
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
James A. Fellows Yates
9d7208504d
Add gecco/run module (#1790) 
* Add gecco/run module

* Fix container URLs

* Apply suggestions from code review

Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
 2022-06-22 13:43:45 +02:00
Mahesh Binzer-Panchal
280eec5317
Add MerquryFK KatComp (#1797) 
Add Kat Comp

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-06-21 09:43:37 +02:00
Adam Talbot
f19ec865aa
vcf2maf module with built in VEP (#1768) 
vcf2maf module created

Additions:
 - vcf2maf module created
 - If VEP is present in PATH, it is added to command
 - If VEP is missing, it is ignored (recommended to skip with --inhibit-vep)
 - VEP version automatically added to versions.yml
 - Uses VEP cache during testing which is added to test-datasets in https://github.com/nf-core/test-datasets/pull/563
 - Default Docker image includes VEP and vcf2maf
 - Test includes without VEP.

Relates to #490
 2022-06-20 18:27:12 +02:00
James A. Fellows Yates
be8d7b3293
Update MALT to older version due to major bug in most recent version (#1796) 
* Rollback version

* Start work rollback to 0.4.1

* Further changes

* Re do dynamic flag creation

* Prettier.
 2022-06-20 08:20:22 +02:00
nvnieuwk
6e7c0e945b
new module vcf2db (#1795) 
* added vcf2db

* fix test.yml

* possible fix for failing tests

* fix version number

* fix test.yml

* removed some comments
 2022-06-17 15:54:02 +02:00
alyssa-ab
c1eb9cce44
Trimmomatic (#1757) 
* Trimmomatic main only first draft

* Add test files

* SE PE Adjustment

* Remove extra reads input

* chore: Remove TODOs

* Apply suggestions from code review

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

* fix(trimmomatic): Handle SE output correctly

Since there's never going to be unpaired reads for SE reads we can get
away with it for SE

* fix(trimmomatic): Use correct elvis operator to handle logic

* fix(trimmomatic): Add hack to work with SE and PE reads

* Update test.yml

* use the PE and SE trimming correctly

* Made user set adaptors

* Add documentation

* test(trimmomatic): Add files to pytest_modules

* test(trimmomatic): Update name of failing test

Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
 2022-06-17 13:18:15 +00:00
Matthias De Smet
f32dc15414
update bclconvert module, as used in nf-core/demultiplex (#1569) 
* update bclconvert module, as used in nf-core/demultiplex

* reconfigure test with new test data

* update test

* formatting

* update outputs, update meta

* update module and test

* update test config, test.yml

* fix linting

* emit logs and reports as dir

* fix typo, recreate test.yml

* fix linting

Co-authored-by: CMGG ICT Team <ict@cmgg.be>
 2022-06-16 15:03:13 +02:00
Matthias De Smet
ecece498f1
samtools/*stats*: use prefix for outputs (#1788) 
* use prefix in flagstat

* use prefix in idxstats

* use prefix in stats

* update test.yml
 2022-06-16 13:42:01 +02:00
Robert A. Petit III
052b9f2fe9
add module for plasmidfinder (#1773) 
* add module for plasmidfinder

* Update test.yml
 2022-06-15 10:25:51 -06:00
Robert A. Petit III
1fe4cb942f
add module for ariba (#1731) 2022-06-15 10:18:31 -06:00
Anders Sune Pedersen
30f72e2482
Optional output from the VEP-moduel (#1775) 
* Making the output from the VEP-moduel (ENSEMBLVEP) optionally vcf, json or tab. #1774

* Trying to fix tests

* Still trying to fix tests

* Fetching the vep-output-file-extension from the args.

* Update meta.yml

* WIP: Adding tests for vep-output json and tab

* updated the test.yml

Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Co-authored-by: nvnieuwk <nicolas.vannieuwkerke@ugent.be>
 2022-06-15 13:52:12 +02:00
nvnieuwk
9dbaffff88
fix bgziptabix extension (#1784) 
* fix bgziptabix extension

* update test.yml
 2022-06-15 10:33:10 +02:00
Mahesh Binzer-Panchal
0af6adef55
Add MerquryFK PloidyPlot (#1780) 2022-06-14 20:50:58 +02:00
Mahesh Binzer-Panchal
e91e99db30
Add GeneScopeFK (#1781) 2022-06-14 20:49:06 +02:00
Mahesh Binzer-Panchal
8ded6d441a
Add MerquryFK (#1778) 
* Add MerquryFK

* Change resource allocation
 2022-06-14 16:36:02 +02:00
Mahesh Binzer-Panchal
fd5aea0b76
Add FastK/Histex (#1776) 2022-06-14 16:30:37 +02:00
nvnieuwk
1a4ab76618
new module rtgtools/pedfilter (#1777) 
* new module rtgtools/pedfilter

* removed checksum due to the presence of a date in the file
 2022-06-14 16:02:18 +02:00
Mahesh Binzer-Panchal
4e308c131e
FastK/fastK (#1739) 
* Add FastK/FastK

* Add ktab and prof outputs

* Add the hidden files necessary for the optional files

* Update image

* Apply suggestions from code review

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

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
 2022-06-14 13:39:52 +02:00
Thomas A. Christensen II
8b2a473f58
New module: krakentools/kreport2krona (#1746) 
* Add module definition for kreport2krona

* Add metadata for kreport2krona module

* Add tests for kreport2krona

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
 2022-06-13 20:14:44 +02:00
Maxime U. Garcia
b689b8ed88
TIDDIT - add --skip_assembly when no bwa specified (#1769) 
add --skip_assembly when no bwa specified
 2022-06-13 17:02:59 +02:00
Maxime U. Garcia
680b6c5b04
Update tiddit to 3.1.0 (#1767) 
* update TIDDIT to 3.1.0

* update VCF too as version is in file
 2022-06-13 16:24:34 +02:00
Merlin Szymanski
8f199c4fa4
Create atlas/splitmerge Module (#1756) 
* Add atlas/splitmerge module

* Finish the tests for atlas/splitmerge

* Prettier

* Update modules/atlas/splitmerge/meta.yml

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

* Remove curly brackets from meta.yml parameters

For single-file outputs, as reviewed

* Lintung: Remove trailing white-space

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-06-13 15:09:32 +02:00
Robert A. Petit III
81232af296
add module for mcroni (#1750) 
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
 2022-06-13 15:04:01 +02:00
Mahesh Binzer-Panchal
c1761293d8
Merge branch 'master' into busco_md5sum_patch 2022-06-13 10:53:36 +02:00
Mahesh Binzer-Panchal
575b2f00d3 Change busco multi-fasta test md5sum to contains 2022-06-13 08:51:41 +00:00
WackerO
f1b3174501
Merge branch 'master' into mpileup_bgzip 2022-06-13 09:48:47 +02:00
FriederikeHanssen
5b27af025a
Merge branch 'master' into manta_convert 2022-06-13 09:29:50 +02:00
FriederikeHanssen
e5b0c7ed25
Update tests/modules/manta/convertinversion/main.nf 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-06-13 09:26:35 +02:00
WackerO
c3b6ec8f3b Merge branch 'master' of https://github.com/nf-core/modules into mpileup_bgzip 2022-06-13 08:31:01 +02:00
WackerO
dc6c09e083 samtools mpileup now bgzips mpileup files 2022-06-11 13:32:53 +02:00
Rike
650076cacf add manta conversion script 2022-06-11 13:01:18 +02:00
Taniguti
547f483b74
Merge branch 'master' into haplocheck 2022-06-10 20:39:33 -03:00
Jasmin F
7027719c67
Merge branch 'master' into r-ampir 2022-06-10 14:57:24 +02:00
jasmezz
088b5b14f6 Merge branch 'r-ampir' of github.com:jasmezz/modules into r-ampir 2022-06-10 12:54:47 +02:00
jasmezz
39388abc04 Add file name collision check + TSV output 2022-06-10 12:54:39 +02:00
Alexander Peltzer
a0747b1405 Remove empty file md5sum 2022-06-10 11:53:28 +02:00
Alexander Peltzer
63f47551a8 Fix empty test having md5sum 2022-06-10 11:52:30 +02:00
Alexander Peltzer
1fbe69cfcc Updated and fixed tests 2022-06-10 11:46:23 +02:00
Alexander Peltzer
8dfe8b795f Merge remote-tracking branch 'refs/remotes/origin/cellranger-7.0.0' into cellranger-7.0.0 2022-06-10 11:23:15 +02:00
Alexander Peltzer
4928dfad34 Trying to fix tests 2022-06-10 11:22:45 +02:00
Alexander Peltzer
570a43ba4c Fix tests 2022-06-10 11:21:03 +02:00
Thiseas C. Lamnidis
9948e9fe21
Merge branch 'master' into sexdeterrmine 2022-06-10 11:03:18 +02:00
James A. Fellows Yates
c9db677a45
Merge branch 'master' into r-ampir 2022-06-09 19:28:37 +02:00
jasmezz
5841f11edb Replace MD5 with contains check 2022-06-09 18:15:27 +02:00
jasmezz
ecf1d146ab Add full user options for AMPir 2022-06-09 16:59:00 +02:00
Maxime U. Garcia
878a5a8093
Merge branch 'master' into update_spark 2022-06-09 15:49:31 +02:00
Rike
30262d1fdd remove variable checksum 2022-06-09 15:44:12 +02:00
Rike
a5583143c4 update checksum 2022-06-09 15:38:28 +02:00
jasmezz
ba53e09b64 Implement suggestions from code review 2022-06-09 15:37:35 +02:00
Rike
95633c6853 update checksum 2022-06-09 15:30:47 +02:00
Nicolas Vannieuwkerke
c50df9ad04 fix test.yml 2022-06-09 15:14:37 +02:00
Nicolas Vannieuwkerke
81fff7384d small fix and typo 2022-06-09 15:08:02 +02:00
Nicolas Vannieuwkerke
14d38e43cf fix test.yml 2022-06-09 14:58:20 +02:00
nvnieuwk
bf73b6d376
Merge branch 'master' into new-module-gatk4/reblockgvcf 2022-06-09 14:57:20 +02:00
Nicolas Vannieuwkerke
fe9e4ece00 new module gatk4/reblockgvcf 2022-06-09 14:56:55 +02:00
nvnieuwk
6d10909e9f
Update tests/modules/ensemblvep/main.nf 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-06-09 11:55:41 +02:00
nvnieuwk
e88a4ff70b
Merge branch 'master' into add-optional-fasta-parameter-to-ensemblvep 2022-06-09 11:54:22 +02:00
Nicolas Vannieuwkerke
e60323b757 typo 2022-06-09 11:53:59 +02:00
Nicolas Vannieuwkerke
7947bc662c added an extra test without fasta 2022-06-09 11:53:16 +02:00
Nicolas Vannieuwkerke
a3202e41ec prettier 2022-06-09 11:47:24 +02:00
Nicolas Vannieuwkerke
5ccf6fbcc9 add optional fasta argument to ensemblvep 2022-06-09 11:45:27 +02:00
SusiJo
0204d2374b Merge remote-tracking branch 'origin/master' into gatk_spark 2022-06-09 09:33:17 +02:00
James Fellows Yates
4d7afa21e2 Add GATK indelrealigner tests 2022-06-08 21:14:08 +02:00
James A. Fellows Yates
1fc0d3de4b
Merge branch 'gatk3-indelrealigner' into upstream-for-indel 2022-06-08 20:30:19 +02:00
James A. Fellows Yates
4a2157e5ab
Merge branch 'master' into gatk-realigntargetcreator 2022-06-08 20:15:02 +02:00
Taniguti
89bffe3a5e
Merge branch 'master' into haplocheck 2022-06-08 15:00:06 -03:00
Ramprasad Neethiraj
1d67489056 update test 2022-06-08 16:36:02 +02:00
Ramprasad Neethiraj
0b090a6b6d Merge branch 'master' of https://github.com/nf-core/modules into rhocall 2022-06-08 16:34:34 +02:00
Taniguti
d037f0ec97
Merge branch 'master' into haplocheck 2022-06-08 10:47:38 -03:00
Ramprasad Neethiraj
3cabdfac20
Merge branch 'master' into update_roh 2022-06-08 15:04:34 +02:00
Ramprasad Neethiraj
c079ee2025 fix test 2022-06-08 14:48:16 +02:00
Matthias De Smet
c005a5e007 formatting 2022-06-08 14:42:58 +02:00
Matthias De Smet
100b3f244c
Apply suggestions from code review 
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
 2022-06-08 14:24:55 +02:00
Lucas Taniguti
b2afb3b2ee fix: string interpolation and test input access 2022-06-08 09:08:59 -03:00
Matthias De Smet
71e3056813
Merge branch 'master' into update/multiqc 2022-06-08 14:03:26 +02:00
Matthias De Smet
439d2a9e67 update mqc inputs 2022-06-08 13:48:27 +02:00
Lucas Taniguti
abaec30889 tests: add stub 2022-06-08 08:46:22 -03:00
Lucas Taniguti
f26979c44e tests: add input to test_data.config 2022-06-08 08:10:25 -03:00
Taniguti
d5e077a2e9
Merge branch 'master' into haplocheck 2022-06-08 07:31:28 -03:00
Maxime U. Garcia
7230bf2174
Merge branch 'master' into update_tiddit 2022-06-08 11:16:01 +02:00
Taniguti
3be549534d
Apply suggestions from code review 
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
 2022-06-07 14:09:04 -03:00
Ramprasad Neethiraj
16e5e6093c Merge branch 'master' of https://github.com/nf-core/modules into rhocall 2022-06-07 14:45:09 +02:00
SusiJo
745e47cd33 add versions.yml 2022-06-07 14:38:43 +02:00
Ramprasad Neethiraj
65a0fb959f rhocall 2022-06-07 14:37:03 +02:00
SusiJo
e78ad2f88b Merge remote-tracking branch 'origin' into gatk_spark 2022-06-07 14:00:26 +02:00
Matthias De Smet
bffd1c562b
Merge branch 'master' into update/multiqc 2022-06-07 13:59:00 +02:00
SusiJo
dbca9e8b36 adjusted prefix + test + authors 2022-06-07 13:58:57 +02:00
Matthias De Smet
e5bf87aec3 possible fix for name collisions 2022-06-07 13:58:27 +02:00
Taniguti
a2e2d50494
Merge branch 'master' into haplocheck 2022-06-07 08:16:22 -03:00
Ramprasad Neethiraj
9d6697bdea template 2022-06-07 12:14:40 +02:00
Nicolas Vannieuwkerke
771425e7a0 add threads to calibratedragstrmodel 2022-06-07 12:11:18 +02:00
SusiJo
1368956d88 Merge remote-tracking branch 'origin/master' into gatk_spark 2022-06-07 11:00:33 +02:00
James A. Fellows Yates
d292f822e4
Merge branch 'master' into gatk-realigntargetcreator 2022-06-03 21:33:22 +02:00
James A. Fellows Yates
d2b240a17a
Merge branch 'master' into gatk-unifiedgenotyper 2022-06-03 21:24:09 +02:00
Robert A. Petit III
24ca2ed464
Merge branch 'master' into rp3-add-snippy 2022-06-03 13:01:05 -06:00
MaxUlysse
97e66015ca add test + fix issues 2022-06-03 15:51:02 +02:00
SusiJo
230224700e change prefix 2022-06-03 13:20:45 +02:00
SusiJo
1db7771ea9
Merge branch 'nf-core:master' into gatk_spark 2022-06-03 13:17:35 +02:00
MaxUlysse
f1a5cc07db restructure tiddit/sv + test (just one for now) 2022-06-03 13:00:29 +02:00
MaxUlysse
40996cdbe1 update tiddit/cov + more tests 2022-06-03 12:07:16 +02:00
MaxUlysse
36ffd4fbf7 Merge remote-tracking branch 'upstream/master' into update_tiddit 2022-06-03 11:38:33 +02:00
Rike
2c9e2f5e73 Update TIDDIT to 3.0.0 2022-06-03 10:52:50 +02:00
James Fellows Yates
a565d9072a Add GATK UnifiedGenotyper 2022-06-02 21:39:39 +02:00
James Fellows Yates
544b62df45 Star work on GATK UG 2022-06-02 21:11:17 +02:00
James Fellows Yates
9a4f22e8d1 Merge branch 'gatk-realigntargetcreator' of github.com:jfy133/nf-core-modules into gatk-realigntargetcreator 2022-06-02 20:32:03 +02:00
James Fellows Yates
c469a2b35e Fux tests 2022-06-02 20:32:00 +02:00
James A. Fellows Yates
abc619a3e2
Merge branch 'master' into gatk-realigntargetcreator 2022-06-02 20:24:24 +02:00
SusiJo
1b93cde9ff
Merge branch 'master' into gatk_spark 2022-06-02 16:24:39 +02:00
Nicolas Vannieuwkerke
b4b1f3b81d add intervals to calibratedragstrmodel 2022-06-02 16:20:12 +02:00
nvnieuwk
e107d61069
Update tests/modules/gatk4/haplotypecaller/test.yml 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-06-02 14:20:15 +02:00
nvnieuwk
e419d306df
Update tests/modules/gatk4/haplotypecaller/test.yml 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-06-02 14:20:10 +02:00
nvnieuwk
2ce1cf3329
Update tests/modules/gatk4/haplotypecaller/test.yml 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-06-02 14:20:04 +02:00
nvnieuwk
a6c4276ad7
Update tests/modules/gatk4/haplotypecaller/test.yml 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-06-02 14:19:57 +02:00
Nicolas Vannieuwkerke
e53d091a6d added dragstr model to haplotypecaller 2022-06-02 14:08:09 +02:00
nvnieuwk
a339f9818a
Merge branch 'master' into new-module-gatk4/CalibrateDragstrModel 2022-06-02 13:42:56 +02:00
nvnieuwk
4b430e8ece
Merge branch 'master' into new-module-gatk4/CalibrateDragstrModel 2022-06-02 13:41:20 +02:00
Matthias De Smet
f58771c47f
Merge branch 'master' into update/untar 2022-06-02 13:38:53 +02:00
nvnieuwk
eadab8e002
Merge branch 'master' into new-module-gatk4/CalibrateDragstrModel 2022-06-02 13:18:36 +02:00
Nicolas Vannieuwkerke
2a45d42868 added the calibratedragstrmodel module 2022-06-02 13:17:06 +02:00
SusiJo
2f3ddc90fb added fasta_fai as input + changed if statements 2022-06-02 12:57:50 +02:00
Matthias De Smet
51be617b1c fix untar output dir 2022-06-02 11:09:55 +02:00
SusiJo
7742661784 Merge remote-tracking branch 'upstream/master' into cnvkit_bam 2022-06-02 10:51:43 +02:00
SusiJo
a21cfb666e changed container + add cram2bam conversion 2022-06-02 10:38:05 +02:00
SusiJo
9fc9be3e7b Merge remote-tracking branch 'origin/master' into cnvkit_bam 2022-06-01 17:35:47 +02:00
SusiJo
f6953b5147 adjust cnvkit/batch for germline mode 2022-06-01 17:35:02 +02:00
Nicolas Vannieuwkerke
8470f3cb7e linting 2022-06-01 09:20:20 +02:00
James A. Fellows Yates
5a94794793
Merge branch 'master' into r-ampir 2022-06-01 09:18:54 +02:00
Nicolas Vannieuwkerke
d4f3df4677 Updated the test 2022-06-01 09:17:05 +02:00
nvnieuwk
e4f51d6f59
Merge branch 'master' into new-module-gatk4/ComposeSTRTableFile 2022-06-01 08:59:19 +02:00
Alexander Peltzer
9ac3cf342a
Merge branch 'master' into gatk-realigntargetcreator 2022-05-31 21:12:59 +02:00
James Fellows Yates
7633d7816b Add GATK(3)/realignertargetcreator 2022-05-31 20:35:54 +02:00
James A. Fellows Yates
615cb0722f
Merge branch 'master' into fix-filtlong 2022-05-31 20:25:16 +02:00
James Fellows Yates
c1ac3fbb59 Skeleton 2022-05-31 20:13:48 +02:00
James Fellows Yates
df22cd80df Fix config for tests 2022-05-31 20:07:52 +02:00
FriederikeHanssen
19037ed8f4
Merge branch 'master' into get_tbi_files_from_gatk4_mergevcfs 2022-05-31 17:42:27 +02:00
Nicolas Vannieuwkerke
1166fb5150 prettier 2022-05-31 16:13:38 +02:00
Nicolas Vannieuwkerke
ec41ea6082 fix test.yml 2022-05-31 16:12:05 +02:00
Nicolas Vannieuwkerke
80366924fd added gatk4/composestrtablefile 2022-05-31 16:08:13 +02:00
asp8200
98bb45cf4e Updating test for gatk4/mergevcfs 2022-05-31 13:59:56 +00:00
SusiJo
84f584875e change string array 2022-05-31 15:50:31 +02:00
James A. Fellows Yates
edc9e83a7d
Merge branch 'master' into fix-filtlong 2022-05-31 15:47:39 +02:00
James Fellows Yates
3e20ca7e9a Don't hardcode forced output names 2022-05-31 15:46:28 +02:00
SusiJo
58389e550d test json array 2022-05-31 15:41:50 +02:00
SusiJo
49135415ae
Merge branch 'master' into gatk_spark 2022-05-31 15:36:55 +02:00
SusiJo
941760f75d ran prettier 2022-05-31 15:36:02 +02:00
SusiJo
35e296cd7d added brackets 2022-05-31 15:35:34 +02:00
SusiJo
37b543e3e7 changed to tab 2022-05-31 15:29:27 +02:00
SusiJo
810564deca
Merge branch 'master' into gatk_spark 2022-05-31 15:24:58 +02:00
nvnieuwk
a6c7635b73
Merge branch 'master' into add-tbi-to-bcftools-concat 2022-05-31 15:20:03 +02:00
Nicolas Vannieuwkerke
51b0a6e4f3 Added optional input of index files to bcftools/concat 2022-05-31 15:15:58 +02:00
SusiJo
9ef09e6add adjusted newlines 2022-05-31 14:54:39 +02:00
SusiJo
205576279f ran prettier again 2022-05-31 14:50:55 +02:00
James Fellows Yates
430def06fa Switch from md5sum to string due to conda flakiness 2022-05-31 14:45:41 +02:00
SusiJo
d484aa1906 adjusted tabs 2022-05-31 14:45:23 +02:00
SusiJo
e083bfafa0 ran prettier 2022-05-31 14:38:45 +02:00
SusiJo
1e396d767f Merge remote-tracking branch 'upstream/master' into gatk_spark 2022-05-31 14:36:14 +02:00
SusiJo
ea526051a4 new test.yml 2022-05-31 14:35:42 +02:00
SusiJo
3117b2973c added test for metrics 2022-05-31 14:35:29 +02:00
SusiJo
e0e8273f74 adjusted input to use queryname sorted bams 2022-05-31 14:35:18 +02:00
James Fellows Yates
723852bf3d Fixes running without shortreads, and also ensures all tests produce non-empty fastq.gz files 2022-05-31 13:38:18 +02:00
James Fellows Yates
7ffe98ac8b Add gatk/indelrealigner 2022-05-30 21:12:21 +02:00
jtangrot
6ae405c5da prettier 2022-05-30 13:35:12 +02:00
jtangrot
6aac5c2c40 Update test 2022-05-30 13:30:27 +02:00