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1733 commits

Author SHA1 Message Date
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
Mahesh Binzer-Panchal
f8bd7902d9 Update Git SHA messagre 2022-06-10 11:01:40 +00:00
Mahesh Binzer-Panchal
25c742dc69 Commit suggestions from code review 2022-06-10 10:56:56 +00:00
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
Mahesh Binzer-Panchal
6a1cbce0f5
Update tests/test_versions_yml.py 
Co-authored-by: Fabian Egli <fabianegli@users.noreply.github.com>
 2022-06-10 12:54:08 +02:00
Mahesh Binzer-Panchal
e75dd10667
Merge branch 'master' into allow_git_sha_versions 2022-06-10 12:53:50 +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
Mahesh Binzer-Panchal
0479544e02 Allow Git commit SHA's as version numbers 2022-06-10 09:46:14 +00:00
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