Alexander Peltzer
013035eb5c
Improved kbtools/count ( #1884 )
...
* Improved kbtools/count
* Update test.yml
removing TODO statements
* Update main.nf
Co-authored-by: Felipe Marques de Almeida <almeidafmarques@gmail.com>
2022-07-14 14:27:56 +02:00
WackerO
c29b3fe11a
Updated container versions for fgbio ( #1878 )
...
* Updated container versions for fgbio groupreadsbyumi and callmolecularconsensusreads
* Corrected fgbio call container, trying to fix fgbio group tests
* Removed incorrect line
2022-07-14 13:51:34 +02:00
Matthias De Smet
9294259eea
Module/bcl2fastq ( #1883 )
...
* add bcl2fastq
* test fixes
* fixed tests
* add tests to workflow
* change container source
2022-07-14 13:18:21 +02:00
Mahesh Binzer-Panchal
1de4bd46b7
Add Merqury ( #1647 )
...
* Add merqury files
* Remove md5sum for completeness stats file
* update container and test output
* Update modules/merqury/meta.yml
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* Explicitly set thread usage for meryl
* Remove empty file md5sum
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
2022-07-14 10:38:50 +02:00
Alexander Ramos Díaz
b4452a4881
Add ENTREZDIRECT/ESUMMARY ( #1833 )
...
* first commit
* entrezdirect/esummary fixed version definition
* resolved suggestion
* updated main.nf
* changed output definition
* output: XML file
* output definition: XML file
* updated XML format in tests
* updated test file
* version: esummary instead of entrezdirect
* output file pattern: *.esummary.xml
* updated test file
* updated versions
* restored versions stdout
* updated test file
* changed xml_esummary pattern
* changed entrezdirect to esummary version
* updated test file
* Update modules/entrezdirect/esummary/meta.yml
changed output file pattern: "*.xml"
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/entrezdirect/esummary/meta.yml
updated keywords
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/entrezdirect/esummary/main.nf
Output file pattern: *.xml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/entrezdirect/esummary/main.nf
Output file pattern: *.xml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/entrezdirect/esummary/main.nf
database as separate input channel
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* removed blank spaces in input definition
* database as separate channel
* conditional script for stdin
* updated input definition
* entrez-direct version:16.2_1
* all input channels are separate
* ignore stderr, catch xml stdout
* removed blank lines
* added ids file input
* updated test
* conditional script for input
* removed bad definition of input file
* updated test file
* Update modules/entrezdirect/esummary/main.nf
changed input definition: ui, uids_file
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/entrezdirect/esummary/meta.yml
added uids_file description
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/entrezdirect/esummary/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* input: uid or uids_file
* updated input
* added uids_file to input
* input file as optional input
* input file as optional input in each test
* new conditional script
* unpdated test file
* single input definition
* added error messages
* updated test
* removed cat from command output
* Update modules/entrezdirect/esummary/main.nf
added comment on use of grep in output
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* added comment
* removed blank spaces
* input file: empty list
* input file: empty list
* removed comment at wrong position
* optional file defined as empty list
* updated successful test
* Apply suggestions from code review
Accepted suggestions.
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
* Update modules/entrezdirect/esummary/main.nf
Fixed comment.
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
* Update modules/entrezdirect/esummary/main.nf
Updated grep in output file.
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
* added tail -n+3 before output
* updated successful test
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
2022-07-13 11:26:58 -06:00
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
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 )
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* 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 )
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* 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 )
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* 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 )
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* 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
8b2a473f58
New module: krakentools/kreport2krona ( #1746 )
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* 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 )
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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 )
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* 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 )
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* 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
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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
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