nvnieuwk
720027275c
small update to samtools/merge ( #1896 )
2022-07-18 11:37:45 +02:00
Anders Sune Pedersen
ffe0375048
DRAFT: Extend output from snpeff ( #1895 )
...
* Extending output from snpEff
* Test of additional output-files from snpEff
* Removing some md5 checks
2022-07-16 20:08:52 +02:00
SusiJo
535975eb81
Update bcftools/stats for WES ( #1893 )
...
update bcftools/stats
2022-07-15 20:55:59 +02:00
WackerO
6720d88f4e
Fgbio tmpdir modification ( #1890 )
...
* Updated container versions for fgbio groupreadsbyumi and callmolecularconsensusreads
* Corrected fgbio call container, trying to fix fgbio group tests
* Removed incorrect line
* Changed tmp-dir to .
* Update modules/fgbio/groupreadsbyumi/main.nf
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* Update modules/fgbio/fastqtobam/main.nf
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* Added callmol and sortbam
* fixed typo in callmol container
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-07-15 11:20:58 +02:00
louperelo
1368164eb5
add module hamronization/amrfinderplus ( #1888 )
...
* add module hamronization/amrfinderplus
* deleted comments
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-07-15 10:54:42 +02:00
Júlia Mir Pedrol
9bda3dc7f0
Add new module: Pear ( #1779 )
...
* create pear module
* add command and tests
* remove md5sum from known empty file
* add force -f to gzip and gunzip to avoid problems with symbolic links
* apply suggestions from review
2022-07-15 10:28:31 +02:00
nickhsmith
edfe28a5e0
Variant recalibration ( #1885 )
...
* update tests
* update
* update
* make the manta inputs consistant for germline/somatic/tumoronly
* match chromosomes to cram file (chr21)
* undo genotypegvfs
* undo genotypegvfs
* update VariantRecalibrator
* lint
* add '--resource:' tag
Co-authored-by: Smith Nicholas <smith@in.tum.de>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-07-15 09:21:34 +02:00
Matthieu Muffato
9deff5222e
Fixed the MD5 checksum ( #1881 )
2022-07-15 08:52:03 +02:00
Mahwash Jamy
3531824af8
Update DIAMOND module to output log file ( #1879 )
...
* Update DIAMOND module to output log file
* Updating DIAMOND module to output log file - with jfy133 suggestions
Co-authored-by: Mahwash Jamy <mahwashjamy@n183-p186.eduroam.kth.se>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-07-14 16:18:28 +02:00
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
Maxime U. Garcia
f48a24770e
more generic name because of multiple extension ( #1880 )
2022-07-14 11:42:00 +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
Harshil Patel
589f39c39e
Add manual version definition for artic modules ( #1867 )
2022-07-12 11:33:51 +01:00
Erik Danielsson
49366ef275
Add CITATION.cff file for the nf-core publication ( #1865 )
...
* Add CITATION.cff file for nf-core publication
* Update .editorconfig .cff files
2022-07-12 10:15:32 +02:00
WackerO
b2a8464e3e
This updates the fgbio container version ( #1863 )
...
* This updates the fgbio container version
* Also updated conda install command
2022-07-11 16:17:54 +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
Sébastien Guizard
2f1eca7467
Adjust requested ressources for gstama/merge, isoseq3/refine, lima, ultra/align ( #1858 )
...
Reduce requested resources
2022-07-07 11:10:18 +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
Aleksei Korzhenkov
848ee9a215
Improve descriptions for modules with missing
...
Description and keywords
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-07-06 12:03:08 +02:00
Alexander Peltzer
5138acca09
Fix MultiQC conda ( #1856 )
2022-07-06 10:16:34 +02:00
Sima Rahimi
16536b6936
removed extra ) in the version strings ( #1850 )
2022-07-05 15:24:08 +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
Jose Espinosa-Carrasco
fa37e06626
Add stub run to gunzip module ( #1849 )
2022-07-04 17:33:55 +02:00
Jasmin F
92c420e7d0
Prokka: Fix typo in variable name ( #1846 )
...
Fix typo in variable name
2022-07-04 15:04:59 +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
Jasmin F
b3acfc54f5
antismashlite: Support GBK input ( #1840 )
...
* Support non-GFF input
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Fix linting error
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-07-01 09:29:53 +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
Simon Pearce
d6102dab6d
NGSCheckMate doesn't generate a pdf for only one sample, made optional output ( #1839 )
...
NGSCheckMate doesn't generate a pdf if only one sample is included, made optional
Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-06-30 17:43:34 +01:00
Simon Pearce
a363c12d71
Set randomseed for UMI tools if not otherwise set ( #1837 )
...
Set randomseed if not otherwise set
Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
2022-06-30 16:30:38 +01:00
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
