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Author SHA1 Message Date
WackerO
8214b73700
SVDB_MERGE bgzip (#1910) 
* Started (again) to work on bgzipping SVDB_MERGE output

* Updated test yml

* SVDB_MERGE now bgzips output

* Fixed singularity, renamed tests in test.yml

Co-authored-by: Cloud User <centos@oskar-instance.novalocal>
 2022-07-20 10:54:06 +02:00
James A. Fellows Yates
f91abed951
RGI/main export versions as explicit emission strings (#1909) 
* Export versions  as explicit emission strings in addition to versions.yml for compatibility with hAMRonization

* Update YML
 2022-07-20 10:33:53 +02:00
Adam Talbot
7e8ad56688
module FASTP: Support for interleaved FASTQ (#1891) 
* 1882 FASTP now supports interleaved FASTQ files

Changes:
 - single_end FASTP pipes the FASTQ file
 - Using args, it can be configured for interleaved in `--interleaved_in`
 - Out is automatically interleaved if input is paired end.
 - Removed md5sum checks for FASTQ files as compression seemed to cause
 differences
 - Instead, we check inside the FASTQ files for content.

Relates to #1882

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
 2022-07-19 16:27:15 +01:00
nvnieuwk
8d4373b4e8
added bcftools convert (#1906) 
* added bcftools convert

* Update modules/bcftools/convert/main.nf

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>

* updated test.yml

* Update modules/bcftools/convert/main.nf

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>

* added automatic output type detection

* linting

* removed a trailing whitespace

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
 2022-07-19 15:09:40 +02:00
Matthias De Smet
6b9a6a5b29
bamsormadup: add extra test case, fix single file input (#1905) 2022-07-19 13:52:37 +02:00
louperelo
8002e373b5
Amrfinderplus: add db-version to versions.yml (#1899) 
* not yet working: add db version to versions.yml

* next try: db version number not in versions.yml

* Fix amrfinderplus versioning

* Update main.nf

* Apply suggestions from code review

* Update main.nf

* Dump version for syncrony with run

* Update test.yml

* Apply suggestions from code review

Co-authored-by: James Fellows Yates <jfy133@gmail.com>
 2022-07-19 09:52:36 +02:00
Matthias De Smet
035e418369
Biobambam/bamsormadup: Fix name collision (#1900) 
* Fix name collision

Add stageAs to avoid name collisions

* fix version check

* fix test
 2022-07-18 15:43:02 +02:00
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
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
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
Matthias De Smet
253f8c1b0e
snapaligner: fix quotes (#1835) 
Fix quotes
 2022-06-30 11:15:15 +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
Zhe Wang
0f1e736212
update kb-python version (#1823) 
Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
 2022-06-29 11:19:34 +02:00
Alexander Peltzer
08376da684
Bump MultiQC to v1.13a (dev) (#1814) 
* Bump MultiQC to v1.13a (dev)

* Update main.nf

Predicted new container names ;-)
 2022-06-29 08:40:42 +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
Matthias De Smet
a9521de5ac
bclconvert: Update Dockerfile (#1819) 
* Update Dockerfile

* Output only top level InterOp files

* Update tag
 2022-06-28 11:11:16 +01:00
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
Alexander Peltzer
b573ff053e
Bugfix for CellRanger Dockerfile (#1812) 
Bugfix to enable Singularity support
 2022-06-27 11:07:33 +02:00
Mahesh Binzer-Panchal
233fa70811
Update manual versioning (#1813) 2022-06-27 10:35:41 +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
Felipe Marques de Almeida
e1a3ae6bf5
make module output meta map (#1803) 2022-06-23 12:43:06 +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
Sébastien Guizard
8296a28346
Remove a blank line (#1793) 2022-06-17 10:58:24 +01:00
Maxime U. Garcia
757c20c8eb
Same version on conda and in the dockerfile (#1791) 2022-06-16 16:25:54 +02:00
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
FriederikeHanssen
1ac223ad43
GATK/Getpileupsummaries: If no intervals use variants instead (#1787) 
If no intervals use variants instead
 2022-06-16 15:00:01 +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
WackerO
f1b3174501
Merge branch 'master' into mpileup_bgzip 2022-06-13 09:48:47 +02:00
WackerO
24e05f6097
Update modules/samtools/mpileup/main.nf 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-06-13 09:35:34 +02:00
FriederikeHanssen
5b27af025a
Merge branch 'master' into manta_convert 2022-06-13 09:29:50 +02:00
FriederikeHanssen
b8ff8e32e3
Update modules/manta/convertinversion/main.nf 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-06-13 09:26:29 +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
dd6c514710 Fix linting 2022-06-11 13:12:56 +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
James A. Fellows Yates
01d4a1fa3a
Apply suggestions from code review 2022-06-10 14:46:58 +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
Gisela Gabernet
5a16cf7bae
Merge branch 'master' into cellranger-7.0.0 2022-06-10 11:19:57 +02:00
Alexander Peltzer
62c4b59d10
Update main.nf 2022-06-10 11:05:59 +02:00
Thiseas C. Lamnidis
9948e9fe21
Merge branch 'master' into sexdeterrmine 2022-06-10 11:03:18 +02:00
Thiseas C. Lamnidis
fe855a1c23
Apply suggestions from code review 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-06-10 11:03:01 +02:00
Alexander Peltzer
cfcd93f3e7
Update Dockerfile 2022-06-10 10:56:13 +02:00
Alexander Peltzer
61d87bb2bc
Update main.nf 2022-06-10 10:54:06 +02:00
Alexander Peltzer
e499abe572
Update main.nf 2022-06-10 10:53:48 +02:00
Alexander Peltzer
8032833e6e
Update main.nf 2022-06-10 10:53:09 +02:00
Alexander Peltzer
e36b79201d
Update Dockerfile 2022-06-10 10:52:13 +02:00
James A. Fellows Yates
c9db677a45
Merge branch 'master' into r-ampir 2022-06-09 19:28:37 +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
jasmezz
ba53e09b64 Implement suggestions from code review 2022-06-09 15:37:35 +02:00
Rike
6a4732ef3b similar issues arise with bqsrspark, also use broadinstitute container 2022-06-09 15:29:00 +02:00
Rike
8e8f4c9c51 remove singulairty container 2022-06-09 15:16:11 +02:00
nvnieuwk
873215c8ae
Update modules/gatk4/reblockgvcf/main.nf 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-06-09 15:11:18 +02:00
Rike
89a6a03e38 fix container tag 2022-06-09 15:09:19 +02:00
Nicolas Vannieuwkerke
81fff7384d small fix and typo 2022-06-09 15:08:02 +02:00
Rike
b9e397ff15 use broadinstitute container 2022-06-09 15:06:46 +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
Rike
ef5b0dd977 gatk4 version update to 4.2.6.1 2022-06-09 14:54:19 +02:00
nvnieuwk
e88a4ff70b
Merge branch 'master' into add-optional-fasta-parameter-to-ensemblvep 2022-06-09 11:54:22 +02:00
Nicolas Vannieuwkerke
5ccf6fbcc9 add optional fasta argument to ensemblvep 2022-06-09 11:45:27 +02:00
SusiJo
cda434611f fix conda with openjdk 1.8 2022-06-09 10:24:39 +02:00
SusiJo
0204d2374b Merge remote-tracking branch 'origin/master' into gatk_spark 2022-06-09 09:33:17 +02:00
James A. Fellows Yates
70f7f07a37
Apply suggestions from code review 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-06-09 08:33:37 +02:00
James Fellows Yates
939653a47e Changes after code review 2022-06-09 08:26:04 +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
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
Lucas Taniguti
f5615c3db6 fix: stub output name 2022-06-08 10:10:24 -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
e5f8924fab
Update modules/multiqc/main.nf 
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
 2022-06-08 14:41:10 +02:00
Ramprasad Neethiraj
ea4dc866e0 add index 2022-06-08 14:38:55 +02:00
Ramprasad Neethiraj
1648d2fcba add index 2022-06-08 14:36:25 +02:00
Matthias De Smet
7b018acabb
Update modules/multiqc/main.nf 
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
 2022-06-08 14:36:13 +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
f1e33ca6e0 update mqc command 2022-06-08 14:02:04 +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
Taniguti
d5e077a2e9
Merge branch 'master' into haplocheck 2022-06-08 07:31:28 -03:00
MaxUlysse
07eff4346f fix path to symbolic links 2022-06-08 11:46:45 +02:00
Maxime U. Garcia
4935bb98cb
Apply suggestions from code review 
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
 2022-06-08 11:38:02 +02:00
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
Matthias De Smet
d196552e06 update input 2022-06-07 16:33:17 +02:00
Ramprasad Neethiraj
16e5e6093c Merge branch 'master' of https://github.com/nf-core/modules into rhocall 2022-06-07 14:45:09 +02:00
Ramprasad Neethiraj
17a4e93142 fix versions.yaml 2022-06-07 14:43:35 +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
Nicolas Vannieuwkerke
4c7ef30fb6 changed to label to medium 2022-06-07 12:17:14 +02:00
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
0d087b4890
Update modules/gatk/realignertargetcreator/main.nf 2022-06-03 21:33:54 +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
James A. Fellows Yates
e827a042ce
Update modules/gatk/unifiedgenotyper/main.nf 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-06-03 21:24:03 +02:00
Robert A. Petit III
d7cec801b2
Update main.nf 2022-06-03 13:05:43 -06:00
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
MaxUlysse
f9ac4e28e9 cover all use cases 2022-06-03 15:37:10 +02:00
SusiJo
e2bb56608c change prefix output 2022-06-03 13:50:45 +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
Matthias De Smet
cf9d62fc83
Merge branch 'master' into bump/picard 2022-06-02 22:09:42 +02:00
James Fellows Yates
a565d9072a Add GATK UnifiedGenotyper 2022-06-02 21:39:39 +02:00
James Fellows Yates
a14855dbe8 Start meta 2022-06-02 21:22:21 +02:00
James Fellows Yates
544b62df45 Star work on GATK UG 2022-06-02 21:11:17 +02:00
James Fellows Yates
de88adc926 Standardise parameters (no tests yet until realigntarget creator ready) 2022-06-02 20:35:34 +02:00