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Author SHA1 Message Date
Ramprasad Neethiraj
a8e6a88163
update options (#1959) 
* update options

* update test
 2022-08-22 16:26:05 +02:00
Alexander Ramos Díaz
37c6d4a1a1
Add module: goat/taxonsearch (#1866) 
* first commit

* single taxon input

* added .tsv output

* input: single taxon or file with taxon identifiers

* updated input and output

* removed wrong tool description

* added tests

* ext.args = '-l -b'

* fixed wrong input names

* updated test file

* Update modules/goat/taxonsearch/main.nf

simple version output

Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>

* removed 'NO_FILE' from input definition

* added ! in if statement

* optional input: empty list

* successful updated test

* added test with file

* remove blank spaces in include {}

* added test with taxa file

Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
 2022-08-18 08:34:58 -06:00
nickhsmith
454e0acc09
Mpileup intervals (#1955) 
* update tests

* update

* update

* make the manta inputs consistant for germline/somatic/tumoronly

* match chromosomes to cram file (chr21)

* undo genotypegvfs

* undo genotypegvfs

* include intervals

* update md5 with interval

Co-authored-by: Smith Nicholas <smith@in.tum.de>
 2022-08-16 14:16:35 +02:00
Matthieu Muffato
458f4396a6
Added support for task.ext.args (#1954) 
* Added support for `task.ext.args`

* Renamed the module since it can now process any sort of BED file
 2022-08-16 12:05:25 +01:00
nvnieuwk
eab173f2bb
Added java options to vardict java (#1695) 
* Added java options to vardict java

* updated test.yml

* correctly added java options

* Added automatic version numbers for vardictjava

* possible fix for version number in conda

* removed the cram tests

* linting

* Update modules/vardictjava/main.nf

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>

* Update modules/vardictjava/main.nf

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>

* removed the version line

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
 2022-08-10 14:13:03 +02:00
Ramprasad Neethiraj
94619a3faf
Add genmod (#1950) 
* add annotate

* add models

* add compound

* add score

* update annotate recipe

* update meta and main

* main updates

* add test for annotate

* update all tests

* refactor

* update tests

* fix conda issue

* review suggestions
 2022-08-09 14:48:29 +02:00
Annick Renevey
47cc7a77bf
add stub for stringtie (#1949) 
* add stub for stringtie

* add ballgown file to test.yml

* add ballgown file to test.yml forward
 2022-08-09 10:11:37 +02:00
Annick Renevey
cd22a76c78
Add stub star align genomegenerate (#1948) 
* correct md5sum for updated star/samtools

* merge changes in align test.yml

* update md5sum for star genomegenerate

* update md5sum for star align
 2022-08-09 09:42:19 +02:00
Annick Renevey
ac1c6ad710
add stub for picard/collectwgsmtrics (#1945) 
* add stub for picard/collectwgsmtrics

* fix conda build needs to be >2.0 error and typo
 2022-08-09 09:33:15 +02:00
Annick Renevey
479e0638d1
add stub for kallisto/index (#1944) 2022-08-09 09:23:55 +02:00
Annick Renevey
b034029b59
add stub for cat/fastq (#1943) 
* add stub for cat/fastq

* prettier linting
 2022-08-09 09:18:37 +02:00
Sofia Stamouli
734d0db607
Update module: Use report insted of results for centrifuge/kreport (#1929) 
* Use report insted of results for kreport

* Update modules/centrifuge/kreport/meta.yml

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-07-27 14:24:06 +02:00
Matthieu Muffato
31409f5e72
Added the samtools/dict module (#1922) 
* Added the samtools/dict module

* samtools/dict is single-threaded
 2022-07-26 22:13:19 +01:00
Matthieu Muffato
30b0485912
Added support for meta in bwamem2/index (#1921) 
* Added support for meta in bwamem2/index

* Added missing description of the input meta map (fasta file)

* Made bwamem2/mem aware of the meta map the index carries

* The output meta map needs to be same as the input bam file

Don't merge it with the index's

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-07-26 21:48:47 +01:00
Alexander Ramos Díaz
4ed5dc4593
new (fixed) module: entrezdirect/esearch (#1927) 
* added module files

* latest version

* latest version

* latest version

* latest version

* updated test, failing

* added comment on why to use tail -n+3

* same as latest test

* moved args to the end of script

* updated test

* double quotes for esearch input

* removed tail -n+3, stderr is redirected by nextflow

* changed single to double quotes

* Update modules/entrezdirect/esearch/main.nf

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

* Update modules/entrezdirect/esearch/meta.yml

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

* Update meta.yml

removed default from database parameter

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-07-26 09:07:38 -06:00
Alexander Ramos Díaz
ad426cb18c
new (fixed) module: entrezdirect/xtract (#1926) 
* first commit: module files

* last version main.nf

* modules/entrezdirect/xtract/meta.yml

* updated file

* updated test

* Update modules/entrezdirect/xtract/main.nf

changed name of output file

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

* Update modules/entrezdirect/xtract/meta.yml

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

* Update tests/modules/entrezdirect/xtract/main.nf

Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>

* Update tests/modules/entrezdirect/xtract/main.nf

Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>

* updated test, removed esummary input file

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
 2022-07-26 08:58:49 -06:00
Alexander Ramos Díaz
f420d97ca2
renamed output in entrezdirect/esummary: xml (#1928) 
* renamed output: xml

* removed tail -n+3 from output

* removed comment

* removed blank space

* removed blank space

* updated test
 2022-07-26 08:33:02 -06:00
Jasmin F
7f7f6bc913
Add module hamronization/abricate (#1925) 
* Add hamronization/abricate

* Update input pattern in meta.yml

* Update location of hamronization test data

* Apply suggestions from code review
 2022-07-26 12:55:53 +02:00
nvnieuwk
c363d8c37c
added gvcftools/extractvariants (#1924) 
* added gvcftools/extractvariants

* linting

* Update modules/gvcftools/extractvariants/meta.yml

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>

* Update modules/gvcftools/extractvariants/main.nf

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>

* added uncompressed input handling

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
 2022-07-25 13:30:35 +02:00
Luca Cozzuto
a8b0fce8ce
Tailfindr (#1904) 
* adding tailfindr module

* replacing the container

* removing todo

* removing todo and fixing meta.yml

* Update modules/tailfindr/main.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Update modules/tailfindr/main.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Update modules/tailfindr/meta.yml

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Update modules/tailfindr/main.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Update tests/modules/tailfindr/test.yml

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Update modules/tailfindr/meta.yml

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Update modules/tailfindr/meta.yml

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Update modules/tailfindr/main.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Update modules/tailfindr/main.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Update main.nf

* Update meta.yml

* Update modules/tailfindr/main.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Update meta.yml

* Update main.nf

* adding pytest

* Update main.nf

* Update modules/tailfindr/main.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Update test.yml

* Update main.nf

* Update main.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
 2022-07-22 16:20:53 +02:00
Luca Traverso
c9dc0a82d0
New Module: atlas/recal (#1915) 
* commit 08/07

* fixed formatting

* atlas recal commit - corrected formatting

* Fix tests

* Fix meta.yml

* Prettier

* Delete nextflow

* yaml > yml

* Delete meta.yaml

* Fix test

* Forgot to run prettier?

Co-authored-by: ltcrod <luca_traverso@kickseed.localdomain>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-07-22 15:36:53 +02:00
nvnieuwk
8656636f0d
update for bcftools merge (#1908) 
* update for bcftools merge

* Update modules/bcftools/merge/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* Update modules/bcftools/merge/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* updated test.yml

* added the bed file to the main input tuple

* merged all output into one output channel

* added a test for bcf.gz output

* Update modules/bcftools/merge/main.nf

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

* updated the tests

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
 2022-07-20 11:22:51 +02:00
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
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
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
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