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Author SHA1 Message Date
Annick Renevey
53108b6b51
add stub for qualimap/rnaseq (#1946) 
Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
 2022-08-09 15:24:35 +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
James A. Fellows Yates
5644df8d43
Update module: Gecco fix to no file generated if no hits found (#1930) 
* Make gene and cluster TSVs optional output in case no hits found

* update indicating optional output

* Apply suggestions from code review

Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>

Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
 2022-07-27 15:19:43 +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
ce06694af8
Added support for ext.args in samtools/faidx (#1919) 
ext.args was not used in the actual command-line

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-07-26 21:51:47 +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
Maxime U. Garcia
e5b44499ef
update multiqc and strelka modules version to have the same as the other modules using these ones (#1914) 
* update multiqc version in CUSTOM_DUMPSOFTWAREVERSIONS

* update stelka version in  STRELKA_GERMLINE

Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
 2022-07-21 11:44:07 +02:00
WackerO
6b011dd148
SVDB MERGE samtools version (#1913) 
* Started (again) to work on bgzipping SVDB_MERGE output

* Updated test yml

* SVDB_MERGE now bgzips output

* Fixed singularity, renamed tests in test.yml

* Added samtools version

Co-authored-by: Cloud User <centos@oskar-instance.novalocal>
 2022-07-20 12:42:40 +02:00
louperelo
839bc6b1ad
Amrfinderplus add tool and db version as output (#1912) 
* 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

* add tool and db version to output

* Apply suggestions from code review

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

* Update meta.yml

Co-authored-by: James Fellows Yates <jfy133@gmail.com>
 2022-07-20 11:55:44 +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
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
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