Commit graph

1815 commits

Author SHA1 Message Date
Daniel Lundin
8bc5236371
Add hmmer/eslreformat (#2009)
* Created hmmer/eslalimask from template

* esl-alimask module with --rf-is-mask test case

* Add optional file output

* Add hmmer to test name

* Move from process_single to process_low

* Test for versions.yml, plus content

* Prettier

* Avoid gzipping input alignment

* hmmer/eslreformat from template

* Started on main.nf

* meta.id to prefix

* Continued work

* Fix version string so it's from *this* tool

* hmmer/eslreformat

* Prettier

* Get tests/config/pytest_modules.yml back

* Delete extra hmmer/eslalimask in pytest_modules.yml

* More prettier

* Fix path to versions.yml in test

* Remove 'format' param

* Fix problems with format param deletion

* Document format param
2022-09-05 15:21:09 +02:00
Daniel Lundin
b5e3d16d80
Added hmmer/eslalimask (#1999)
* Created hmmer/eslalimask from template

* esl-alimask module with --rf-is-mask test case

* Add optional file output

* Add hmmer to test name

* Move from process_single to process_low

* Test for versions.yml, plus content

* Prettier

* Avoid gzipping input alignment

* meta.id to prefix

* Fix version string so it's from *this* tool
2022-09-05 14:01:33 +02:00
Adam Talbot
e7845e2472
1976 msisensor2 (#1977)
* msisensor2: Add msisensor2 module

* msisensor2/scan module added

* msisensor2 tests added

Changes:
 - tests added for msisensor2 from the msisensor2 github repo. No
 available tests from NF-Core test repo.

Relates to #1976

* msisensor2 slight bump in stuff

* msisensor2: Replaced spelling of 'tumour' with 'tumor'

* msisensor2: fix linting, testing and containers

Relates to #1976

Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-09-05 13:00:18 +02:00
nvnieuwk
5a30294eec
Update for the delly/call module (#2008)
* updated the delly/call module

* Update modules/delly/call/meta.yml

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

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-09-05 12:09:55 +02:00
Matthias De Smet
36049bf544
Fgbio/fastqtobam (#1980)
* fix samtools stats thread usage

* fix samtools stats thread usage (#1975)

* fix samtools stats thread usage

* fix checksums

* Fix/samtools flagstat (#1979)

* fix samtools stats thread usage

* flagstat: fix threads

* Update busco to v5.4.3 and tar small files (#1970)

* Update busco to v5.4.3 and tar small files

* Fix file contain strings

* Swap md5sums to contains for variable files

* Simplify and generalize module

* add test.yml

* Update modules/fgbio/fastqtobam/meta.yml

Co-authored-by: Moritz E. Beber <midnighter@posteo.net>

* add support + tests for cram output

* more tweaks

* update test.yml

* prettier

* try to fix tests

* fix tests

* prettier

* drop checksum for cram

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
2022-09-05 11:57:55 +02:00
nvnieuwk
09acfad211
new module gatk4/collectreadcounts (#1998)
* added the module

* updated test.yml

* Update modules/gatk4/collectreadcounts/main.nf

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* small fix

* tests update

* linting

* tests update (again)

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-09-05 10:49:13 +02:00
tamuanand
57b43ed3de
New module - BBMap clumpify (#1978)
* Update meta.yml by fixing html pattern expected 

Fixed html pattern typo:

Before: pattern: "*.thml"

After fix: pattern: "*.html"

* main.nf for bbmap_clumpify

* meta.yml for bbmap_clumpify

* bbmap/clumpify via Gitpod and @mahesh-panchal guide

* small changes to tests

* explicit mention of output file pattern - *.clumped.fastq.gz

* Update modules/bbmap/clumpify/main.nf

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

* Update modules/bbmap/clumpify/main.nf

Accepted @mahesh-panchal suggestions

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

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
2022-09-05 08:23:08 +02:00
nvnieuwk
a509eda8a4
New module: Whamg (#1994)
* added whamg

* linting

* linting
2022-09-02 13:33:48 +02:00
nvnieuwk
49825425bb
Update delly/call version (#1991)
updated version + added tests
2022-09-02 10:08:41 +02:00
Louis LENEZET
01d6d4c286
Creation of Glimpse Chunk (#1985)
* Creation of Glimpse Chunk
Add sub tools chunk with configuration and needed files for unitest.

* Code linting correction

* Prettier ran
Newline deleted in nextflow.config

* New final line and white spaces

* Change Pytest.yml to work as a subtool.

* Control for the parameters deleted.
Control for the size/count of the window and buffer not needed.
They have some defaults value.

* Changed the different recommended part by @nvnieuwk

Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
2022-09-01 10:01:49 +02:00
Edmund Miller
2f1555bf77
feat(pints): Add initial caller module (#1983)
* feat(pints): Add initial caller module

* docs(pints): Add initial documentation

* chore: Add TODOs

* test(pypints): Use docker image for singularity

The image doesn't exist yet for some reason

* test(pints): Remove unidirectional peaks hash

* style(pints): Align emits
2022-08-31 14:04:48 +00:00
Moritz E. Beber
3a138c2d27
Update bracken (#1982)
* chore: update version

* tests: update use of kraken2 module
2022-08-30 15:15:48 +02:00
Matthias De Smet
ee46c19d03
new module: Picard/fastqtosam (#1911)
* add Picard FastqToSam

* Update test.yml

* update tests

* possible fix?

* fixed!

* Update modules/picard/fastqtosam/main.nf

Co-authored-by: Moritz E. Beber <midnighter@posteo.net>

* Update modules/picard/fastqtosam/main.nf

Co-authored-by: Moritz E. Beber <midnighter@posteo.net>

* simplify tests

* fix tests

* revert version check

Co-authored-by: CMGG ICT Team <ict@cmgg.be>
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
2022-08-30 14:27:00 +02:00
Mahesh Binzer-Panchal
89a84538be
Update busco to v5.4.3 and tar small files (#1970)
* Update busco to v5.4.3 and tar small files

* Fix file contain strings

* Swap md5sums to contains for variable files
2022-08-30 10:25:01 +02:00
Matthias De Smet
bbb99cb8d6
Fix/samtools flagstat (#1979)
* fix samtools stats thread usage

* flagstat: fix threads
2022-08-29 13:11:58 +02:00
Matthias De Smet
f4eab79459
fix samtools stats thread usage (#1975)
* fix samtools stats thread usage

* fix checksums
2022-08-29 12:05:47 +02:00
Daniel Lundin
98642619bd
Add hmmbuild (#1960)
* Fixing test.yml

* hmmbuild passing tests

* Output meta

* Linting problem

* Linting problem again

* Fix prettier

* Update modules/hmmer/hmmbuild/meta.yml

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

* Fix missing prefix

* Accept mxfile param

* Output gzipped hmm

* Moved input file for test to modules branch

* Update modules/hmmer/hmmbuild/meta.yml

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

* Describe mxfile

* Get LENG  80 check back

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-08-25 09:39:40 +02:00
Adam Talbot
7bfbce94b0
Added fq/lint module (#1968)
* Added fq/lint module

Additions:
 - fq/lint module, which checks paired end FASTQ files and confirms they
 are valid.

Relates to #1967

* fq/lint linting

* Correct Singularity image

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

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-08-24 10:20:39 +02:00
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
James A. Fellows Yates
b02e648c22
Add MOTUS/MERGE (#1734)
* Add motus/merge module, missing test yml

* Fix prefix

* Fix polymersase

* Update test meta.yml

* Try new version system

* Typo fix

* Clairfy docs for the version file

* Switch to directory auto detection

* Now with the change and not just meta

* Remove now unneeded input parameter from test

* Fix input type check

* Try adding db requirement to fix docker issue

* Update modules/motus/merge/main.nf

* Fix input

* Apply suggestions from code review

* Fix md5sums

* Replace debugging db location with actual

* Fix contains due to further varialbility

* Indenting
2022-07-07 09:47:41 +02:00
Adam Talbot
43d05d5482
fix (1852): picard/collectmultiplemetrics supports CRAM (#1853)
* fix (1852): picard/collectmultiplemetrics supports CRAM

Changes:
 - Add .fai input to Picard CollectMultipleMetrics
 - Now supports CRAM effectively.
 - Will break existing pipelines!

Fixes #1852

* 1852 Update meta.yml to include .fai
2022-07-06 19:05:53 +02:00
Alexander Peltzer
ed5594bee3
Bump version of kallistobustools/count (#1834)
* Bump version of kallistobustools/count

* Trying to update the entire call of kbtools for scrnaseq

* Improved tests for kallistobustools/count

* Add memory, remove workflow as this is passed as args now

* Update modules/kallistobustools/count/main.nf

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>

* adding missing value

* workflow properly chained together

* changing --workflow to ext.args

* fix intron channel

* fixed checking whether filename is empty or not

* bump indentation

* fixed if else

* Fix linting

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Felipe Marques de Almeida <almeidafmarques@gmail.com>
2022-07-05 13:28:57 +02:00
James A. Fellows Yates
aed45dd766
Add MultiVCFAnalyzer (#1845)
* Add MultiVCFAnalyzer

* Fix versions

* Fix tests due to md5sum var

* Apply suggestions from code review

* Linting

* Apply suggestions from code review

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-07-05 09:47:10 +02:00
James A. Fellows Yates
6702d2e145
Add MEGAN/DAA2INFO (#1848)
* Add daa2info

* Add right flag in the config

* Fix config

* Apply suggestions from code review

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

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2022-07-05 09:36:22 +02:00
Sébastien Guizard
60c65fb386
New modules: ultra/index and ultra/align (#1830)
* Add ultra/index and ultra/align modules

* Correct tag and prefix

* Fix typos

* Remove SAMTOOLS SORT from test

* Update: Convert sam to bam

* Add tag to docker image

* Fix typo

* Add args2 for samtools
2022-07-04 07:46:49 +01:00
James A. Fellows Yates
0e9fd9370a
Fix Krona ktimporttaxonomy to allow multiple input files and simplifies database input (#1841)
* Remove quotes around input reports variable for ktImportTaxonomy as prevents supplying multiple files

* Add using prefix for output files

* Tweak meta reflecting more flexible input database specification

* Linting

* Fix finding the correct directory

* Update main.nf

* Fix database inport

* Prettier
2022-07-01 15:18:29 +02:00
James A. Fellows Yates
7d0ddbc8ab
Add atlas/call (#1809)
* Add atlas/call

* Apply suggestions from code review

* Update modules/atlas/call/main.nf

Co-authored-by: Thiseas C. Lamnidis <thisseass@gmail.com>

* Apply suggestions from code review

Co-authored-by: Thiseas C. Lamnidis <thisseass@gmail.com>
2022-07-01 15:06:07 +02:00
louperelo
057a889d3b
new module hamronization/rgi (#1844)
* new module hamronization/rgi

* remove comments

* Update modules/hamronization/rgi/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-07-01 12:03:08 +02:00
Harshil Patel
b96066565a
Add ffq module (#1842) 2022-07-01 08:59:13 +02:00
Júlia Mir Pedrol
bd0fa881f6
Add new module: Flye (#1164)
* changing mv by gzip

* changing mv by gzip

* first module creation

* add test.yml

* add flye to pyestes_modules.yml

* update flye module

* delete functions.nf

* generate test.yml

* fix contains from test.yml

* test file assembly_info.txt with regex

* check that file contains at least contig_1

* fix typo in contains

* update version

* split fastq file for raw runs

* use asm-coverage to reduce memory usage

* fix module name error

* add genome-size

* decrease coverage

* change test data for raw runs

* add coverage and genome size

* Apply comments from code review

Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com>

* after many trys, add a stub run

* remove md5sum for stub run

* Apply suggestions from code review

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

* fix review comments

* Apply suggestions from code review

Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com>

* no hardcoded version in stub run

* Update modules/flye/main.nf

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

Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
2022-06-30 22:45:55 +02:00
Matt Olm
031fbd37aa
Instrain profile (#1822)
* add instrain profile

* module instrain/profile

* add instrain profile

* module instrain/profile

* instrain profile

* Update modules/instrain/profile/main.nf

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

* Update modules/instrain/profile/meta.yml

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

* Update modules/instrain/profile/meta.yml

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

* Update modules/instrain/profile/meta.yml

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

* Update modules/instrain/profile/main.nf

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

* Update modules/instrain/profile/main.nf

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

* Update modules/instrain/profile/main.nf

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

* update

* linting

* Apply suggestions from code review

* Update modules/instrain/profile/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-06-30 18:44:41 +02:00
Jose Espinosa-Carrasco
82fdff4fb4
Add khmer unique-kmers.py module (#1838) 2022-06-30 16:23:30 +01:00
Matthias De Smet
44baf85bcc
snapaligner: improve index detection (#1836)
* improve index detection

* fix escaping
2022-06-30 12:19:46 +02:00
James A. Fellows Yates
486eebfd29
Update RGI: add database version reporting to module (#1824)
* Add rgi database version to module as fixed within the container/environment

* Remove check of the version file

* Or rather check for existance of the versions file not contents

* Delete main.nf

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-06-29 16:30:51 -06:00
Mahesh Binzer-Panchal
b67556e29f
Add FastK/Merge (#1828)
* Add FastK/Merge

* Update modules/fastk/merge/main.nf

* Update modules/fastk/merge/meta.yml

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
2022-06-29 18:04:36 +02:00
Annick Renevey
80746895e2
Update Arriba to 2.3.0 (#1827)
* update test files md5sum

* update test files md5sum, again
2022-06-29 14:39:13 +02:00
Matthias De Smet
e2755cb039
add extra output from snap aligner (#1826) 2022-06-29 12:37:38 +02:00
nvnieuwk
d596571a03
added an optional vcf index to bcftools/norm (#1821)
* added an optional vcf index to bcftools/norm

* updated test.yml for failing conda tests
2022-06-28 16:18:12 +02:00
SusiJo
98ffb09002
Added output files to ASCAT (#1820)
* add unzip alleles + loci

* fix the partial absolute prefix path

* exchanged deprecated function + added metrics

* updated meta

* tested logRCorrection + cram input

* added BED for WES

* added outputs + alleleCounter version

* test samtools chr operations, fixed cancerit conda

* ch formatting, fasta, bed input

* comment out local tests

* added metrics, bed, ref_fasta

* rm print statement

* added stub outputs

* rm versions.yml

* fix linting

* rm fictitious md5sums for stub-run

* try fixing top-level of stub versions.yml

* ordered inputs alphabetically, ref_fasta -> fasta

* rm R system command, adjust meta.yml

* prettier yml

* added outputs + prefix to outputs

* added test-yml outputs

* change underscores to dots
2022-06-28 14:45:57 +02:00
Adam Talbot
009f7c691c
Add module: gatk4/leftalignandtrimvariants (#1808)
* Added: gatk4/leftalignandtrimvariants

Additions:
 - GATK4/LeftAlignAndTrimVariants module
 - Use sars-ncov2 test data as this normalises a larger INDEL correctly.

Fixes #1801

* fixup: Added index to output spec

* fixup: Pattern of tbi output corrected to 'tbi'

* gatk4/leftalignandtrimvariants: Added intervals

Changes:
 - gatk4/leftalignandtrimvariants now supports optional interval as BED
 file
 - Tests added with and without interval. Not test BED file excludes all
 variants so no variants are actually normalised.

Fixes #1801

* fixup: leftalignandtrimvariants vcf->tbi fix

* fixup: gatk4/leftalignandtrimvariants Intervals added to meta.yml
2022-06-28 10:44:08 +02:00
Merlin Szymanski
b6fe5d2643
Add Atlas/PMD (#1810)
* add atlas/pmd
* update atlas/pmd tests
* Add atlas/PMD module
* Remove comment
* Run Prettier
* Incorporate Review by @jfy133

Co-authored-by: maxibor <maxime.borry@gmail.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-06-24 16:53:51 +02:00
FriederikeHanssen
9b51362a53
Proposal: Rename output from fastp module (#1802)
* Rename output from fastp module

* UPdate tests

* fix alignment

* prettier

* Update modules/fastp/main.nf

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

* apply review suggestion -sf

* typo

* update md5

* update md5

* try with human data

* revert, human data also doesn't work

* use contains instead

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
2022-06-24 10:01:14 +02:00
nvnieuwk
1363130410
small changes to vcfanno (#1804)
removed a redundant input field from vcfanno

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
2022-06-24 08:58:26 +02:00
Matthias De Smet
5e2325956c
bump bclconvert version (#1806) 2022-06-24 07:14:42 +02:00
Mahesh Binzer-Panchal
a7193dc628
Add MerquryFK KatGC (#1798)
* Add KAT GC

* Add additional container warning
2022-06-23 20:57:15 +02:00
2f0b192404
Add KAIJU2KRONA module (#1800)
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-06-23 16:38:50 +00:00
SusiJo
7daba6a13f
Update ASCAT module (#1805)
* add unzip alleles + loci

* fix the partial absolute prefix path

* exchanged deprecated function + added metrics

* updated meta

* tested logRCorrection + cram input

* added BED for WES

* added outputs + alleleCounter version

* test samtools chr operations, fixed cancerit conda

* ch formatting, fasta, bed input

* comment out local tests

* added metrics, bed, ref_fasta

* rm print statement

* added stub outputs

* rm versions.yml

* fix linting

* rm fictitious md5sums for stub-run

* try fixing top-level of stub versions.yml

* ordered inputs alphabetically, ref_fasta -> fasta

* rm R system command, adjust meta.yml

* prettier yml
2022-06-23 17:06:00 +02:00
James A. Fellows Yates
9d7208504d
Add gecco/run module (#1790)
* Add gecco/run module

* Fix container URLs

* Apply suggestions from code review

Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
2022-06-22 13:43:45 +02:00
Mahesh Binzer-Panchal
280eec5317
Add MerquryFK KatComp (#1797)
Add Kat Comp

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-06-21 09:43:37 +02:00
Adam Talbot
f19ec865aa
vcf2maf module with built in VEP (#1768)
vcf2maf module created

Additions:
 - vcf2maf module created
 - If VEP is present in PATH, it is added to command
 - If VEP is missing, it is ignored (recommended to skip with --inhibit-vep)
 - VEP version automatically added to versions.yml
 - Uses VEP cache during testing which is added to test-datasets in https://github.com/nf-core/test-datasets/pull/563
 - Default Docker image includes VEP and vcf2maf
 - Test includes without VEP.

Relates to #490
2022-06-20 18:27:12 +02:00
James A. Fellows Yates
be8d7b3293
Update MALT to older version due to major bug in most recent version (#1796)
* Rollback version

* Start work rollback to 0.4.1

* Further changes

* Re do dynamic flag creation

* Prettier.
2022-06-20 08:20:22 +02:00