Commit graph

1815 commits

Author SHA1 Message Date
Ashot Margaryan
d8ba32c6b5
Somalier relate (#2001)
* Working version of somalier relate

* few changes

* new changes

* corrected test.yml

* updated container paths and file paths

* changed container and inputFile paths

* changed left padding

* requested changes

* Update modules/somalier/relate/main.nf

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

* Update modules/somalier/relate/main.nf

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

* Update modules/somalier/relate/main.nf

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

* Update modules/somalier/relate/main.nf

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

* Update modules/somalier/relate/meta.yml

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

* Update modules/somalier/relate/meta.yml

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

* Update modules/somalier/relate/meta.yml

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

* requested changes

* requested changes

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-09-19 13:22:24 +02:00
James A. Fellows Yates
90aef30f43
Set process label to process_single for modules with no task.cpus usage (#2076)
* Set process label to `process_single` for modules with no `task.cpus` usage

* Fix tests of 'borked' modules

* prettier

* More modules are single-threaded and can use process_single

* Adding process_single to hmmer/esl* modules

* Fix failing tests

* Prettier

Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
2022-09-19 11:54:47 +02:00
Daniel Lundin
46ad627a73
Add gappa/examineassign (#2079)
* Created gappa/examineassign from template

* Test passing

* Run only when taxonomy is set

* Revert adding taxonomy to when

* Add period after prefix

* Fix test

* Add some keywords

* Add one more keyword
2022-09-19 11:49:42 +02:00
Daniel Lundin
b6f18f8733
eslreformat: descriptive suffix (#2081) 2022-09-19 09:49:00 +02:00
Ashot Margaryan
f62e4cf5f0
Added Somalier extract module (#1986)
* Added Somalier extract module

* changed somalier_dbg4 to somalier for versions.yml

* added  and minor changes in meta.yml

* Apply suggestions from code review

* Update main.nf

* Typo in quay.io rl

* updated the input

* new updates

* linting

* linting

* changed the test.yml

* Update modules/somalier/extract/main.nf

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

* Update modules/somalier/extract/main.nf

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

* Update modules/somalier/extract/meta.yml

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

* Update modules/somalier/extract/main.nf

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

* Update tests/modules/somalier/extract/main.nf

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

* Update modules/somalier/extract/main.nf

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

* Update tests/modules/somalier/extract/test.yml

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

* last changes

* Update modules/somalier/extract/meta.yml

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

* Update modules/somalier/extract/meta.yml

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

* Update modules/somalier/extract/main.nf

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-09-19 08:58:17 +02:00
Rafal Stepien
38383cfaef
Update eido/validate module (#2071)
* Update eido/validate module

* Update modules/eido/validate/meta.yml

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-09-16 09:00:03 -04:00
Rafal Stepien
9764eef361
Update eido/convert module (#2072)
* Update eido/validate module

* Update modules/eido/convert/meta.yml

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-09-16 08:54:40 -04:00
Matthias De Smet
b98f1b77d1
Bump bcl-convert version (#2077)
* Update main.nf

* update test.yml

* prettier
2022-09-16 14:34:52 +02:00
James A. Fellows Yates
54ff289487
Update mOTUs to remove now unused channel (#2075)
* Update main.nf

* Update meta.yml

* Re-add logos as not staged in a way that works with MultiQC config files

* Update main.nf

* Remove now unnecessary input channel

* Remove unused channel from tests
2022-09-16 10:23:21 +02:00
James A. Fellows Yates
8372df6fb2
Update MOTUS/MERGE (#2068)
* Update main.nf

* Update meta.yml

* Re-add logos as not staged in a way that works with MultiQC config files

* Add meta to mOTUs merge

* Put tests back to use downloaded db

* Apply suggestions from code review

* Fix test text string

* md5sum -> contains

* Update nextflow.config
2022-09-15 19:45:43 +02:00
Edmund Miller
4963ca0570
Add bases2fastq (#2054)
* feat(bases2fastq): nf-core modules create

* test(bases2fastq): Update tests

* docs(bases2fastq): Update meta.yml

* test: Add untar rundir
2022-09-15 13:50:33 +00:00
Ramprasad Neethiraj
513b5fcab9
update stub for svdb/merge (#2066)
update stub

Co-authored-by: Annick Renevey <47788523+rannick@users.noreply.github.com>
2022-09-15 14:20:09 +02:00
Daniel Lundin
847bebc0ab
Make hmmer/hmmalign output files with correct prefix (#2067) 2022-09-15 14:06:18 +02:00
James A. Fellows Yates
4b1d4bf401
Update MULTIQC for an additional custom config (#2063)
* Update main.nf

* Update meta.yml

* Re-add logos as not staged in a way that works with MultiQC config files

* Add support for secondary custom configs
2022-09-15 13:53:15 +02:00
Ramprasad Neethiraj
8572bc8865
Update stub for ucsc/wigtobigwig (#2065)
update stub
2022-09-15 13:12:05 +02:00
Matthias De Smet
b63b9f752d
Fix for nested directories in tar archive (#2062)
* Fix for nested directories in tar archive

* fix untar for tar with a single directory

* prettier
2022-09-15 11:32:36 +02:00
James A. Fellows Yates
978087354e
Update METAPHLAN3_METAPHLAN3 to correct module name (#2056)
* Update main.nf

* Update meta.yml

* Re-add logos as not staged in a way that works with MultiQC config files

* Fix MeaPhlAn3 module name

* Fix metayaml

* Fix meta.yml
2022-09-15 09:09:55 +02:00
Daniel Lundin
885e724e07
Add postprocessing option to hmmer/eslreformat (#2061)
* Add postprocessing option to hmmer/eslreformat

* Update tests/modules/hmmer/eslreformat/nextflow.config

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

* Update modules/hmmer/eslreformat/main.nf

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
2022-09-14 18:43:50 +02:00
Ramprasad Neethiraj
67652c7c4d
add stub to picard/addorreplacereadgroups (#2057)
add stub
2022-09-14 15:44:47 +02:00
Lucpen
cad9133c71
Add haplogrep2 (#2030)
* feat added haplogrep classify

* feat made module

* fix added correct container

* feat removed md5sum

* fix trying to fix issue with version.yml

* fix some small things

* fix version

* fix on meta.yml

* fix stub run

* fix Apply suggestions from code review

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>

* fix Apply suggestions from code review2

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>

Co-authored-by: Taniguti <ltaniguti@gmail.com>
Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
2022-09-14 14:58:02 +02:00
James A. Fellows Yates
393dbd6dda
Update UNTAR to account for file-only or multi-directory tar archives (#2055)
* Update main.nf

* Update meta.yml

* Re-add logos as not staged in a way that works with MultiQC config files

* Fix when only files or multiple directories

* Add test for only-files tar

* Fix bash check
2022-09-14 10:40:45 +02:00
Rafal Stepien
c9b29c7686
Add eido/convert module (#2051)
* Add eido/convert module

* Run prettier

* Update modules/eido/convert/main.nf

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

* Update modules/eido/convert/main.nf

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

* Update extension format

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-09-13 12:17:29 -04:00
Rafal Stepien
2456ef7d99
Add eido/validate module (#2048)
* Add eido/validate module

* Apply first batch of updates after code review

* Remove readlink, update sed, update paths

* Move sample table index parameter to config

* Update tests/modules/eido/validate/test.yml

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

* Update tests/modules/eido/validate/test.yml

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

* Update tests/modules/eido/validate/test.yml

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

* Update tests/modules/eido/validate/test.yml

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

* Update modules/eido/validate/main.nf

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-09-13 10:27:28 -04:00
James A. Fellows Yates
36bcd675ae
Update METAPHLAN3/MERGEMETAPHLANTABLES (#2041)
* Update main.nf

* Update meta.yml

* Re-add logos as not staged in a way that works with MultiQC config files

* Add meta to mergemetaphlan3 tables

* Actually combine the data together
2022-09-13 14:37:46 +02:00
James A. Fellows Yates
ee0346b4d1
Update KRAKENTOOLS/COMBINEKREPORTS (#2043)
* Update main.nf

* Update meta.yml

* Re-add logos as not staged in a way that works with MultiQC config files

* Add meta to combinekreports
2022-09-13 14:31:27 +02:00
Matthieu Muffato
d75b37fef1
Upgraded getchromsizes to support meta and output the gzi index (#2046)
* This process is single-threaded

* Added meta to match the other nf-core modules

* "custom" is not a great name

* Newer modules have a stub

* To match the other modules

* self promotion

* Output the gzi file too, if there is one

* More Fasta extensions

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-09-12 13:17:13 +01:00
James A. Fellows Yates
2c70c1c195
Fix duplicated input in single-end fastp command (#2034)
* Update main.nf

* Update meta.yml

* Re-add logos as not staged in a way that works with MultiQC config files

* Removes duplicate input to single end  FASTP

* Fix md5sums

* Separate interleaved from normal SE command to continue supporting `split_by_lines`

* Simplify save_trimmed_fail

* Update modules/fastp/meta.yml
2022-09-09 11:08:52 +02:00
nvnieuwk
65800cee75
new module gatk4/collectsvevidence (#2039) 2022-09-09 10:58:47 +02:00
Matthieu Muffato
c736d26b7e
bedToBigBed AutoSql option (#1981)
* Added missing "ucsc" tags (as per the convention)

* Added support for the -as input file

* Added a test
2022-09-09 09:27:47 +01:00
Daniel Lundin
e97d4cd32b
epang: Output gzipped jplace (#2037)
* Output gzipped jplace
2022-09-09 09:54:03 +02:00
Matthieu Muffato
4f78d40b11
New module: fasta_windows (#1956)
* New module for fasta_windows

* Upgraded the code and the test to v2.4

* Standard list of Fasta file extensions

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

* Output file (and/or directory) names SHOULD just consist of only ${prefix}

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-09-09 08:41:38 +01:00
Daniel Lundin
b444b084fa
Add gappa/examinegraft (#2035) 2022-09-09 09:26:41 +02:00
nvnieuwk
bf09fdf892
new module: svtk/standardize (#2031)
* new module: svtk/standardize

* linting

* fixed tests
2022-09-08 15:03:08 +02:00
Matthieu Muffato
3eb99152ce
Added the optional .gzi output of "samtools faidx" (#1935) 2022-09-08 13:35:23 +01:00
James A. Fellows Yates
16eee433b8
Update MultiQC to re-add staging logos as a separate input channel (#2032)
* Update main.nf

* Update meta.yml

* Re-add logos as not staged in a way that works with MultiQC config files
2022-09-08 12:36:15 +02:00
James A. Fellows Yates
8d2fedadff
Multiqc sep logo (#2028)
* Separate MultiQC config from logo input channel

* Update meta.yml

* Update main.nf

* Add test for new check

* md5sum -> contains

* Remove logo input channel from MultiQC
2022-09-08 10:47:08 +02:00
Matthieu Muffato
73e062cf5e
Added the meta map to minimap2/index (#1934) 2022-09-08 09:27:14 +01:00
Daniel Lundin
74b569b66a
Add epang/place (#2023)
* Created epang module from template

* Module seems to be working

* Namechange to epang_place

* Move model to meta map

* Fix linting problems

* Prettier

* Forgot --threads!

* Moved module to epang

* Move reference file params

* Directory output

* Make all args optional

* Added inputs for three other types of file arguments

* Update modules/epang/main.nf

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

* Add directory to output doc, reorder the other

* Make model specification less hardcoded

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-09-08 10:05:57 +02:00
James A. Fellows Yates
31166227d3
Modify MULTIQC: separate logo from config file (#2027)
* Separate MultiQC config from logo input channel

* Update meta.yml

* Update main.nf

* Add test for new check

* md5sum -> contains
2022-09-08 09:12:53 +02:00
Robert A. Petit III
1ade577ef6
add snippy/core module (#1855)
* add snippy-core module

* Update modules/snippy/core/meta.yml

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

* Update tests/modules/snippy/core/main.nf

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

* Update tests/modules/snippy/core/main.nf

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

* Update modules/snippy/core/main.nf

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

* Update main.nf

* update test

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-09-08 06:58:10 +02:00
Robert A. Petit III
a5976c50be
add module for pbptyper (#2005)
* add module for pbptyper

* add optional database parameter
2022-09-07 15:29:03 -06:00
James A. Fellows Yates
940d7fe9d6
Move MetaPhlAn3 to a subcommand and add mergemetaphlantables (#2026)
* Move MetaPhlAn3 to a subcommand and add mergemetaphlantables

* Add mergemetaphlantables tests

* Add mergemetaphlantables to test config

* Apply suggestions from code review

* Revert now unnecessary input channel name change and now document

* Update modules/metaphlan3/mergemetaphlantables/main.nf

* Require database directory and more details in description
2022-09-07 21:58:03 +02:00
Robert A. Petit III
3ef618fed2
add module for pasty (#2003)
* add module for pasty

* run prettier

* line up those commas

* Update main.nf
2022-09-07 09:29:28 -06:00
louperelo
eae945721d
new module: deepbgc/pipeline (#2014)
* not working yet (db not found)

* modify deeparg/download module to return db-path

* 🪄

* Prettier

* add test.yml

* much prettier

* test.yml delete md5 for pot. empty files

* adapt test.yml

* test.yml again

* 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>
2022-09-07 14:59:01 +02:00
nvnieuwk
f2264c1052
New module: scramble (#2015)
* added scramble/clusteridentifier

* linting

* added cluster_analysis

* added a comment to the mei ref

* added reference comments

* linting
2022-09-07 13:19:18 +02:00
FriederikeHanssen
e726b1730d
MD finally supports cram output (#2019)
* MD finally supports cram output

* publish crai file

* fix test output

* fix mv

* figure out if contains breaks stuff

* remove variable checksum

* add contains check

* remove variable checksum

Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-09-07 11:04:58 +02:00
James A. Fellows Yates
d27b7a6fda
Add bracken/combinebrackenoutputs (#2022)
* Add combinebrackenoutputs

* Prettier and relax tests contains

* 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>
2022-09-07 09:18:21 +02:00
James A. Fellows Yates
fe3e18eaee
Add krakentools/combinekreports (#2018)
* Add krakentools_combinekreports

* Update test.yml

* Update main.nf

* Update tests/modules/krakentools/combinekreports/test.yml

* Prettier

* Update modules/krakentools/combinekreports/main.nf

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

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-09-06 11:32:30 -06:00
louperelo
04dfb65335
Deepbgcdownload (#2010)
* deepbgc_download first version

* with test.yml

* Apply suggestions from code review

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

* Apply suggestions from code review

* delete trailing whitespace main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-09-05 16:51:21 +02:00
nvnieuwk
30102f3b20
Another update to delly/call (#2011)
small update
2022-09-05 16:06:56 +02:00