Commit graph

673 commits

Author SHA1 Message Date
Robert A. Petit III
9e0abcc443
add module for ssuisero (#1329)
* add module for ssuisero

* Update main.nf

* Update meta.yml

Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
2022-02-27 20:04:03 -07:00
Robert A. Petit III
55bee0b02e
add module for hpsuisero (#1331)
* add module for hpsuisero

* Update meta.yml

* Update main.nf

Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
2022-02-27 17:58:35 -07:00
Sateesh
8a20253f40
update args & convert to bam (#1355) 2022-02-25 11:06:39 -07:00
Priyanka Surana
3e6be50600 Adjusted Augustus Config Path settings. Suggested by @mahesh-panchal 2022-02-25 13:26:23 +00:00
Priyanka Surana
3cffa96efe Merge branch 'master' of https://github.com/nf-core/modules into busco 2022-02-25 13:12:53 +00:00
Sateesh
4c59984d7b
Seqkit pair (#1348)
* add seqkit pair module

* local tests

* local tests

* fix workflow name

* fix workflow name

* fix version indentation

* fix version indentation

* fix version indentation

* fix review comments

* fix review comments

* fix github usernames

* minor fix

* add meta unpaired output

Co-authored-by: Peri <rrx8@cdc.gov>
2022-02-24 15:07:35 +01:00
Michael J Cipriano
6400317623
Gatk4 selectvariants (#1346)
* initial commit

* tested

Co-authored-by: Cipriano <rrn8@cdc.gov>
Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-02-24 09:51:48 +01:00
Ramprasad Neethiraj
ee915a43e4
update svdb merge (#1274)
* update svdb merge

* fix undefined variable error

* remove prio join in the script block

* fix error

* fix error again

* update tests and refactor
2022-02-24 09:49:30 +01:00
Hunter Seabolt
1016c9bd1a
Seqtk seq (#1340)
* Initial commit of seqtk/seq module files

* pytest.yml

* updated module and tests code, need to finish modules/main.nf

* Initial commit of seqtk/seq module files

* pytest.yml

* updated module and tests code, need to finish modules/main.nf

* Adding code and configs for seqtk/seq module

* Re-tested module following minor code update

* removed trailing whitespace errors

* Changed variable name  to  following reviewer suggestions

Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
2022-02-23 17:02:51 +01:00
Michael J Cipriano
f144171ddc
Faqcs (#1339)
* Initial module creation

* Update test.yml

* Update test.yml

* Update test.yml

* Update meta.yml

Co-authored-by: Cipriano <rrn8@cdc.gov>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-02-23 16:30:22 +01:00
Sateesh
a25423dbb9
Gatk4 combinegvcfs (#1342)
* add gatk4/combinegvcfs module

* update gatk4/combinegvcfs

* loop to create a string adding -V to each vcf file

* add contains for variable md5

* rm whitespace

* meta in output

* fix indentations

* fix indentations

* move tmpdir to args and update conda version

Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-02-23 16:29:29 +01:00
Moritz E. Beber
938387d10d
feat: add hmmsearch module and tests (#1273)
* feat: add hmmsearch module and tests

* chore: set medium resource requirements

* tests: look for correct output

* fix: add when condition

* Apply suggestions to meta.yml

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

* refactor: create gzip compressed output

* docs: describe compressed in-/output

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-02-23 15:32:33 +01:00
Priyanka Surana
c20f836450
Merge branch 'nf-core:master' into busco 2022-02-23 11:40:21 +00:00
James A. Fellows Yates
f9d25aad7f
Switch to native mandatory gzipped reading for hmmalign (#1343)
* fix: remove left-over unnecessary code

* Update main.nf

* Update hmmer/hmmalign command to natively accept gzipped input

* Making @drpatelh happy

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

Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
2022-02-23 09:59:24 +00:00
Mei Wu
2597c31d6b
refactored vcfanno (#1266)
* final refactor: using tarball instead
2022-02-21 11:49:21 +01:00
Robert A. Petit III
15d39f841a
add amrfinderplus module (#1284)
* add amrfinderplus module

* Update test.yml

* Update main.nf

* Update main.nf

* Update test.yml

* Update test.yml

* Update test.yml

* Update main.nf

* Update meta.yml

* Update meta.yml

* Update main.nf

* Update test.yml

* Update test.yml
2022-02-19 23:02:23 +00:00
Sateesh
a0d91e4a93
Picard addorreplacereadgroups (#1305)
* add picard-addorreplacereadgroups

* add picard_addorreplacereadgroups

* add new line to main.nf

* remove trailing whitespaces

* remove trailing whitespaces

* change to output in test yml

* add when directive

* picard 2.26.10 -> 2.26.9

* picard 2.26.10 -> 2.26.9 test yml

Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-02-18 19:59:06 -07:00
Sateesh
927dbfed04
Picard cleansam (#1306)
* add picard-cleansam

* add picard/cleansam

* update test yml with output

* picard 2.26.10 -> 2.26.9

* add output to test yml

Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-02-18 19:17:58 -07:00
Sateesh
62e5d1f0b3
Picard createsequencedictionary (#1310)
* add picard/createsequencedictionary module

* add picard-CreateSequenceDictionary

* add picard/createsequencedictionary/

* add contains to test yml

* update test yml contains

* update test yml contains

Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-02-18 18:49:12 -07:00
Sateesh
f655e5dea2
Picard fixmateinformation (#1315)
* add picard-fixmateinformation

* add picard-fixmateinformation

* fix trailing whitespace

* fix trailing whitespace

Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-02-18 18:18:05 -07:00
Robert A. Petit III
be798861c6
add module for abricate (#1280)
* add module for abricate

* rename abricate/abricate to abricate/run

* Update test.yml

Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
2022-02-18 18:00:21 -07:00
Robert A. Petit III
45466684e7
add mobsuite_recon module (#1270)
* add mobsuite_recon module

* Update main.nf

* Update nextflow.config

* Update test.yml

Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
2022-02-18 17:52:38 -07:00
Robert A. Petit III
425939a108
add module for legsta (#1319) 2022-02-18 17:42:18 -07:00
Robert A. Petit III
439763bf2c
add module for sistr (#1323)
* add module for sistr

* Update test.yml
2022-02-18 17:33:48 -07:00
Robert A. Petit III
8055c5d1c3
add module for rgi (#1321)
* add module for rgi

* fix extension

* fix test yaml

* Update main.nf

* Update main.nf
2022-02-18 17:23:44 -07:00
Harshil Patel
cab399507b
Patch fix artic/minion and ivar/variants modules (#1326) 2022-02-18 17:36:09 +00:00
FriederikeHanssen
e31f1ff3b1
add qualimap with cram files + remove val from qualimap/bam, instead use empty list as everywhere else (#1320)
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-02-18 09:43:53 +01:00
FriederikeHanssen
3f364e2f31
add mergemutectstats (#1314)
* add mergemutectstats

* correct md5sum

* Update modules/gatk4/mergemutectstats/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-02-18 09:38:55 +01:00
FriederikeHanssen
fdb1664885
Add deeptools bamcoverage (#1316)
* Add deeptools bamcoverage

* remove todo string

* Add in when

* fix c&p version format error

* Fix md5sums

Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-02-18 09:35:41 +01:00
FriederikeHanssen
fcd483e1b5
intervallisttobed (#1312)
* intervallisttobed

* correct md5sum
2022-02-17 16:32:26 +01:00
FriederikeHanssen
8c8be7d7c6
Add gatherpileupsummaries (#1311)
* Add gatherpileupsummaries

* fix checksum

* Update modules/gatk4/gatherpileupsummaries/main.nf

* Add in when
2022-02-17 15:05:21 +01:00
Hunter Seabolt
a69faefee8
Seqtk rename (#1304)
* Added seqtk/rename module and tests code

* Updated files and testing code for seqtk rename

* Added meta map to seqtk/rename module def

* updated prefix parameter usage

* updated test.yml to remove local filepaths --> change to output

* Added empty line to main.nf
2022-02-16 17:28:08 +01:00
Moritz E. Beber
7560689375
feat: add sourmash sketch (#1287)
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 12:30:28 +01:00
Matthias Hörtenhuber
e745e167c1
Fix formatting in yaml files, add yamllint config (#1279)
* fix yml formatting

* allow fastq.gz and fq.gz as file input, add meta.yml and test

* fix yaml files

* Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test"

This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4.

* prettier magic!

* fix comments for yamllint

* remove node version number

* fix linting errors

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 11:15:27 +00:00
Harshil Patel
12b0bc5aa9
Bump Pangolin version to 3.1.20 (#1296)
* Bump Pangolin version to 3.1.20

* Fix md5sum
2022-02-15 10:46:20 +00:00
FriederikeHanssen
967fb22ded
Update versions (#1292)
* Update versions

* update checksums + remove variables as input for applyvqsr

* sneak in removal of values and provide them via modules.config

* update another checksum

* more checksums

* move vairable to config

* remove controlfreec, wrong branch

* add line break
2022-02-15 11:29:36 +01:00
Matthieu Muffato
04e82ec61a
First version of the biobambam/bammarkduplicates2 module (#1247)
* First version of the biobambam/bammarkduplicates2 module

* Fixed the path of versions.yml

* Regenerated the checksums as the previous files were generated with a single core

* Added the `when:` block, as per #1261

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

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-14 16:30:48 +00:00
Simon Pearce
78e2e76b24
New module: ichorCNA (#1182)
* hmmcopy/mapCounter

* update test

* Remove bam tag

* Remove /tmp/ path from test.yml

* Update modules/hmmcopy/mapcounter/meta.yml

Incorporate formatting changes

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

* Update modules/hmmcopy/mapcounter/meta.yml

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

* Update tests/modules/hmmcopy/mapcounter/main.nf

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

* ichorCNA run

* Add panel of normals code

* Try and fix tests

* Edit string detection in tests

* Fix linting issues

* Just failing END_VERSIONS

* Fixed versions.yml

* Added DOI

* Optional name for file

* Add when command

* Updated when

* Update modules/ichorcna/createpon/main.nf

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-02-11 16:56:13 +01:00
Priyanka Surana
e55664b0c3
Merge branch 'master' into busco 2022-02-11 10:43:56 +00:00
James A. Fellows Yates
a9050b8ab6
Fix test data paths for hmmer/hmmalign (#1272)
* fix: remove left-over unnecessary code

* Update main.nf
2022-02-10 13:14:44 +01:00
Ramprasad Neethiraj
d0240fee1e
update manta to enable jointcalling (#1218)
* update manta to enable jointcalling

* fix lint errors

* fix error

* update comment

* remove comment

* suggestions from code review

* add stub
2022-02-10 10:37:31 +01:00
FriederikeHanssen
f5d5926516
Update intervals (#1278)
* Match target bed to input files

* Intervals in getpileupsumamries

* more interval updates

* change targets in strelka

* remove leftover channel

* fix checksums

* add new test vcfs

* add new test vcfs

* Update modules/freebayes/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-02-10 10:34:22 +01:00
FriederikeHanssen
c8ebd0de36
Add msisensorpro (#1267)
* Add msisensorpro

* remove absolute paths

* fixing tests

* fix msisensorpro tests

* Update modules/msisensorpro/msi_somatic/main.nf

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

* Update modules/msisensorpro/msi_somatic/main.nf

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

* add when back in

* add when back in

* Update modules/msisensorpro/msi_somatic/main.nf

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

* update description

* Update main.nf

* Update main.nf

* Update main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-02-09 21:05:49 +01:00
Ramprasad Neethiraj
45acc79667
Update mosdepth (#1256)
* nf-core create

* svdb merge module and test

* remove to-do from test.yml

* version

* update meta.yml

* mosdepth update

* update md5sums

* add stub

* add stub

* remove svdb

* remove merge

* Add tests

* code linting fix

* undo previous commit

* revert code linting fix
2022-02-09 12:45:55 +00:00
Ramprasad Neethiraj
f44e6c74b4
Add svdb/merge (#1233)
* nf-core create

* svdb merge module and test

* remove to-do from test.yml

* version

* update meta.yml

* add stub

* add when
2022-02-04 15:29:44 +01:00
Benjamin Wingfield
e687c7025a
New module: plink2/extract (#1228)
* add plink2_extract

* fix test yml path

* Update modules/plink2/extract/main.nf

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

* Update modules/plink2/extract/main.nf

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

* compress output

* add DOI

* make outputs less ambiguous

* update test for compressed output

* brain is dumb

* Update modules/plink2/extract/main.nf

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-02-03 10:42:56 +00:00
Katarzyna Kamieniecka
f112e4d701
bamcmp (#1244)
* New module added bamcmp

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
2022-02-02 16:38:41 +00:00
Harshil Patel
aa2eca6997
Bump versions for Pangolin and Nextclade (#1255) 2022-02-02 15:19:46 +00:00
Danilo Di Leo
aa97b1be3e
Transdecoder predict (#1251)
* create transdecoder/longorf module

* module transdecoder

* main.nf

* transdecoder/longorf ready to PR

* review comments update

* transdecoder/predict module create

* test transdecoder/predict module

* fix pytest

* pytest passed

* removed whitespace

* Update meta.yml

* Update meta.yml

Co-authored-by: Danilo Di Leo <danilo.dileo@lnu.se>
Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
2022-02-02 09:46:07 +01:00
Ramprasad Neethiraj
fc4bd3a2d2
Add svdb/query (#1249)
* first commit

* add test data
2022-02-01 20:46:10 +01:00
Felipe Marques de Almeida
53b324281f
Raven assembler (#1087)
Adding a new module for [Raven](https://github.com/lbcb-sci/raven), a De novo genome assembler for long uncorrected reads.
2022-02-01 11:47:01 +01:00
Danilo Di Leo
a74e8436cc
Transdecoder longorf (#1230)
* create transdecoder/longorf module

* module transdecoder

* main.nf

* transdecoder/longorf ready to PR

* review comments update

* transdecoder_longorf reviewed main.nf

* removed predict

* test.yml updated

* pytest run

Co-authored-by: Danilo Di Leo <danilo.dileo@lnu.se>
2022-01-31 13:34:38 +01:00
Maxime Borry
7026122ec8
Freebayes: compress with bgzip (#1243)
* move to bgzip
* update freebayes test results
2022-01-31 10:11:39 +01:00
Sébastien Guizard
080320765c
New module: bamtools/convert (#1219)
* 📦 NEW: Add bamtools/convert module

* 👌 IMPROVE: Update output channel name, Add tests for each output format

* 👌 IMPROVE: Add error test

* 🐛 FIX: Remove custom tags

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2022-01-28 09:58:25 +00:00
GCJMackenzie
08db860938
Update mergebam syntax and sample specific unmapped channel (#1238)
* initial commit to setup branch

* workflow finished

* Update nextflow.config

* tumour to tumor, getpileup passed as nomral and tumor

* paired_somatic renamed to tumor_normal_somatic

* Apply suggestions from code review

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

* Update subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf

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

* updated index names in meta.yml

* changed index file names in main script and test

* Apply suggestions from code review

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

* Apply suggestions from code review

* fixed bug from changes

* Apply suggestions from code review

* modified yml to allow new subworkflow testing

* Update test.yml

* Update test.yml

* updated to follow the new mergebam syntax, also made unaligned input sample specific

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-01-27 15:30:27 +00:00
Priyanka Surana
8fdd5abe1d
Merge branch 'nf-core:master' into busco 2022-01-27 14:44:08 +00:00
Priyanka Surana
b412e6dabc Busco module commit with nf-core v2.2 c1 2022-01-27 14:36:18 +00:00
Harshil Patel
d70526c806
Bump Nextclade version to 1.10.1 (#1236) 2022-01-27 12:53:14 +00:00
James A. Fellows Yates
c3bacb9fdd
Add deeparg (#1234)
* Add deeparg download data

* Tweak downloaddata test.yml

* Add deeparg tests

* Apply suggestions from code review

* Fix output file paths in test

* Fix tests again md5sum to string
2022-01-26 15:19:16 +01:00
Regina Hertfelder Reynolds
1b24005f07
Add bcl2fastq2 to cellranger dockerfile (#1115)
* refactor: add bcl2fastq to cellranger dockerfile

bcl2fastq required for the cellranger mkfastq module and was therefore
added to the cellranger dockerfile. Further, cellranger was updated to
the latest version, 6.1.2., with naming and containers across
cellranger modules updated accordingly.

* chore: add bcl2fastq zip to .gitignore

* style: fix code linting error

* test(cellranger): Add tiles to mkfastq

* additional dockerfile for mkfastq

* update readme and dockerfiles

* update readme

* fix: update container for mkfastq

* docs: correct typos in readme

* test: update md5sum following cellranger update

* test: update md5sum following cellranger update

* fix: new line for external args in mkfastq

* test: update mkfastq tiles argument

* test: comment out mkfastq tests until smaller test data found

* test: stub-run mkfastq test until smaller test data found

* test: fix incorrect file path for mkfastq

Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
2022-01-25 19:58:22 +01:00
Jose Espinosa-Carrasco
9573e7e53d
Bump version 0.1.5 to chromap/chromap (#1223)
* Bump version 0.1.5 to chromap/chromap

* Bump conda samtools version to 1.14

* Get read of inconsistent md5sum in conda

* Bump version in conda and retry md5 checks

* genome index md5 hash removed, conda failed
2022-01-20 19:00:20 +01:00
Mei Wu
435ca4100a
New module/vcfanno (#1204)
* boilerplate

* tests passed

* fixed regex

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2022-01-20 08:46:31 +00:00
Harshil Patel
bb90e4fb78
Remove bcftools and ivar module customisations (#1217)
* Remove customisation from bcftools modules

* Add save_mpileup option to bcftools/mpileup

* Remove params.save_mpileup from ivar/consensus

* Update meta.ymls
2022-01-18 16:04:56 +00:00
Jose Espinosa-Carrasco
4e9cc84514
Bump chromap index version (#1216)
* Bump chromap version

* Update md5 hash

* Remove md5 check, variable with conda
2022-01-18 12:24:21 +01:00
FriederikeHanssen
1287ba48fe
Update version & add intervals usage (#1214)
* Update version & add intervals usage

* Fix config when passing intervals as file

* Use proper paths
2022-01-17 16:40:31 +01:00
Harshil Patel
796dbb573e
Add nextclade/datasetget and nextclade/run modules (#1210)
* Remove old nextclade module

* Add nextclade/datasetget and nextclade/run modules

* Fix ECLint

* Add reference and tag as inputs to datasetget module

* Fix tests

* Adjust spacing
2022-01-17 11:46:15 +01:00
Abhinav Sharma
6243c3792c
module: deepvariant (#572)
* Add stubs for deepvariant [ci skip]

* Update the stubs for deepvariant [ci skip]

* functional with google docker image

* cleanup

* consume docker container within singularity executor

* update the meta.yml file and ask for review

* tweak the input channel shape and test data

* tweak input data [ci skip]

* update for the new syntax

* remove the functions and rename meta vars

* Update the arguments mechanism

* update chr, region and checksum

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-01-17 12:25:36 +02:00
Michael L Heuer
c9587d76e2
Update dsh-bio to version 2.0.7, add support for compressed GFA 1.0 format (#1207)
* Update dsh-bio to version 2.0.7, add support for compressed GFA 1.0 format

* fix ci failures

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2022-01-17 09:24:40 +00:00
Harshil Patel
280712419d
Add new vcflib/vcfuniq module (#1208)
* Add new vcflib/vcfuniq module

* Rename module from vcfutils to vcfuniq

* Fix tests

* Compress output by default

* Fix ECLint
2022-01-14 18:18:11 +00:00
Harshil Patel
b4c6b430d0
Remove params call in ivar variants module (#1203)
* Remove params call in ivar variants module

* Update main.nf
2022-01-12 16:43:26 +00:00
FriederikeHanssen
598d7abdb2
Log4j again (#1202)
* Log4j again

* Update checksums
2022-01-12 13:55:54 +01:00
Mei Wu
30e64becaa
ucsc/wigtobigwig: add meta map (#1199)
* add meta info

* updated meta.yml

* Apply suggestions from code review

* Update test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-01-11 21:31:37 +00:00
Harshil Patel
e751e5040a
Bump software versions for viralrecon modules (#1198)
* Bump software versions for viralrecon modules

* Remove custom params.save_unaligned from bowtie2_align

* Unify samtools modules and error if input and output names are the same

* Fix ALL the tests
2022-01-07 17:52:39 +00:00
emnilsson
c4549c0ecd
Editing the CAT/CAT module to handle single files (#1196)
* Removed if-statement to only run on more than 1 file, now it will run on single files as well.

* Added a test for running the cat_cat module on a single file.

* Created a new test.yml with nf-core modules create-test-yml -t cat/cat

* Edited test.yml to not include paths and md5sums for versions.yml, and also removed sometimes variable md5sums
2022-01-06 16:41:36 +00:00
Gwenna Breton
2d4b0f7787
Bcftools sort new syntax (#1169)
* Added files for bcftools/sort

* Fixed output format and removed md5 checksum

* Change input to avoid identical in/output names

* Created rows for bcftools/sort in pytest_modules.yml
2022-01-05 12:15:54 +01:00
Robert A. Petit III
bf5edb8614
add module for mash dist (#1193)
* add module for mash dist

* fix lint

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2022-01-04 17:29:49 +01:00
FriederikeHanssen
a6e0629e24
Change intervals to be part of sample specific input (#1189)
* Change intervals to be part of sample specific input

* Fix some tests

* Update checksum

* Update intervals

* Update intervals

* Try out gavins idea for adding the file

* update test line

* update test line

* update test line

* revert contains line
2021-12-23 12:58:20 +01:00
Robert A. Petit III
5320ab7e6c
Fix kleborate inputs (#1172)
* Fix kleborate inputs

* Update test.yml

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
2021-12-22 11:39:35 +00:00
FriederikeHanssen
50eafb19c6
Update version for log4j vulnerability (#1176)
* Update version for log4j vulnerability

* update checksums

* update checksums

* update checksums

* Remove todo string

* remove werid output paths

* remove werid output paths

* remove werid output paths

* Update various checksums

* Update various checksums

* Remove unstable md5sums

* Update md5sums

* Fix pileupsummary

* Fix genotypegvcfs

* Update test files mutect2

* hm genotypevcf updated again

* Update some mutect checksums and whatnot

* Fix last mutect checksum

* Apply suggestion to use mtochondria data instead
2021-12-20 17:10:49 +01:00
Simon Pearce
02218ab5a0
hmmcopy/mapCounter (#1175)
* hmmcopy/mapCounter

* update test

* Remove bam tag

* Remove /tmp/ path from test.yml

* Update modules/hmmcopy/mapcounter/meta.yml

Incorporate formatting changes

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

* Update modules/hmmcopy/mapcounter/meta.yml

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

* Update tests/modules/hmmcopy/mapcounter/main.nf

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

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-12-17 15:39:50 +00:00
Harshil Patel
ce8c781bb4
Provide BAI when running rseqc/tin (#1177)
* Provide BAI when running rseqc/tin

* Add md5sum

* Add proper md5sums

* md5sum not md5

* Add xls to meta.yml
2021-12-17 10:00:09 +00:00
SusiJo
3eff67f54d
Added new module snpsift/split (#1031)
* added new module snpsift/split

* added options.args

* added .vcf.gz to input

* removed test and updated to new NF DSL2 syntax

* Updated to new NF DSL2 syntax

* added option to join vcf files

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-12-17 09:08:14 +01:00
GCJMackenzie
54e0ac4ed9
add module: Variantrecalibrator (#1088)
* committing to pull updated nf-core files

* saving changes to checout other branch

* committing progress so far, difficulty with test data

* uploading to be used as draft PR

* fix linting error in meta.yml

* attempt to group reference inputs together

* updated input format for resources

* meta.yml updated with new resource names

* added output channel for recal index

* module only takes single vcf file input now

* committing to checkout

* update to new syntax, remove indel test for now

* updated to use memory options and new test data

* Update modules/gatk4/variantrecalibrator/main.nf

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

* Update main.nf

* Update modules/gatk4/variantrecalibrator/main.nf

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

* remove duplicate test keys from test_data.config

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-12-16 10:54:49 +00:00
GCJMackenzie
9f8d9fb615
Add applyvqsr (#1101)
* initial commit to setup branch

* workflow finished

* Update nextflow.config

* tumour to tumor, getpileup passed as nomral and tumor

* paired_somatic renamed to tumor_normal_somatic

* Apply suggestions from code review

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

* Update subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf

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

* updated index names in meta.yml

* changed index file names in main script and test

* Apply suggestions from code review

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

* Apply suggestions from code review

* fixed bug from changes

* Apply suggestions from code review

* modified yml to allow new subworkflow testing

* Update test.yml

* Update test.yml

* add applyvqsr

* added memory options, new test data used

* Update main.nf

* Update main.nf

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-12-16 08:44:50 +00:00
Harshil Patel
67571c4e79
Add RSeqC tin.py module (#1174)
* Add RSeqC tin.py module

* Fix EC lint for unrelated hmmcopy module

* Remove md5sum for empty file
2021-12-15 21:26:43 +00:00
Simon Pearce
ae92159762
New subtool: hmmcopy/generatemap (#1168)
* Initial structure

* Working with local singularity image

* Working generateMap.pl script

* Remote not working bioconda

* Working generateMap with biocontainer

* Lint changes

* Updated hmmcopy container version to be consistent

* Fix failing test

* Remove path to perl

* No hardpath to script

* Update main.nf

Moved version outside of process, add support for zipped fasta file

* Revert to not allowing gzip via pipe, as perl script can't cope

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
2021-12-15 16:57:42 +01:00
GCJMackenzie
61376425fb
BugFix: add missing tbi output channel to genotypeGVCFs (#1153)
* initial commit to setup branch

* workflow finished

* Update nextflow.config

* tumour to tumor, getpileup passed as nomral and tumor

* paired_somatic renamed to tumor_normal_somatic

* Apply suggestions from code review

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

* Update subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf

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

* updated index names in meta.yml

* changed index file names in main script and test

* Apply suggestions from code review

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

* Apply suggestions from code review

* fixed bug from changes

* Apply suggestions from code review

* modified yml to allow new subworkflow testing

* Update test.yml

* Update test.yml

* added output channel for tbi files, tweaked method of adding blank inputs for gendb tests

* Update main.nf

* Update main.nf

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-12-14 16:10:08 +00:00
Mingda Jin
826a5603db
Stage fastq for concat in subfolders to avoid name collision issue (#1107)
* Stage fastq for concat in subfolders in task workdir

* Update main.nf

* Update test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-12-13 19:18:27 +00:00
Harshil Patel
0fafaeebf5
Revert PR #1147 (#1166)
* Revert PR #1147

* Fix md5sum for crai file
2021-12-13 16:15:20 +00:00
James A. Fellows Yates
be85289981
Update metabat2 output channels and compression (#1111)
* feat: each output type has dedicated channel replace bgzip with gzip can only zip one at a time

* Add condition moving of unbinned files

* fix: solution for moving sometimes non-existant files

* fix: update meta.yml to add the new channels

* fix: remove most of the checksums due to variability

* fix: tweaking of output

* Update modules/metabat2/metabat2/main.nf

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Fix find commands

* Fix find commands

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
2021-12-09 15:00:32 +01:00
Anan Ibrahim
1f3f2b18bb
Add new module macrel/contigs (#1109)
* Add new module macrel/contigs

* removed trailing whitespace

* removed whitespace

* linting cleanup

* Apply suggestions from code review

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

* Updated the test.yml

It didnt upload the updated version earlier for some reason :(

* Update test.yml

* Update test.yml

* Update test.yml as generated by pytest

* Update test.yml

* updated the version issue

* Update tests/modules/macrel/contigs/test.yml

* Update modules/macrel/contigs/main.nf

* Update modules/macrel/contigs/main.nf

* Update pytest_modules.yml

* Update pytest_modules.yml

* Update modules/macrel/contigs/main.nf

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

* Zipped all fasta outputs

* Update main.nf

* Update test.yml

* Update test.yml

* Update main.nf

* Update main.nf (gzip -n)

* Update test.yml

* Update main.nf

* Update main.nf

* Update test.yml

* Update tests/modules/macrel/contigs/test.yml

* Update modules/macrel/contigs/main.nf

* Apply suggestions from code review

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

Co-authored-by: darcy220606 <ananhamido@hotmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-12-09 13:17:50 +01:00
Francesco L
a68c563e54
Added UMI sub-workflow (#1098)
* added code for subworkflow fgbio call umi consensus

* ironing out a few typos etc

* fixing last things

* fixed md5sum - lets see if it changes

* removing file accidentally deleted

* tidy indents

* added bwamem2 alternative

* fixed entry for both tests

* changed name second test workflow entry

* fixed workflow entry names

* fixed md5sum for file generated with bwamem2

* added syntax new DSL2

* added new config location in test command line

* added new config location in test command line

* use of prefix instead of suffix because modules have been changed in this way

* explicit alias to bwa mem1 to avoid confusion

* removed param that should be an ext optional argument in fgbio groupreadsbyumi

* missing colon in config

* missing colon in module config too

* order list alphabetically

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

* remove params from body

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

* improving readability of input structure

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

* reverting to mandatory input

* fixed tests and workflow take values

* remove param

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

* simplify tests params

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

* formatting inputs for readability

* factoring in changes to bwamem2_mem and bwa_mem sort/view inputs

* updating test md5sum for grouped file following code update in bwamem

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
2021-12-09 11:16:40 +01:00
FriederikeHanssen
a9dd46f010
add gatk4/gatherbqsr (#1130)
* nf-core modules create

* add module files

* indent

* remove templte code

* manually revert pytest changes from tools

* manually revert pytest changes from tools

* add include statement back in

Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-12-08 23:43:36 +01:00
Maxime U. Garcia
ca3ae9ff4f
feat: update dragmap to follow new bwa/mem + bwamem2/mem logic (#1146) 2021-12-08 23:19:37 +01:00
Maxime U. Garcia
1765225042
Add new boolean sort_bam as input to be able to chose between sort and view in bwamem and bwamem2mem (#1125)
* feat: view is now in args2 so we can use sort

* forgot one split_cpus

* feat: update with new logic

* fix: add more info

* fix: remove split_cpus logic
2021-12-08 14:31:27 +00:00
Mahesh Binzer-Panchal
d473a247d2
Replace remaining task.ext.suffix with task.ext.prefix (#1117)
* Replace remaining task.ext.suffix with task.ext.prefix
2021-12-07 15:00:43 +01:00
Maxime U. Garcia
3b366c7c6a
greatly simplify syntax (#1121) 2021-12-07 11:18:12 +01:00
FriederikeHanssen
7006699ff8
Update version & prefix (#1120)
* Update version & prefix

* Fix indentation
2021-12-07 10:22:32 +01:00
Maxime U. Garcia
98b024c0e4
Fix syntax for extra containers for ensemblvep and snpeff (#1105)
* fix: correct syntax for task.ext.use_cache

* Apply suggestions from code review

* fix: simplify logic

* fix: update to new syntax
2021-12-06 12:59:49 +01:00
Maxime Borry
e0aa89141f
Add meta information to samtools/faidx (#1114)
* add meta to samtools/faidx
2021-12-06 11:37:04 +01:00
Edmund Miller
f3ffa69b8d
Dragmap (#1108)
* feat(dragmap): Add initial hastable module

* feat(dragmap): Add initial align module

* test(dragmap): Remove md5sum

Forgot sam files have a header. Might pipe this through samtools.

* build(dragmap): Add mulled container

* chore(dragmap): Update prefix

* feat(dragmap): Output a bam file

* feat(dragmap): Add log files

* Update modules/dragmap/align/meta.yml

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-12-06 09:56:41 +01:00
Edmund Miller
e2ba70ed9a
Add Cell Ranger mkfastq, mkgtf, and count (#979)
* feat(cellranger): Add initial count module

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>

* feat(cellranger): Add mkgtf module

* test(cellranger): Fix count test with mkgtf

* fix(cellranger): Generalize gtf attribute filters

* chore: Add .gitignore for cellranger tar

* build(cellranger): Update dockerfile

https://joshtronic.com/2021/09/12/fixed-repository-debian-security-buster-updates-changed-suite-from-stable-to-oldstable/

* Apply suggestions from code review

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>

* Apply suggestions from code review

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

* Update modules/cellranger/mkgtf/main.nf

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

* style: Capitalize README

* test(cellranger): Update pytest_modules

* feat(cellranger): Add initial mkfastq module

* ci: Update pytest modules

* refactor(cellranger): Update modules to new syntax

* docs(cellranger): Update meta files

There is some terrible copy-pasting going on.

* fix(cellranger): Add args

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-12-02 14:27:20 +00:00
Harshil Patel
9d0cad583b
Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110)
* Add comment line for consistency

* Remove all functions.nf

* Remove include functions.nf and publishDir options

* Replace options.args3 with task.ext.args3 - 3 modules

* Replace options.args3 with task.ext.args3 - 17 modules

* Replace {task.cpus} with task.cpus

* Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with

* Add def args = task.ext.args line to all modules in script section

* Replace options.args with args and args_list

* Initialise args2 and args3 properly

* Replace container syntax

* Revert container changes for cellranger/mkref

* Replace getProcessName in all modules

* Replace getSoftwareName in all modules

* Unify modules using VERSION variable

* Replae options.suffix with task.ext.suffix

* Remove NF version restriction for CI

* Bump NF version in README

* Replace task.process.tokenize logic with task.process

* Minor tweaks to unify syntax in tests main.nf

* Add a separate nextflow.config for each module

* Transfer remaining module options to nextflow.config

* Remove addParams from tests main.nf

* Remove TODO statements

* Use -c to import module specific config

* Bump NF version to 21.10.3

* Fix tests for artic/minion

* Fix broken publishDir syntax

* Standardise and fix obvious failing module tests

* Remove kronatools to krona

* Comment out tags in subworkflow test.yml

* Fix failing module tests

* Add consistent indentation to nextflow.config

* Comment out subworklow definitions

* Fix kallistobustools/ref

* Fix rmarkdownnotebook

* Fix jupyternotebook

* Quote task.process

* Add plink2/vcf to pytest_modules.yml

* Remove NF_CORE_MODULES_TEST from pytest CI

* Fix more tests

* Move bacteroides_fragilis to prokaryotes folder

* Fix cooler merge tests

* Fix kallistobustools/count tests

* Fix kallistobustools/ref tests

* Update test_10x_1_fastq_gz file for kallistobustools/count tests

* Fix bcftools/query tests

* Fix delly/call tests

* Fix cooler/zoomify tests

* Fix csvtk/split tests

* Fix gatk4/intervallisttools tests

* Fix gatk4/variantfiltration

* Fix pydamage/filter tests

* Fix test data for unicycler

* Fix gstama/collapse module

* Fix leehom tests

* Fix metaphlan3 tests

* Fix pairtools/select tests

* Update nextflow.config

* Update nextflow.config

* feat: update syntax

* Fix arriba tests

* Fix more failing tests

* Update test syntax

* Remove comments from tests nextflow.config

* Apply suggestions from code review

* Fix kallistobustools/count module

* Update dumpsoftwareversions module

* Update custom/dumpsoftwareversions

* Add args2 to untar module

* Update leftover modules

* Remove last remaining addParams

* Change syntax from task.ext.suffix to tast.ext.prefix

* Change nextflow.config in all tests to use ext.prefix instead of ext.suffix

Co-authored-by: JoseEspinosa <kadomu@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
2021-12-02 12:39:55 +00:00
louperelo
1f8f86b793
takes gunzip out of fargene main.nf (#1090)
* takes gunzip out of fargene main.nf

* update definition of input

* options.args -> args

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-11-29 14:32:23 +01:00
Harshil Patel
20d8250d9f
Update all modules to new NF DSL2 syntax (#1099)
* Add comment line for consistency

* Remove all functions.nf

* Remove include functions.nf and publishDir options

* Replace options.args3 with task.ext.args3 - 3 modules

* Replace options.args3 with task.ext.args3 - 17 modules

* Replace {task.cpus} with task.cpus

* Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with

* Add def args = task.ext.args line to all modules in script section

* Replace options.args with args and args_list

* Initialise args2 and args3 properly

* Replace container syntax

* Revert container changes for cellranger/mkref

* Replace getProcessName in all modules

* Replace getSoftwareName in all modules

* Unify modules using VERSION variable

* Replae options.suffix with task.ext.suffix

* Remove NF version restriction for CI

* Bump NF version in README

* Replace task.process.tokenize logic with task.process

* Minor tweaks to unify syntax in tests main.nf

* Add a separate nextflow.config for each module

* Transfer remaining module options to nextflow.config

* Remove addParams from tests main.nf

* Remove TODO statements

* Use -c to import module specific config

* Bump NF version to 21.10.3

* Fix tests for artic/minion

* Fix broken publishDir syntax

* Standardise and fix obvious failing module tests

* Remove kronatools to krona

* Comment out tags in subworkflow test.yml

* Fix failing module tests

* Add consistent indentation to nextflow.config

* Comment out subworklow definitions

* Fix kallistobustools/ref

* Fix rmarkdownnotebook

* Fix jupyternotebook

* Quote task.process

* Add plink2/vcf to pytest_modules.yml

* Remove NF_CORE_MODULES_TEST from pytest CI

* Fix more tests

* Move bacteroides_fragilis to prokaryotes folder

* Fix cooler merge tests

* Fix kallistobustools/count tests

* Fix kallistobustools/ref tests

* Update test_10x_1_fastq_gz file for kallistobustools/count tests

* Fix bcftools/query tests

* Fix delly/call tests

* Fix cooler/zoomify tests

* Fix csvtk/split tests

* Fix gatk4/intervallisttools tests

* Fix gatk4/variantfiltration

* Fix pydamage/filter tests

* Fix test data for unicycler

* Fix gstama/collapse module

* Fix leehom tests

* Fix metaphlan3 tests

* Fix pairtools/select tests

* Update nextflow.config

* Update nextflow.config

* feat: update syntax

* Fix arriba tests

* Fix more failing tests

* Update test syntax

* Remove comments from tests nextflow.config

* Apply suggestions from code review

* Fix kallistobustools/count module

* Update dumpsoftwareversions module

* Update custom/dumpsoftwareversions

* Add args2 to untar module

* Update leftover modules

* Remove last remaining addParams

Co-authored-by: JoseEspinosa <kadomu@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
2021-11-26 07:58:40 +00:00
Annick Renevey
45985ff6f0
Peddy nf core2 2dev0 (#1048)
* Updated module to fit nf-core2.2dev0 templates

* Updated module to fit nf-core2.2dev0 templates

* Linked test files to nf-core/test-dataset branch:raredisease raw files

* Change order of input: vcf and tbi with meta, ped without

* Change order of input: vcf and tbi with meta, ped without/adapt test

* Change order of input: vcf and tbi with meta, ped without/adapt test, bugfix

* Indent and rename files

* Update modules/peddy/main.nf

Removed newline

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

* Update modules/peddy/main.nf

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

* Update modules/peddy/main.nf

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

* Update modules/peddy/main.nf

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

* Update modules/peddy/meta.yml

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

* Update modules/peddy/meta.yml

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

* Update modules/peddy/main.nf

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

* Update modules/peddy/main.nf

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

* Update pytest_modules.yml

* Update main.nf

* Apply suggestions from code review

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-21 20:14:09 +00:00
Florian De Temmerman
1455498152
CNVkit: Make targets file optional when running in WGS mode (#1030)
* Make targets.bed optional when running in wgs mode

* added test for cram

* Update test_data_config with new reference.cnn

* Update main.nf to allow tumor-only running

Still need a unit-test for this. Almost ready, but needs this file as input https://github.com/nf-core/test-datasets/blob/modules/data/generic/cnn/reference.cnn

* re-writing previous changes, but now it wont crash the entire CI-setup

* fixing overlooked merge conflict

* last overlooked merge-conflict

* move all files to batch subfolder

* adding an optional input for a reference file (needed when running germline and tumoronly)

* minor typo

* update meta.yml

* aligning code, renaming cnvkit to cnvkit_batch, renaming tumorbam to tumor, normalbam to normal

* Update pytest_modules.yml

Co-authored-by: EC2 Default User <ec2-user@ip-172-31-21-198.us-west-2.compute.internal>
Co-authored-by: Lasse Folkersen <lassefolkersen@gmail.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-21 19:56:57 +00:00
Abhinav Sharma
15fd90ffe8
Add phyloflash module (#786)
* initial stubs [ci skip]

* remove comments and add main command [ci skip]

* design iteration [ci skip]

* add new standard functions.nf [ci skip]

* update the version string [ci skip]

* accomodate the db stubs and single/double ends [ci skip]

* add FIXME for missing info [ci skip]

* Accomodate the results folder [ci skip]

* Update main.nf

* Apply suggestions from code review

* Update main.nf

* Apply suggestions from code review

* Add version file to stubs [ci skip]

* Tweak the output dir pattern [ci skip]

* Update modules/phyloflash/main.nf

* Update modules/phyloflash/main.nf

* Update modules/phyloflash/main.nf

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-21 19:43:58 +00:00
Sébastien Guizard
c25c3fe466
Update: uLTRA (#1081)
* 👌 IMPROVE: Update .gitignore

* 📦 Add ultra module

* 👌 IMPROVE: Update test input

* 👌 IMPROVE: Update and clean code

- Update to last versions.yml file
- Update meta.yml
- Correct typos

* 👌 IMPROVE: Update output channels + Rename following subtool

* 👌 IMPROVE: Remove old ultre files

* 👌 IMPROVE: Update of pytest_modules.yml

* 👌 IMPROVE: Update test.yml

* 👌 IMPROVE: Keep md5sum as much as possible

* 👌 IMPROVE: Remove old ultra files

* 👌 IMPROVE: Update of pytest_modules.yml

* 👌 IMPROVE: Update test.yml

* 👌 IMPROVE: Keep md5sum as much as possible

* 🐛 Fix: add unsaved modifications

* 🐛 FIX: Remove one inconstant md5sum

* 🐛 FIX: Grab software name using ${getSoftwareName(task.process)}

* 🐛 FIX: Remove md5sums for pickle files (not constant).

* Update modules/ultra/pipeline/main.nf

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

* Update modules/ultra/pipeline/main.nf

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

* 👌 IMPROVE: update output directory, update meta.yml

* 👌 IMPROVE: Use modules to gunzip and sort gtf

* 🐛 FIX: Set up channel correctly

* 👌 IMPROVE: Remove pickles files and databases

Those data might be useful in a debugging purpose.

* Apply suggestions from code review

* Update main.nf

* 🐛 FIX: Update uLTRA to version 0.0.4.1 + remove $(pwd)

* 👌 IMPROVE: Sort tags in test.yml

* align order of input between main.nf and meta.yml. Add ksahlin as co-author (he did update his package to overcome the pwd-problem

* Update main.nf

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Lasse Folkersen <lassefolkersen@gmail.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2021-11-21 13:00:53 +00:00
James A. Fellows Yates
d30bf235b1
update: gunzip to include meta input tuple (#1082)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* feat: add megahit module, currently decompressed output

* Update main.nf

* Update tests/modules/megahit/test.yml

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Apply suggestions from code review

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

* feat: compress all outputs, remove md5sums due to gz stochasicity

* fix: wrong conda channel for pigz

* fix: broken singleend tests and update meta.yml

* Missed one

* Apply suggestions from code review

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

* fix: pigz formatting

* Apply suggestions from code review

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

* Apply suggestions from code review

* Add bamUtil trimBam

* Update modules/bamutil/trimbam/main.nf

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

* Update modules/bamutil/trimbam/main.nf

* Changes after code-review

* YAML lint

* update: add (optional) meta to input tuple

* YAML linting

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2021-11-21 12:41:03 +00:00
Robert A. Petit III
29c669766d
add bakta module (#1085)
* add bakta module

* Update main.nf

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-21 12:17:25 +00:00
Robert A. Petit III
5ebe62612c
add ectyper module (#948)
* add ectyper module

* fix-lint

* try zcat

* Update main.nf

* fix lint

* Update main.nf

* Apply suggestions from code review

Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>

* Update main.nf

* pass lint

* Update main.nf

* fix lint

Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-21 12:14:02 +00:00
Maxime Borry
72c94dbed9
Add new module: Das Tool (#1004)
* add pydamage module

* remove TODOs

* split module by subcommands

* update version parsing

* remove forgotten TODOs

* update module names

* remove old holistic module

* Update modules/pydamage/analyze/main.nf

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

* add keywords

* update resource requirement

* Update modules/pydamage/filter/main.nf

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

* Update modules/pydamage/filter/meta.yml

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

* merge from upstream

* update pydamage from upstream

* add freebayes

* update pydamage test from upstream

* fix meta.yml

* update functions.nf

* update test.yml

* update version parsing

* update version parsing

* fix indentation

* Update modules/freebayes/main.nf

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

* Update modules/freebayes/main.nf

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

* Update modules/freebayes/main.nf

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

* add optional inputs

* Update modules/freebayes/main.nf

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

* add bed test

* add metabat2 module

* only freebayes

* remove metabat2

* update md5sum because of vcf including date of the day

* add keyword

* rescue conflicted files

* attempt to fix ECLint

* add pytest workflow for metabat

* remove -

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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

* Update modules/metabat2/metabat2/meta.yml

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

* Update modules/metabat2/metabat2/meta.yml

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

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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

* add optional inputs/outpus

* remove trailing whitespace

* compressing and removing not reproducible md5sums

* follow symlinks while decompressing

* add dastool/scaffolds2bin

* add dastool

* remove non reproducible md5sum check for compressed files

* Update tests/modules/metabat2/metabat2/main.nf

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

* Update tests/modules/metabat2/metabat2/main.nf

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

* split tests

* export env variable

* remove metabat2 from PR

* fix linting errors

* remove traling whitespace

* Update modules/metabat2/jgisummarizebamcontigdepths/main.nf

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

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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

* Update modules/metabat2/metabat2/main.nf

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

* Update modules/metabat2/metabat2/meta.yml

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

* answer PR comments and switch to bgzip

* PR review updates

* update from PR review

* update test files

* add bacillus fragilis alignments

* switch tests to bacillus fragilis

* add string check

* update test string

* add pr comment answer

* last fixes for PR review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-19 08:33:29 +01:00
FriederikeHanssen
19035c99d1
Add thread option to samtools modules (#1069)
* add thread option to samtools modules

* fix tests

* fix tests

* fix tests

* Fix naming to fix tests

* cpus-1 to account for mainthread

* remove thread in ampliconclip, docu doesn't report this param

* add -1 to all other applicable samtools modules

* Update samtools version

* Update checksums

* retrigger GHA after update

* Update modules/samtools/fastq/main.nf

Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>

* Update modules/samtools/fixmate/main.nf

Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>

* Update modules/samtools/flagstat/main.nf

Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>

* Update modules/samtools/index/main.nf

Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>

* Update modules/samtools/merge/main.nf

Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>

* Update modules/samtools/stats/main.nf

Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>

* Update modules/samtools/view/main.nf

Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>

* Fix md5sum fixmate

* Fix md5sums

* sth funny with the fixmate checksums

* more md5sums updates

Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>
2021-11-18 22:24:47 +01:00
Jose Espinosa-Carrasco
4e5b6ed843
Fix picard markduplicates (#1084)
* Fix picard/markduplicates with new options syntax

* Delete md5sum for bam files and add contains for metrics.txt

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-18 21:54:14 +01:00
praveenraj2018
43a1c1c6d1
Update in GATK4 variantfiltration: Added vcf_index to vcf tuple; output to vcf.gz format. (#1083)
* Added vcf_index to vcf tuple; output to vcf.gz format.

* Fix: extra new line in meta.yml.

* addressed review feedback

* fix: editorconfig error

* fix: gatk memory flag

* fix: editorconfig error

* fix: Indentation 

fix: Indentation

* Fix: lint editorconfig error

Removed one extra space

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2021-11-18 21:47:40 +01:00
praveenraj2018
691feeafdc
GATK4 SplitNCigarReads: fasta_fai_dict tuple is now split into separate input channels (#1076)
* fasta_fai_dict tuple is now split into separate input channels

* fix: lint errors

* fix: pytest errors

* Update modules/gatk4/splitncigarreads/meta.yml

* Update modules/gatk4/splitncigarreads/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-11-16 15:09:30 +01:00
Robert A. Petit III
bc8899f1bf
[fix] hicap module allow optional outputs (#937)
* make hicap outputs optional

* update test data

* typo

* Update main.nf

* use mkfifo

* Update main.nf

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-16 09:23:07 +00:00
Sateesh
d5f6985607
add new nucmer module (#945)
* add new nucmer module

* Apply suggestions from code review

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

* update tests with file produced by input

* Update main.nf

* Update meta.yml

Co-authored-by: Michael Cipriano <mcipriano@gmail.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 22:05:34 +00:00
JIANHONG OU
52c541b080
Cooler cload (#634)
* rebuild cooler cload.

* update test file path of cload.

* add pytest for cload

* update to version.yml

* update the test data path

* Update tests/modules/cooler/cload/main.nf

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

* Update modules/cooler/cload/main.nf

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

* Update tests/config/test_data.config

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

* Update main.nf

Remove a lonely curly bracket.

* Update test.yml

Updated with new workflows.

* update the test files

* merge the conflicts.

* update the test.yml

* update for change of cooler/dump

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 21:43:55 +00:00
Robert A. Petit III
c2bba7a65d
add clonalframeml module (#974)
* add clonalframeml module

* Update main.nf

* try recommended gzip

* Update main.nf

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2021-11-15 19:43:53 +00:00
tamara-hodgetts
13b8a16f4a
Add module get_chrom_sizes (#1063)
* hifiasm copied from fastqc

* hifiasm tests init from fastqc

* meta.yml init; test.yml and main.nf for printing version

* Add hifiasm version printing

* Removed spaced on an empty line

* Reverted hifiasm from main

* init getchromsizes

* add tests for getchromsizes

* Included meta.yml

* removed whitespace

* Moved getchromsizes to custom folder

* Update modules/custom/getchromsizes/main.nf

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

Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: Svyatoslav Sidorov <svet.sidorov@gmail.com>
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
Co-authored-by: Tamara Hodgetts <hodgett@crick.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 19:22:12 +00:00
Robert A. Petit III
2294ff7826
add ncbi-genome-download module (#980)
* add ncbi-genome-download module

* Update modules/ncbigenomedownload/main.nf

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 18:32:53 +00:00
SusiJo
ad46010385
Added new module csvtk/split (#1014)
* added module csvtk/split

* removed todo statement

* adjusted meta map names

* changed tests to use generic input files

* added module in pytest

* updated test-data paths

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 18:29:55 +00:00
Edmund Miller
2af071ed0d
Fix subworkflows seperate from modules (#933)
* ci: Remove pytest_subworkflows

* ci(bam_sort_samtools): Depend on paths-filter instead of pytest-workflow

Co-authored-by: Harshil Patel <drpatelhh@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* ci: Revert back to one job branch

* ci(align_bowtie2): Run tests that depend on bam_sort_samtools

* ci: Fix anchor not being created yet

* ci: Update sra_fastq tags and pytest_modules

* fix(bam_sort_samtools): Update nextflow.config with params

* test(subworkflows): Update gatk_create_som_pon tags

* ci: Point to subworkflow_hacks branch of nf-core tools

Co-authored-by: Harshil Patel <drpatelhh@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-11-15 18:18:46 +00:00
avantonder
527ccdb419
Add Miniasm module (#962)
* add racon

* add miniasm module

* edit miniasm module

* edit miniasm module

* Update tests/modules/racon/main.nf

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

* Update tests/modules/racon/test.yml

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

* Update modules/miniasm/meta.yml

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

* Update main.nf

Add some spaces.

* Update meta.yml

Correct DOI

* Update main.nf

* Apply suggestions from code review

* Update tests/modules/miniasm/test.yml

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 17:50:56 +00:00
mjakobs
466b964b37
add Kronatools KTImportTaxonomy (#928)
* created and initialised krona module

* Added kronatools/ktimporttaxonomy module

* removing previous redundant work

* added contains info for html

* edited contains in test.yml

* Update get versions

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

* remove old syntax

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

* rewording module description

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

* added detailed keywords

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

* update syntax and tool version

* fixed meta.yml issues

* remove contains line from test.yml

* re-wrote module after nf-core/tools update - should work now

* removed md5

* Update modules/kronatools/ktimporttaxonomy/main.nf

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

* update meta save

* removed typo

* double quotes to single quotes around html

* re-ran test, which updated md5

* removed md5

* 'classifier' removed to fix linting

* update version

* removed erroneous ktimporttaxonomy2

* Updated input to include meta and database

* fixed tab issues in yaml

* added `contains` to test.yml

* edited `contains` in test.yml

* trying another `contains`

* retrying `contains`

* contains with extra line

* removed classifier from tag

* Apply suggestions from code review

* Update meta.yml

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 17:40:46 +00:00
avantonder
8d9e8ae839
Add Medaka module (#992)
* add racon

* add medaka module

* add medaka module

* add medaka module

* add medaka module

* add medaka module

* add medaka module

* Indentation

* Apply suggestions from code review

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

* Update main.nf

* Update main.nf

* Apply suggestions from code review

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 17:26:37 +00:00
JIANHONG OU
4398056204
Macs2 calllpeak (#1038)
* Add tests and yml file for macs2/callpeak

* add format option for macs2

* update macs2/callpeak to accept format argument

* update test.yml

* update the container version.

* try to fix the issue in conda container.

* Update conda and containers

* Going back to previous container versions

Co-authored-by: JoseEspinosa <kadomu@gmail.com>
2021-11-15 18:17:40 +01:00
Maxime U. Garcia
3426834744
feat: fastaidx -> fai (#1073) 2021-11-15 18:03:02 +01:00
Maxime U. Garcia
5b1ce484b9
feat: _idx -> _tbi (#1074)
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 17:49:20 +01:00
James A. Fellows Yates
632587a7fc
Add bamutil/trimbam (#1060)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* feat: add megahit module, currently decompressed output

* Update main.nf

* Update tests/modules/megahit/test.yml

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Apply suggestions from code review

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

* feat: compress all outputs, remove md5sums due to gz stochasicity

* fix: wrong conda channel for pigz

* fix: broken singleend tests and update meta.yml

* Missed one

* Apply suggestions from code review

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

* fix: pigz formatting

* Apply suggestions from code review

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

* Apply suggestions from code review

* Add bamUtil trimBam

* Update modules/bamutil/trimbam/main.nf

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

* Update modules/bamutil/trimbam/main.nf

* Changes after code-review

* YAML lint

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
2021-11-15 16:44:12 +00:00
louperelo
eff515891d
new module fargene (#1068)
* new module fargene

* Update main.nf

* Update modules/fargene/main.nf

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 16:42:48 +00:00
JIANHONG OU
7ad42eae1b
Cooler zoomify (#514)
* add software/cooler

* fix the wrong files uploaded.

* create a branch for cooler/zoomify

* Apply suggestions from code review

* update functions.nf to new version.

* update the test file to test-datasets.

* update the test method of zoomify

* update dump test file.

* update version.txt to version.yml

* Update modules/cooler/dump/main.nf

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

* fix the output bug of versions update to pytest_modules.yml

* update the test file path and fix the output versions.

* Update modules/cooler/dump/main.nf

* indent

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 17:18:02 +01:00
mjakobs
f93c2f2604
add Krona_db module (#995)
* add Krona_db module

* removed md5 sum

* Update tests/modules/kronatools/kronadb/main.nf

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

* added input information

* removed trailing white spaces

* changed krona version to 2.7.1

* Apply suggestions from code review

* Update modules/kronatools/kronadb/meta.yml

* Update modules/kronatools/kronadb/main.nf

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>
2021-11-15 16:01:46 +00:00
Sébastien Guizard
4a9bfec61d
New module: Ultra (#871)
* 👌 IMPROVE: Update .gitignore

* 📦 Add ultra module

* 👌 IMPROVE: Update test input

* 👌 IMPROVE: Update and clean code

- Update to last versions.yml file
- Update meta.yml
- Correct typos

* 👌 IMPROVE: Update output channels + Rename following subtool

* 👌 IMPROVE: Remove old ultre files

* 👌 IMPROVE: Update of pytest_modules.yml

* 👌 IMPROVE: Update test.yml

* 👌 IMPROVE: Keep md5sum as much as possible

* 👌 IMPROVE: Remove old ultra files

* 👌 IMPROVE: Update of pytest_modules.yml

* 👌 IMPROVE: Update test.yml

* 👌 IMPROVE: Keep md5sum as much as possible

* 🐛 Fix: add unsaved modifications

* 🐛 FIX: Remove one inconstant md5sum

* 🐛 FIX: Grab software name using ${getSoftwareName(task.process)}

* 🐛 FIX: Remove md5sums for pickle files (not constant).

* Update modules/ultra/pipeline/main.nf

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

* Update modules/ultra/pipeline/main.nf

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

* 👌 IMPROVE: update output directory, update meta.yml

* 👌 IMPROVE: Use modules to gunzip and sort gtf

* 🐛 FIX: Set up channel correctly

* 👌 IMPROVE: Remove pickles files and databases

Those data might be useful in a debugging purpose.

* Apply suggestions from code review

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 15:57:58 +00:00
Michael J Cipriano
0754d49db8
Initial commit mummer module (#940) 2021-11-15 16:53:41 +01:00
santiagorevale
1a4c7cec1b
New modules added: issues #200 and #310 (#884)
* New modules added: issues #200 and #310

* Update main.nf

* Update meta.yml

* Update tests/modules/gatk4/genotypegvcfs/main.nf

* Apply suggestions from code review

* Update main.nf

* Updating tests for GenomicsDB input and adding the path for this test resource to test_data.config

* Some minor changes on one of the test files I forgot to include

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: GCJMackenzie <43276267+GCJMackenzie@users.noreply.github.com>
2021-11-15 15:43:06 +00:00
JIANHONG OU
a6ca2b006b
Cooler merge (#515)
* add software/cooler

* fix the wrong files uploaded.

* create a branch for cooler/merge

* remove the bin_size from metadata.

* update the test_data to test-datasets

* update pytest_modules.yml

* update the test file from single input file to two input file.
update the output file from hdf5 to bedpe.

* update the version.txt to version.yml and functions.nf

* change version.yml to versions

* update the test file path and fix the output versions.

* Update meta.yml

Correct "version" to "versions"

* Update main.nf

Fix typo

* Update main.nf

Remove some spaces

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
2021-11-15 15:18:43 +00:00
Robert A. Petit III
b5b3ff16ce
add module for fastq-scan (#935)
* add module for fastq-scan

* change fastq to reads

* remove uncompressed support

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 15:41:36 +01:00
Robert A. Petit III
7be60774b6
add module for tbprofiler (#947)
* add module for tbprofiler

* Update test.yml

* Update meta.yml

Co-authored-by: Abhinav Sharma <abhi18av@users.noreply.github.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 15:35:55 +01:00
James A. Fellows Yates
2c3c87a10f
Add leehom module (#1052)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* feat: add megahit module, currently decompressed output

* Update main.nf

* Update tests/modules/megahit/test.yml

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Apply suggestions from code review

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

* feat: compress all outputs, remove md5sums due to gz stochasicity

* fix: wrong conda channel for pigz

* fix: broken singleend tests and update meta.yml

* Missed one

* Apply suggestions from code review

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

* fix: pigz formatting

* Apply suggestions from code review

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

* Apply suggestions from code review

* Add leeHom module

* Update modules/leehom/main.nf

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

* Update modules/leehom/main.nf

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

* Update modules/leehom/main.nf

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

* Update modules/leehom/main.nf

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

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 15:26:06 +01:00
Benjamin Wingfield
b012b349c1
New module: plink2/vcf (#1006)
* implement plink2 VCF import

* fix yaml indentation

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2021-11-15 13:55:18 +00:00
Ilya Pletenev
c48244b677
Add new module 'ataqv/ataqv' (#998)
* Add new module 'ataqv/ataqv'

* Update main.nf

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 12:51:40 +00:00
Daniel Straub
661bdb645e
Change Spades input (#1039)
* Change spades module

* correct meta map description

* adjust memory handling

* remove trailing whitespace

* fix hmm input

* Update modules/spades/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 11:53:07 +00:00
Daniel Straub
171a2a2dbf
Unicycler with long read input (#1041)
* Unicycler with long read input

* tests and md5sums

* remove unstable md5sums

* Update modules/unicycler/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 11:48:56 +00:00
JIANHONG OU
9475960928
Bwa index (#1040)
* fix a bug that the prefix is not handled by index.

* build the test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 11:26:01 +00:00
alexandregilardet
94851901d5
add new module pmdtools/filter #847 (#963)
* commit but won't be used because pmdtools should have a submodule

* added submodule pmdtools/filter

* removed pmdtools module created before deciding to design two submodules

* oops forgot to remove a TODO

* removed white space meta.yml, removed v in version and manually added submodule /filter to test

* Update pytest_modules.yml

* Update main.nf

added split_cpus for multi-tools module resources

* Update test.yml

added .pmd extension to match modules/ main.nf

* Update test.yml

update md5sum

* Update singularity and docker build in main.nf

From build 4 to 5 in order to match the conda one

* Update modules/pmdtools/filter/main.nf

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

* Update modules/pmdtools/filter/main.nf

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

* Update modules/pmdtools/filter/main.nf

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

* Update modules/pmdtools/filter/meta.yml

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

* Update modules/pmdtools/filter/meta.yml

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

* Update modules/pmdtools/filter/meta.yml

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

* Update modules/pmdtools/filter/meta.yml

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

* Update modules/pmdtools/filter/main.nf

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

* Update modules/pmdtools/filter/main.nf

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

* Update main.nf adding samtools version

we need both pmdtools and samtools versions

* Update main.nf remove .pmd extension

* Update test.yml md5sum

Because file extension changed

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-11-13 15:09:14 +00:00
Sébastien Guizard
001d5071c2
Update: gstama/collapse (#1057)
* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 📦 NEW: Add galgal6 chr30 test data

* 📦 NEW: Add gd-tama module

* 🐛 FIX (TEMP): Update singularity container address

* 📦 NEW: Add bamtools module

* 📦 NEW: Rewrite and rename module (gstama => gstama/collapse)

* 👌 IMPROVE: ignore test data

* 👌 IMPROVE: Remove junk files

* 👌 IMPROVE: Update output

* 👌 IMPROVE: Add channel for publishing tama's metadata outputs

* 👌 IMPROVE: Update process label

* 🐛 FIX: Use depot.galxyproject.org url for singularity

* 👌 IMPROVE: autoselect running mode

* 🐛 FIX: correct gstama collapse bash test

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update tama package and label

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Update test

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 📦 NEW: Add galgal6 chr30 test data

* 📦 NEW: Add gd-tama module

* 🐛 FIX (TEMP): Update singularity container address

* 📦 NEW: Add bamtools module

* 📦 NEW: Rewrite and rename module (gstama => gstama/collapse)

* 👌 IMPROVE: ignore test data

* 👌 IMPROVE: Update output

* 👌 IMPROVE: Add channel for publishing tama's metadata outputs

* 👌 IMPROVE: Update process label

* 🐛 FIX: Use depot.galxyproject.org url for singularity

* 👌 IMPROVE: autoselect running mode

* 🐛 FIX: correct gstama collapse bash test

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update tama package and label

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Update test

* 👌 IMPROVE: delete unnecessary files

* 👌 IMPROVE: Update + clean

- Remove unnecessary files
- Update to new versions.yml file
- Better output channels

* 👌 IMPROVE: Update meta.yml and output channels

* 👌 IMPROVE: Remove useless files

* 👌 IMPROVE: Remove automatic MODE setup

* 👌 IMPROVE: Applied @jfy133 code modification suggestions

* Update modules/gstama/collapse/meta.yml

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

* 🐛 FIX: Add missing fasta option in meta.yml

* 🐛 FIX: Fix typo

* 🐛 FIX: Update package version

* Update main.nf

* Update meta.yml

* Update modules/gstama/collapse/meta.yml

* Apply suggestions from code review

* Update tests/modules/gstama/collapse/main.nf

* Update main.nf

* 👌 IMPROVE: Update to gs-tama 1.0.3

* Update modules/gstama/collapse/main.nf

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-11 14:57:55 +00:00
Sébastien Guizard
ec15d0f9fd
Update module: pbccs (#1018)
* 📦 NEW: First commit of pbccs module

* 👌 IMPROVE: Remove option from command + rename output (ccs -> bam)

* 👌 IMPROVE: Move .pbi output  into report channel

* 🐛FIX: Correct code after --rq option removal from command line module

- module main.nf: Remove ramaining rq input channel
- Test main.nf: Transfert rq into addParams
- Test test.yml: Update md5sums

* 🐛FIX: Repair additionnal option usage

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: CCS is run in parallel with --chunk option

* 👌 IMPROVE: Add Pbindex in bam ouput channel

* 👌 IMPROVE: Change label to process_low

* 👌 IMPROVE: Define reports files names + add json version of txt report

* 🐛 FIX: Add missing backslashes

* 🐛 FIX: Add missing gz extension

* 🐛 FIX: update ouput channel

* 🐛 FIX: output file name

* 👌 IMPROVE: .gitignore

* 👌 IMPROVE: Update function.nf to last version

* 👌 IMPROVE: Update saveAs in main.nf

* 👌 IMPROVE: Add pbccs module

* 🐛 FIX: Fix Broken test

* 👌 IMPROVE: Update test_data.config

* 🐛 FIX: Fix test

* 👌 IMPROVE: Update path of test dataset files

* 👌 IMPROVE: Remove useless index + Fix Typos

* 📦 NEW: First commit of pbccs module

* 👌 IMPROVE: Remove option from command + rename output (ccs -> bam)

* 👌 IMPROVE: Move .pbi output  into report channel

* 🐛FIX: Correct code after --rq option removal from command line module

- module main.nf: Remove ramaining rq input channel
- Test main.nf: Transfert rq into addParams
- Test test.yml: Update md5sums

* 🐛FIX: Repair additionnal option usage

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: CCS is run in parallel with --chunk option

* 👌 IMPROVE: Add Pbindex in bam ouput channel

* 👌 IMPROVE: Change label to process_low

* 👌 IMPROVE: Define reports files names + add json version of txt report

* 🐛 FIX: Add missing backslashes

* 🐛 FIX: Add missing gz extension

* 🐛 FIX: update ouput channel

* 🐛 FIX: output file name

* 👌 IMPROVE: .gitignore

* 👌 IMPROVE: Update function.nf to last version

* 👌 IMPROVE: Update saveAs in main.nf

* 👌 IMPROVE: Add pbccs module

* 🐛 FIX: Fix Broken test

* 👌 IMPROVE: Update test_data.config

* 🐛 FIX: Fix test

* 👌 IMPROVE: Update path of test dataset files

* 👌 IMPROVE: Remove useless index + Fix Typos

* 🐛 FIX: fill contains args

* 👌 IMPROVE: One output => One Channel

* 👌 IMPROVE: One input => One channel

* 🐛 FIX: Update tests

* 🐛 FIX: Remove TODOs from test.yaml

* 👌 IMPROVE: Revert and keep bam and pbi together

* 🐛 FIX: Remove old rq input from meta.yml

* 👌 IMPROVE: Update test to match input channels

* 👌 IMPROVE: use prefix for for output file name

* 👌 IMPROVE: Update to new versions.yml

* 👌 IMPROVE: Update pbccs from v6.0.0 to v6.0.2

* 👌 IMPROVE: Keep track of the former sample id in meta

* Update modules/pbccs/main.nf

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

* 👌 IMPROVE: remove former_id from meta

* 👌 IMPROVE: Use chunk number in output filename

* 🐛 FIX: Update meta.yml

* 🐛 FIX: Update reports filenames with chunk number.

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-11 14:19:26 +00:00
Maxime U. Garcia
3b600af50e
feat: update gatk4 from 4.2.0.0 to 4.2.3.0 (#1059)
* feat: update gatk4 from 4.2.0.0 to 4.2.3.0

* update md5checksum

* commit all files

* actually checksum was good, but I suspect something fishy with the tests
2021-11-11 08:58:59 +01:00
Robert A. Petit III
4bd530135f
add ngmaster module (#1024)
* add ngmaster module

* add docker container

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-10 11:25:50 -07:00
Maxime U. Garcia
64006e239a
fix: actually do the tests for multiple files (#1058) 2021-11-10 16:26:34 +01:00
Maxime Borry
24707f2144
Fix read indexing in AdapterRemoval module (#1051)
* add pydamage module

* remove TODOs

* split module by subcommands

* update version parsing

* remove forgotten TODOs

* update module names

* remove old holistic module

* Update modules/pydamage/analyze/main.nf

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

* add keywords

* update resource requirement

* Update modules/pydamage/filter/main.nf

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

* Update modules/pydamage/filter/meta.yml

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

* merge from upstream

* update pydamage from upstream

* add freebayes

* update pydamage test from upstream

* fix meta.yml

* update functions.nf

* update test.yml

* update version parsing

* update version parsing

* fix indentation

* Update modules/freebayes/main.nf

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

* Update modules/freebayes/main.nf

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

* Update modules/freebayes/main.nf

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

* add optional inputs

* Update modules/freebayes/main.nf

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

* add bed test

* add metabat2 module

* only freebayes

* remove metabat2

* update md5sum because of vcf including date of the day

* add keyword

* rescue conflicted files

* attempt to fix ECLint

* add pytest workflow for metabat

* remove -

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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

* Update modules/metabat2/metabat2/meta.yml

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

* Update modules/metabat2/metabat2/meta.yml

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

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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

* add optional inputs/outpus

* remove trailing whitespace

* compressing and removing not reproducible md5sums

* follow symlinks while decompressing

* Update tests/modules/metabat2/metabat2/main.nf

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

* Update tests/modules/metabat2/metabat2/main.nf

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

* split tests

* export env variable

* Update modules/metabat2/jgisummarizebamcontigdepths/main.nf

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

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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

* Update modules/metabat2/metabat2/main.nf

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

* Update modules/metabat2/metabat2/meta.yml

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

* answer PR comments and switch to bgzip

* fix read index

* update test.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-10 12:21:12 +00:00
Daniel Lundin
8b4bfb12bb
Add log to output from bbmap/align (#1050) 2021-11-10 10:27:52 +00:00
Mei Wu
7fdeed5b79
Picard/collecthsmetrics (#927)
* added template

* integrated module

* added fasta index info

* test works, have placeholder data for baits until test-data PR is merged

* added new files to config

* updated test files

* fixing fails 

* okay final fix here on the md5sum :face_palm:

* md5sum variable

* update meta.yml to reflect consistency to main.nf

* reverted version so conda works

* Apply suggestions from code review

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

* md5sum can't be generated consistently for output

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
2021-11-10 10:52:54 +01:00
Maxime U. Garcia
1abe23e159
Add CRAM to samtools/index (#1049)
* feat: update samtools/index

* feat: add test

* fix: lint

* fix: output file + md5
2021-11-10 10:30:48 +01:00
Maxime Borry
b399f22af2
Add new module: cmseq/polymut (#918)
* add pydamage module

* remove TODOs

* split module by subcommands

* update version parsing

* remove forgotten TODOs

* update module names

* remove old holistic module

* Update modules/pydamage/analyze/main.nf

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

* add keywords

* update resource requirement

* Update modules/pydamage/filter/main.nf

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

* Update modules/pydamage/filter/meta.yml

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

* merge from upstream

* update pydamage from upstream

* add freebayes

* update pydamage test from upstream

* fix meta.yml

* update functions.nf

* update test.yml

* update version parsing

* update version parsing

* fix indentation

* Update modules/freebayes/main.nf

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

* Update modules/freebayes/main.nf

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

* Update modules/freebayes/main.nf

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

* add optional inputs

* Update modules/freebayes/main.nf

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

* add bed test

* add metabat2 module

* only freebayes

* remove metabat2

* update md5sum because of vcf including date of the day

* add keyword

* rescue conflicted files

* attempt to fix ECLint

* add pytest workflow for metabat

* remove -

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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

* Update modules/metabat2/metabat2/meta.yml

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

* Update modules/metabat2/metabat2/meta.yml

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

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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

* add optional inputs/outpus

* remove trailing whitespace

* first cmseq commit

* compressing and removing not reproducible md5sums

* save intermediate work

* follow symlinks while decompressing

* add cmseq/polymut

* add polymut

* add extra test with optional input file

* remove metabat2

* Update modules/cmseq/polymut/main.nf

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

* Update modules/cmseq/polymut/meta.yml

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

* Update modules/cmseq/polymut/meta.yml

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

* fix file extension

* Update modules/cmseq/polymut/meta.yml

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

* add test without bam index

* split tests in workflows

* answer PR review

* report version from variable

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-09 16:12:51 +01:00
Benjamin Wingfield
6bb4a6a7ee
Implement plink/extract module (#901)
* Implement PLINK_EXTRACT module

* fix plink version number

* Update main.nf

* Update test_data.config

* Update modules/plink/extract/main.nf

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

* just use one channel

* fix test with new channel input

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-09 14:03:13 +00:00
anan220606
6d3d8306e1
Add new module Mapdamage2 (#975)
* Fitst attempt at mapdamage2

* Add new module mapdamage2

* Removed __pycache__/test_versions_yml.cpython-39-pytest-6.2.5.pyc

* Modify main.nf and meta.yml

* Modify main.nf and meta.yml

* Modify main.nf and meta.yml

* Modify meta.yml

* Update pytest_modules.yml

* Apply suggestions from code review

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

* edit the meta.yml and main.nf after reviews

* Update meta.yml

* Update meta.yml

Co-authored-by: AIbrahim <AIbrahim@apate.hki-jena.de>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-11-09 14:05:23 +01:00
Maxime Borry
e0ada7d219
New module: metabat2 (#875)
* add pydamage module

* remove TODOs

* split module by subcommands

* update version parsing

* remove forgotten TODOs

* update module names

* remove old holistic module

* Update modules/pydamage/analyze/main.nf

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

* add keywords

* update resource requirement

* Update modules/pydamage/filter/main.nf

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

* Update modules/pydamage/filter/meta.yml

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

* merge from upstream

* update pydamage from upstream

* add freebayes

* update pydamage test from upstream

* fix meta.yml

* update functions.nf

* update test.yml

* update version parsing

* update version parsing

* fix indentation

* Update modules/freebayes/main.nf

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

* Update modules/freebayes/main.nf

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

* Update modules/freebayes/main.nf

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

* add optional inputs

* Update modules/freebayes/main.nf

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

* add bed test

* add metabat2 module

* only freebayes

* remove metabat2

* update md5sum because of vcf including date of the day

* add keyword

* rescue conflicted files

* attempt to fix ECLint

* add pytest workflow for metabat

* remove -

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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

* Update modules/metabat2/metabat2/meta.yml

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

* Update modules/metabat2/metabat2/meta.yml

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

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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

* add optional inputs/outpus

* remove trailing whitespace

* compressing and removing not reproducible md5sums

* follow symlinks while decompressing

* Update tests/modules/metabat2/metabat2/main.nf

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

* Update tests/modules/metabat2/metabat2/main.nf

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

* split tests

* export env variable

* Update modules/metabat2/jgisummarizebamcontigdepths/main.nf

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

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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

* Update modules/metabat2/metabat2/main.nf

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

* Update modules/metabat2/metabat2/meta.yml

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

* answer PR comments and switch to bgzip

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-08 21:08:26 +01:00
Robert A. Petit III
c10f9eb817
add lissero module (#1026)
* add lissero module

* Update test.yml

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-08 20:52:07 +01:00
Robert A. Petit III
8ca8da46c2
add emmtyper module (#1028)
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-08 20:43:15 +01:00
GCJMackenzie
316aedaaa6
bug fixes: genomicsdbimport (#1035)
* saving changes to checkout

* saving to sort out other branch

* removed yml tracking of files that cant be tracked due to directory name changing between runs

* test data added, ready for pr

* fix eol linting error

* Update modules/gatk4/genomicsdbimport/main.nf

Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>

* merging with master

* update push to show progress

* tests now working untar able to pass data to genomicsdbimport

* commit to checkout

* tests updated, module reworked to simplify and emit updated gendb

* Apply suggestions from code review

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

* update meta.yml 

Priority of input options changed, updated to reflect this

* Update test.yml

name prefix changed in main script, test.yml updated to reflect this

* fix tests due to review changes

* bug fixes, multicalling samples and gendb emissions now fixed

* Update pytest_modules.yml

* Update meta.yml

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-06 15:51:15 +00:00
Robert A. Petit III
729d9ae450
add meningotype module (#1022)
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-06 16:44:26 +01:00
Robert A. Petit III
22aa168622
add scoary module (#1034)
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-06 16:34:39 +01:00
Lasse Folkersen
e560fbbc3e
Imputeme (#882)
* first commit with imputeme as a module. Extensive re-write of imputeme-code, resulting in release v1.0.7 that is runnable in the next-flow framework.


Co-authored-by: EC2 Default User <ec2-user@ip-172-31-21-198.us-west-2.compute.internal>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Pontus Freyhult <pontus_github@soua.net>
2021-11-05 10:25:54 +01:00
Francesco L
02892ef654
New module: Samblaster (#954)
* add base code from samblaster

* added test yml

* fixing versions files, should this be the cause of online lint failures

* removed tmp files that shouldn't be there

* fixing output file name - 1

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

* fixing output file name - 2

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

* fixing output file name - 3

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

* fixing output file name - 4

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

* fixing output file name - 5

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

* fixing output file name - 6

* fixed indent

* fixed input name and updated test.yml file with new name

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-04 18:18:56 +01:00
Robert A. Petit III
fc4f3e8822
add seqsero2 module (#1016)
* add seqsero2 module

* correct lint errors

* Update modules/seqsero2/main.nf

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

* set output directory

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
2021-11-04 07:49:30 +00:00
James A. Fellows Yates
08b71fa85f
New module: gunc run (+ gunc downloaddb) (#880)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* feat: add megahit module, currently decompressed output

* Update main.nf

* Update tests/modules/megahit/test.yml

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Apply suggestions from code review

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

* feat: compress all outputs, remove md5sums due to gz stochasicity

* fix: wrong conda channel for pigz

* fix: broken singleend tests and update meta.yml

* Missed one

* Apply suggestions from code review

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

* fix: pigz formatting

* Apply suggestions from code review

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

* Apply suggestions from code review

* Add GUNC download_db and run commands

* Bump with version without zgrep

* Apply suggestions from code review

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

* Harshil formatting

* Apply suggestions from code review

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

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2021-11-03 17:01:23 +01:00
Maxime U. Garcia
11226d9d98
fix remove md5sum check (#1017) 2021-11-03 11:41:12 +01:00
Maxime U. Garcia
9767b081b9
Merge freebayes subtools (#1015)
* feat: merge freebayes subtools

* fix: typo

* assess comments from review

* fix: path to module
2021-11-03 11:22:06 +01:00
fbdtemme
4619d012e5
Add cram support to Allelecounter module (#1013)
* Add CRAM support to allelecounter

* Update meta.yml

* Rename bam,bai to input,input_index

* Apply suggestions from code review

* Fix reference to renamed variable

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-11-02 17:00:25 +01:00
Simon Pearce
374d81e0b3
readcounter module for hmmcopy (#1001)
* readcounter module for hmmcopy

* Changed version number

* Fix indentation

* Update main.nf

* Update modules/hmmcopy/readcounter/main.nf

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2021-11-02 11:01:13 +00:00
Simon Pearce
cac6dc83bb
gccounter module for hmmcopy (#1003)
* hmmcopy gccounter working

* Update modules/hmmcopy/gccounter/main.nf

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>

* Update main.nf

Changed version to 0.1.1 as the container says

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2021-11-02 09:59:25 +00:00
Simon Pearce
81d65d4978
Samtools fixmate module (#991)
* Samtools fixmate module

* Update modules/samtools/fixmate/meta.yml

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

* Update modules/samtools/fixmate/main.nf

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

* Update main.nf

* Update modules/samtools/fixmate/meta.yml

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

* Update meta.yml

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-11-01 12:12:14 +00:00
Harshil Patel
9fb26ae462
Add IDR module (#908)
* Add IDR module

* Add meta and implement main todos

* Modifying idr tests

* Update tests/config/test_data.config

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

* Update tests/config/test_data.config

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

* Update main.nf

* Update tests/config/test_data.config

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

* Update test with new file name

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-10-30 10:52:13 +02:00
GCJMackenzie
bc8697b766
FIX: Createsomaticpanelofnormals add requested test changes (#983)
* files created for createsompon, script written, meta written, still needs tests

* updated to 2.0.0 method input, however this requires a genomicsDB input now

* script finished, meta yaml updated. Tests working locally, test yaml made, needs genomicsdb example on nf-core to run repository tests

* versions updated, issue with test data not able to download directory

* updated tests to include repo-side data

* Apply suggestions from code review

* Update modules/gatk4/createsomaticpanelofnormals/main.nf

* temp commit to allow checkout

* updated createsompon tests to use tarred gendb

* resolve conflict

* Update tests/modules/gatk4/createsomaticpanelofnormals/main.nf

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

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-29 17:45:32 +01:00
GCJMackenzie
7afb962f0b
New module genomicsdbimport (#857)
* saving changes to checkout

* saving to sort out other branch

* removed yml tracking of files that cant be tracked due to directory name changing between runs

* test data added, ready for pr

* fix eol linting error

* Update modules/gatk4/genomicsdbimport/main.nf

Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>

* merging with master

* update push to show progress

* tests now working untar able to pass data to genomicsdbimport

* commit to checkout

* tests updated, module reworked to simplify and emit updated gendb

* Apply suggestions from code review

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

* update meta.yml 

Priority of input options changed, updated to reflect this

* Update test.yml

name prefix changed in main script, test.yml updated to reflect this

* fix tests due to review changes

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-29 17:21:34 +01:00
FriederikeHanssen
3df4fe6085
add freebayes/somatic and update freebayes/germline (#990)
* add freebayes/somatic and update freebayes/germline to new syntax and cram

* add pytest

* update with new freebayes/germline path
2021-10-29 17:05:06 +02:00
Jose Espinosa-Carrasco
0a7368aa6f
Refactor genrich to avoid params in main (#981)
* Refactor genrich to avoid params in main

* Missed to commit test.yml file
2021-10-29 16:37:39 +02:00
louperelo
a4943a9e57
Mtnucratio (#986)
* add new module samtools_depth

* fixed main.nf for samtools/depth

* add new module mtnucratio

* fix main.nf

* Apply suggestions from code review

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

* Apply suggestions from code review

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

* layout in main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-10-29 15:02:02 +02:00
avantonder
977d96ed0b
Add Racon module to nf-core/modules (#949)
* add racon

* add racon

* add racon

* add racon module

* add racon module

* edit racon module

* edit racon module

* edit racon module

* edit racon module

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2021-10-29 13:33:38 +01:00
Chris Cheshire
2959b4ba07
Bedtools sort add extension choice input (#984)
* hifiasm copied from fastqc

* hifiasm tests init from fastqc

* meta.yml init; test.yml and main.nf for printing version

* Add hifiasm version printing

* Removed spaced on an empty line

* Reverted hifiasm from main

* Added extension input for bedtools sort

* whitespace

* Updated docs

Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: Svyatoslav Sidorov <svet.sidorov@gmail.com>
2021-10-29 13:22:17 +01:00
Francesco L
460a3ed87b
Fgbio group reads by umi (#952)
* adding template for module groupreadsbyumi

* update modules with code

* strategy is required argument so moving it to input rather than options.args

* tests successful committing yml

* added meta to output

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-10-29 14:00:54 +02:00
Daniel Lundin
84cb78cc98
Khmer normalizebymedian (#985)
* Templates for new module

* pe only test passing

* only_pe and only_se passing

* only_pe, only_se, mixed passes

* Multiple pe + se tc passes

* Passing args works

* Add 'interleaved' to description

* Fixed linting message

* Update modules/khmer/normalizebymedian/main.nf

Good point.

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

* Update meta.yml

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
2021-10-29 13:23:34 +02:00
FriederikeHanssen
ac1e6df076
Update to allow cram + update needed to use the gatk4 modules in sarek (#976)
* Make samtools/merge cram compliant

* samtools/stats cram compliance

* update yml file

* samtools/view to deal with crams

* Update tests to make sure cram works

* also fix tmp dir and min mem in one go

* basequalityrecal test for cram + min mem + tmpdir

* update haplotypecaller for sarek

* update haplotype yml

* update markdup to allow multiple bams, take out params to be passed with options.args

* remove TODO statement

* Remove variable md5sum

* add emtpy input to stats module in subworkflows

* subworkflows seem to work now on my side

* Apply code review

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

* replace bam with input to be more inclusive

* rename everywhere

* rename input

* remove variable checksum

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-10-29 13:01:05 +02:00
GCJMackenzie
71945a5b5f
Mutect2 add mitochondria mode and update tests (#967)
* new mitochondria mode added, tests updated to allow for temp fix for test data

* add cram test

* bam/bam_idx renamed to input and input_index

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
2021-10-29 11:27:56 +01:00
Francesco L
4b8c7ac7bd
Bam2fq (#958)
* added template for module

* update main

* added specific code

* wrong variable name in else script

* added tests for both split and nosplit

* docker test successful - updating yaml

* adding echo to version print
2021-10-29 10:46:34 +02:00
Sateesh
5b1fe84bc6
add new assembly scan module (#971)
* add new assembly scan module

* add newline endings

* fix newline ending

* add newline at end

Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-10-29 10:01:23 +02:00
Chris Cheshire
e8b33e6eb1
bedtools/genomecov updated to allow for providing a per-sample scale factor (#799)
* hifiasm copied from fastqc

* hifiasm tests init from fastqc

* meta.yml init; test.yml and main.nf for printing version

* Add hifiasm version printing

* Removed spaced on an empty line

* Reverted hifiasm from main

* Added genomecov scale module

* Updated tagging

* Removed extra module - began merging

* Removed extra module tests

* Updated genomecov to take a scale value

* Updated line endings

* Removed redundant test

* Update tests/modules/bedtools/genomecov/main.nf

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

* Added checking for existing -bg arg

* Update modules/bedtools/genomecov/main.nf

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

* Update modules/bedtools/genomecov/main.nf

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

Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: Svyatoslav Sidorov <svet.sidorov@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-28 17:50:25 +01:00
FriederikeHanssen
1662201102
Add gatk4/estimatelibrarycomplexity (#965)
* Add gatk4/estimatelibrarycomplxity

* forgot to add yml

* Fix placeholder
2021-10-28 17:49:27 +02:00
emnilsson
9402595711
New module seqtk/mergepe (#951)
* First step into creating a seqtk/mergepe module to interleave fastQ input

* First rewrite of main.nf to make the module perform the desired (interleave/merge of pe reads) task

* Modifications to test the new seqtk/mergepe module.

* Improving the seqtk/mergepe module to output single end reads as well, and making sure tests work

* Modified so that gzip uses -n and that single read entries are symlinked with ln -s instead of copied, therefore updated test.yml as well.

* Fix trailing whitespaces

Co-authored-by: Daniel Lundin <daniel.lundin@lnu.se>
2021-10-28 16:53:33 +02:00
Jose Espinosa-Carrasco
fd1189c2f5
Updating test file for optitype (#782)
* Provide an exisiting bam file for optitype

* Update main.nf

Attempt at fixing this with new testing data

* Trying slightly different approach

* Mini fixes, not sure whats wrong here

* Add bam file with NM tags in all reads for optitype

Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
Co-authored-by: Alexander Peltzer <alexander.peltzer@boehringer-ingelheim.com>
2021-10-28 14:24:52 +02:00
Gisela Gabernet
d5183a7fec
new module cellranger mkref (#896)
* add cellranger mkref module

* add cellranger mkref tests

* update test yml chksum

* fix module linting

* fix test yml

* fix getprocessname

* fix versions typo

* fix cellranger test.yml

* fix versions.yml

* test versions.yml

* fix grep version

* fix cellranger version

* add dockerfile and readme

* review container statement

* Update modules/cellranger/mkref/meta.yml

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

* add disclaimers

* change location dockerfile

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-10-28 13:33:57 +02:00
Gisela Gabernet
0b0f87c2f7
add porechop module (#914)
* add module main porechop

* update porechop main

* add porechop functions

* update meta porechop

* add test main porechop

* add porechop pytest yml

* add porechop test.yml

* Update modules/porechop/meta.yml

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

* re-add porechop avoid conflict

* Update modules/porechop/meta.yml

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

* fix prefix suffix

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2021-10-28 13:21:36 +02:00
louperelo
263bbe56d2
add new module samtools/depth (#950)
* add new module samtools_depth

* fixed main.nf for samtools/depth

* 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>
2021-10-28 12:53:21 +02:00
James A. Fellows Yates
e27553b989
Add module: dedup (#907)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* feat: add megahit module, currently decompressed output

* Update main.nf

* Update tests/modules/megahit/test.yml

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Apply suggestions from code review

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

* feat: compress all outputs, remove md5sums due to gz stochasicity

* fix: wrong conda channel for pigz

* fix: broken singleend tests and update meta.yml

* Missed one

* Apply suggestions from code review

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

* fix: pigz formatting

* Apply suggestions from code review

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

* Apply suggestions from code review

* Add dedup (tests and version not working)

* Fix dedup and tests

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
2021-10-28 12:10:21 +02:00
Francesco L
a0bc08732c
Rewritten module fgbio/fastqtobam (#916)
* added template for fastqtobam

* porting old code into new template

* update with missing getprocessname function

* test completed - updating all

* fixed linting issues

* improved reading

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

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-10-27 19:06:06 +02:00
Maxime U. Garcia
80d8e87fa4
adding new manta/germline + manta/tumoronly modules (#906)
* feat: all manta/single to modules

* fix module name

* fix module name

* fix: changes from review comments

* fix: test data
2021-10-27 18:24:48 +02:00
FriederikeHanssen
257078bb39
Update strelka, by enabling BP if Manta candidates are present (#923)
* add BP to strelka/somatic

* merge conflicts

* update strelka modules for BP

* update strelka modules for BP

* apply suggestions from code review
2021-10-27 17:49:54 +02:00
Daniel Straub
12a3f80f33
add filtlong (#919) 2021-10-27 17:00:11 +02:00
FriederikeHanssen
754db250a0
Add Manta/somatic module + (fix tiny strelka params problem, i know bad practice :( ) (#912)
* remove params statement

* add manta/somatic module

* fix strelka target bed thing

* removing checksums should make this pass

* Update modules/manta/somatic/main.nf

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

* fix indentation

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
2021-10-27 16:14:52 +02:00
Matthias Hörtenhuber
b552958341
add paraclu (#909)
* add paraclu

* remove TODOs

* add min_cluster as input parameter, remove option parameters

* add tool_dev_url
2021-10-27 15:48:49 +02:00
Gisela Gabernet
f47c27edfb
Update checksum modules using human GTF (#900)
* update test yml star align

* update test yml stringtie merge

* update star genomegenerate yml

* update test yml rsem calculateexpression

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-26 23:09:04 +01:00
James A. Fellows Yates
bd2baa1e7c
New module: maxbin2 (#895)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* feat: add megahit module, currently decompressed output

* Update main.nf

* Update tests/modules/megahit/test.yml

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Apply suggestions from code review

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

* feat: compress all outputs, remove md5sums due to gz stochasicity

* fix: wrong conda channel for pigz

* fix: broken singleend tests and update meta.yml

* Missed one

* Apply suggestions from code review

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

* fix: pigz formatting

* Apply suggestions from code review

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

* Apply suggestions from code review

* Added, just need to finish tests once we have bacterial data

* Add prelim test data

* Fix version reporting

* Add tests based on proposed test-dataset

* Finalise new testdata

* Fix md5sum issue by removing it...

* Update main.nf

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
2021-10-26 22:07:33 +01:00
James A. Fellows Yates
a740a6ff48
New module: checkm/lineagewf (#899)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* feat: add megahit module, currently decompressed output

* Update main.nf

* Update tests/modules/megahit/test.yml

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Apply suggestions from code review

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

* feat: compress all outputs, remove md5sums due to gz stochasicity

* fix: wrong conda channel for pigz

* fix: broken singleend tests and update meta.yml

* Missed one

* Apply suggestions from code review

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

* fix: pigz formatting

* Apply suggestions from code review

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

* Apply suggestions from code review

* Added but test failing due to null on output channel

* fix prefix variable

* Complete checkm_lineagewf

* Remove TODOs

* Add description of fasta_ext parameter

* Improve meta map for this context

* Update meta.yml

* Update modules/checkm/lineagewf/meta.yml

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

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
2021-10-26 21:54:10 +01:00
Gregor Sturm
2ad98162f3
Notebook modules (#617)
* Draft rmarkdown module

* stub jupyter notebook module

* Create yaml file with params

* Update meta.yml for rmarkdown module

* Add comment on YAML

* Update notebooks module, clean up parametrize.nf

* Two separate channels for parameters and input files

* Fix Rmd render script

* Add tests for rmarkdown

* Fix tests for rmarkdown module

* Update checksums

* Fix tests for jupyter

* Test without Grab()

* Update software versions

* update rmarkdown dependencies

* Draft for multiple versions

* Fix indent of script

* Fix indent in rmarkdown script

* Emit version.syml

* Update modules/rmarkdown/main.nf

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

* Update modules/rmarkdown/meta.yml

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

* Update modules/rmarkdown/meta.yml

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

* Rename rmarkdown to rmarkdownnotebook

* Add rmarkdown mulled biocontainer

* Write sessionInfo to separate log file

* Update rmarkdownnotebook

* Sessioninfo does not have a stable md5sum

* Update jupyternotebook

* Update meta

* Add jupyternotebook biocontainers

* Handle Groovy Gstrings in parameterize

* Update to versions.yml

* Update functions.nf

* Fix versions yaml

* Fix EC lint

* Update modules/rmarkdownnotebook/main.nf

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

* Update modules/jupyternotebook/main.nf

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

* Use official test data

* Harshilify

* Make parameters channel clearer

* Apply suggestions from code review

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

* Apply suggestions from code review

* Update main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-24 20:51:56 +02:00
Sébastien Guizard
0a5ddd0ad0
Update module: bamtools/split (#885)
* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 📦 NEW: Add galgal6 chr30 test data

* 📦 NEW: Add bamtools module

* 👌 IMPROVE: Ignore test data

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 📦 NEW: Add galgal6 chr30 test data

* 📦 NEW: Add bamtools module

* 👌 IMPROVE: Ignore test data

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Update with new versions.yml file

* 🐛 FIX: Update meta.yml + correct typos

* Update modules/bamtools/split/meta.yml

Add bam, split, chunk tags

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

* 🐛 FIX: Correct meta.yml

* 🐛 FIX: Grab software name using ${getSoftwareName(task.process)}

* 🐛 FIX: Update test.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-23 19:39:27 +01:00
GCJMackenzie
3c8ca3fec4
Createsomaticpanelofnormals (#859)
* files created for createsompon, script written, meta written, still needs tests

* updated to 2.0.0 method input, however this requires a genomicsDB input now

* script finished, meta yaml updated. Tests working locally, test yaml made, needs genomicsdb example on nf-core to run repository tests

* versions updated, issue with test data not able to download directory

* updated tests to include repo-side data

* Apply suggestions from code review

* Update modules/gatk4/createsomaticpanelofnormals/main.nf

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-23 19:30:14 +01:00
Sébastien Guizard
8524e6b40f
Update of pbccs (#835)
* 📦 NEW: First commit of pbccs module

* 👌 IMPROVE: Remove option from command + rename output (ccs -> bam)

* 👌 IMPROVE: Move .pbi output  into report channel

* 🐛FIX: Correct code after --rq option removal from command line module

- module main.nf: Remove ramaining rq input channel
- Test main.nf: Transfert rq into addParams
- Test test.yml: Update md5sums

* 🐛FIX: Repair additionnal option usage

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: CCS is run in parallel with --chunk option

* 👌 IMPROVE: Add Pbindex in bam ouput channel

* 👌 IMPROVE: Change label to process_low

* 👌 IMPROVE: Define reports files names + add json version of txt report

* 🐛 FIX: Add missing backslashes

* 🐛 FIX: Add missing gz extension

* 🐛 FIX: update ouput channel

* 🐛 FIX: output file name

* 👌 IMPROVE: .gitignore

* 👌 IMPROVE: Update function.nf to last version

* 👌 IMPROVE: Update saveAs in main.nf

* 👌 IMPROVE: Add pbccs module

* 🐛 FIX: Fix Broken test

* 👌 IMPROVE: Update test_data.config

* 🐛 FIX: Fix test

* 👌 IMPROVE: Update path of test dataset files

* 👌 IMPROVE: Remove useless index + Fix Typos

* 📦 NEW: First commit of pbccs module

* 👌 IMPROVE: Remove option from command + rename output (ccs -> bam)

* 👌 IMPROVE: Move .pbi output  into report channel

* 🐛FIX: Correct code after --rq option removal from command line module

- module main.nf: Remove ramaining rq input channel
- Test main.nf: Transfert rq into addParams
- Test test.yml: Update md5sums

* 🐛FIX: Repair additionnal option usage

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: CCS is run in parallel with --chunk option

* 👌 IMPROVE: Add Pbindex in bam ouput channel

* 👌 IMPROVE: Change label to process_low

* 👌 IMPROVE: Define reports files names + add json version of txt report

* 🐛 FIX: Add missing backslashes

* 🐛 FIX: Add missing gz extension

* 🐛 FIX: update ouput channel

* 🐛 FIX: output file name

* 👌 IMPROVE: .gitignore

* 👌 IMPROVE: Update function.nf to last version

* 👌 IMPROVE: Update saveAs in main.nf

* 👌 IMPROVE: Add pbccs module

* 🐛 FIX: Fix Broken test

* 👌 IMPROVE: Update test_data.config

* 🐛 FIX: Fix test

* 👌 IMPROVE: Update path of test dataset files

* 👌 IMPROVE: Remove useless index + Fix Typos

* 🐛 FIX: fill contains args

* 👌 IMPROVE: One output => One Channel

* 👌 IMPROVE: One input => One channel

* 🐛 FIX: Update tests

* 🐛 FIX: Remove TODOs from test.yaml

* 👌 IMPROVE: Revert and keep bam and pbi together

* 🐛 FIX: Remove old rq input from meta.yml

* 👌 IMPROVE: Update test to match input channels

* 👌 IMPROVE: use prefix for for output file name

* 👌 IMPROVE: Update to new versions.yml

* 👌 IMPROVE: Update pbccs from v6.0.0 to v6.0.2

* 👌 IMPROVE: Keep track of the former sample id in meta

* Update modules/pbccs/main.nf

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

* 👌 IMPROVE: remove former_id from meta

* 👌 IMPROVE: Use chunk number in output filename

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-23 19:09:41 +01:00
Sébastien Guizard
d3369789da
New module: gstama/merge (#813)
* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 📦 NEW: Add galgal6 chr30 test data

* 📦 NEW: Add bamtools module

* 👌 IMPROVE: ignore test data

* 👌 IMPROVE : add test bed files

* 📦 NEW: Add gstama/merge module

* 🐛 FIX: Change process label

* 👌 IMPROVE: do not merge empty bed

* 🐛 FIX: Change 0 lines files detection

* 🐛 FIX: replace spaces by tab

* 🐛 FIX: Remove tuple for report channel and add version output channel

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Update test

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Fix Typos

* 👌 IMPROVE: Updates + clean code

- Update to last versions.yml file
- Better output channels
- Update meta.yml

* 👌 IMPROVE: Correct typo

* 👌 IMPROVE: Remove included filelist creation and add an input channel

* 🐛 FIX: Correct typo

* 👌 IMPROVE: Add filelist file

* 🐛 FIX: tama_merge.py emit a version number

* Update modules/gstama/merge/meta.yml

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

* 👌 IMPROVE: Update meta.yml

* Update main.nf

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-23 19:00:39 +01:00
Sébastien Guizard
481d3c811d
New module: gstama/collapse (#809)
* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 📦 NEW: Add galgal6 chr30 test data

* 📦 NEW: Add gd-tama module

* 🐛 FIX (TEMP): Update singularity container address

* 📦 NEW: Add bamtools module

* 📦 NEW: Rewrite and rename module (gstama => gstama/collapse)

* 👌 IMPROVE: ignore test data

* 👌 IMPROVE: Remove junk files

* 👌 IMPROVE: Update output

* 👌 IMPROVE: Add channel for publishing tama's metadata outputs

* 👌 IMPROVE: Update process label

* 🐛 FIX: Use depot.galxyproject.org url for singularity

* 👌 IMPROVE: autoselect running mode

* 🐛 FIX: correct gstama collapse bash test

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update tama package and label

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Update test

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 📦 NEW: Add galgal6 chr30 test data

* 📦 NEW: Add gd-tama module

* 🐛 FIX (TEMP): Update singularity container address

* 📦 NEW: Add bamtools module

* 📦 NEW: Rewrite and rename module (gstama => gstama/collapse)

* 👌 IMPROVE: ignore test data

* 👌 IMPROVE: Update output

* 👌 IMPROVE: Add channel for publishing tama's metadata outputs

* 👌 IMPROVE: Update process label

* 🐛 FIX: Use depot.galxyproject.org url for singularity

* 👌 IMPROVE: autoselect running mode

* 🐛 FIX: correct gstama collapse bash test

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update tama package and label

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Update test

* 👌 IMPROVE: delete unnecessary files

* 👌 IMPROVE: Update + clean

- Remove unnecessary files
- Update to new versions.yml file
- Better output channels

* 👌 IMPROVE: Update meta.yml and output channels

* 👌 IMPROVE: Remove useless files

* 👌 IMPROVE: Remove automatic MODE setup

* 👌 IMPROVE: Applied @jfy133 code modification suggestions

* Update modules/gstama/collapse/meta.yml

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

* 🐛 FIX: Add missing fasta option in meta.yml

* 🐛 FIX: Fix typo

* 🐛 FIX: Update package version

* Update main.nf

* Update meta.yml

* Update modules/gstama/collapse/meta.yml

* Apply suggestions from code review

* Update tests/modules/gstama/collapse/main.nf

* Update main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-23 18:55:28 +01:00
GCJMackenzie
7676d9d728
Filtermutectcalls (#796)
* first commit with files for filtermutectcalls initialised

* found missing test file that needs to be resolved

* saving config changes

* fixing pytest_module conflict

* finished module, just needs repository side tests added

* test data added, versions file updated

* modified to emit correct versions file

* Update main.nf

* Update test_data.config

* updated test script

* fixed main.nf

* Update main.nf

* Update main.nf

* removed whitespace from test script

* Update test_data.config

* Update .gitignore

* Update test_data.config

* tests changed to new names, main script edited to match comments on learnreads pr

* Update meta.yml

* Apply suggestions from code review

* Update main.nf

* Apply suggestions from code review

* Apply suggestions from code review

* Update main.nf

* Update main.nf

* Update main.nf

* Update main.nf

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-23 18:45:19 +01:00
Jose Espinosa-Carrasco
32f6191aca
New module: genrich (#877)
* Add genrich module

* Rearrange genrich module from genrich/genrich to genrich

* Remove copy/paste code

* Fix meta.yml

* Implement save_duplicates independently of -r opt
2021-10-22 12:22:02 +02:00
Benjamin Wingfield
4ed5e4eff3
New module: ucsc/liftover (#868)
* add liftOver module

* add liftover module tests

* fix getProcessName

* fix tests

* fix out of date function

* version numbers should be numeric

* drop versions.yml from test.yml

* Update modules/ucsc/liftover/main.nf

Remove software name variable

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

* Update tests/modules/ucsc/liftover/main.nf

Use test chain file

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

* add genome_chain_gz to test data config

* update md5sum for new chain test data

* Fix indentation in file declaration

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-10-21 18:04:15 +02:00
Chris Cheshire
4d89d6b2f0
I accidently deleted a branch before the PR merged for PR 800 (#881)
* hifiasm copied from fastqc

* hifiasm tests init from fastqc

* meta.yml init; test.yml and main.nf for printing version

* Add hifiasm version printing

* Removed spaced on an empty line

* Reverted hifiasm from main

* Updated seacr callpeak to include a control threshold

* Whitespace

Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: Svyatoslav Sidorov <svet.sidorov@gmail.com>
2021-10-21 12:28:59 +01:00
Jose Espinosa-Carrasco
b5fa91d0f7
Check only for file being generated (#879) 2021-10-21 11:32:05 +02:00
Maxime Borry
eb04a0f1f6
New module: freebayes (#818)
* add pydamage module

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-10-20 15:19:31 +02:00
James A. Fellows Yates
97fe899f79
fix: reduce number of required input files for damage profiler (#612)
* Reduce number of required input files for damage profiler

* Remove rebugging

* Add optional species list file.

* Working pending updated test-dataset update

* Add genome header to config
2021-10-20 10:02:30 +02:00
Harshil Patel
4e9e732b76
Add strelka/somatic module (#866)
* Add strelka/somatic module

* Fill out meta.yml properly
2021-10-18 22:34:23 +01:00
James A. Fellows Yates
cbfc8eb46c
Pydamage analyzer update (#863)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* feat: add megahit module, currently decompressed output

* Update main.nf

* Update tests/modules/megahit/test.yml

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Apply suggestions from code review

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

* feat: compress all outputs, remove md5sums due to gz stochasicity

* fix: wrong conda channel for pigz

* fix: broken singleend tests and update meta.yml

* Missed one

* Apply suggestions from code review

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

* fix: pigz formatting

* Apply suggestions from code review

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

* Apply suggestions from code review

* Update md5sum due to test-dataset update

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
2021-10-18 15:24:49 +02:00
Sébastien Guizard
1cf207a5b6
Update isoseq3/cluster (#856)
* 📦 NEW: Add isoseq3/cluster module

* 🐛FIX: Fix reports channel and add .pbi to it

* 🐛FIX: Fix report channel definition

* 👌IMPROVE: Move .pbi file into reports channel

* 👌IMPROVE: remove --use_qvs option from command line

* 👌 IMPROVE: Add in addParams removed options from command line

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 👌 IMPROVE: The module accept one channel (primers moved into the first channel)

* 📦 NEW: Add galgal6 chr30 test data

* 📦 NEW: Add bamtools module

* 👌 IMPROVE: Ignore test data

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: add singletons parameter and improve outputs

* 🐛 FIX: Update test with last module model

* 👌 IMPROVE: Add test tag

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Update test data config

* 👌 IMPROVE: Remove pbi from input files

* 👌 IMPROVE: Remove unused index

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Fill contains args

* 📦 NEW: Add isoseq3/cluster module

* 🐛FIX: Fix reports channel and add .pbi to it

* 🐛FIX: Fix report channel definition

* 👌IMPROVE: Move .pbi file into reports channel

* 👌IMPROVE: remove --use_qvs option from command line

* 👌 IMPROVE: Add in addParams removed options from command line

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 👌 IMPROVE: The module accept one channel (primers moved into the first channel)

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: add singletons parameter and improve outputs

* 🐛 FIX: Update test with last module model

* 👌 IMPROVE: Add test tag

* 👌 IMPROVE: Update test data config

* 👌 IMPROVE: Remove pbi from input files

* 👌 IMPROVE: Remove unused index

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Fill contains args

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 📦 NEW: Add galgal6 chr30 test data

* 📦 NEW: Add bamtools module

* 👌 IMPROVE: Ignore test data

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Update code to new versions capture + better output channels

* 👌 IMPROVE: Update with new versions.yml file

* 🐛 FIX: Update meta.yml + correct typos

* 👌 IMPROVE: Clean output file names + correct typo

* 🐛 FIX: Remove bamtools/split module from isoseq3/cluster

* 🐛 FIX: Update output filename pattern

input filename and output filename were the same

* 👌 IMPROVE: Update meta.yml
2021-10-14 11:07:53 +01:00
Mei Wu
d1794d1934
Add TIDDIT cov (#822)
* added template for tiddit/cov

* test finished

* quick fix to meta info

* Apply suggestions from code review

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

* applying suggestions

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-10-13 12:59:35 +02:00
James A. Fellows Yates
7b1e84f7be
Add bcftools/index (#812)
* feat: add bcftools index

* Extend tests to also test gen for TBI

* Update meta.yml

* Update meta.yml
2021-10-13 10:40:04 +02:00
James A. Fellows Yates
359f721cc9
Add MEGAHIT (#810)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* feat: add megahit module, currently decompressed output

* Update main.nf

* Update tests/modules/megahit/test.yml

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Apply suggestions from code review

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

* feat: compress all outputs, remove md5sums due to gz stochasicity

* fix: wrong conda channel for pigz

* fix: broken singleend tests and update meta.yml

* Missed one

* Apply suggestions from code review

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

* fix: pigz formatting

* Apply suggestions from code review

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

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
2021-10-12 16:06:06 +01:00
Moritz E. Beber
de997825de
Add a new module for fasterq-dump (#807)
* chore: use template to create fasterq module

* feat: add fasterq-dump process module

* docs: provide input and output descriptions

* docs: add comment on `--temp`

* fix: use correct variable

* tests: define test output

* refactor: address review comments

* refactor: remove vdb-config input

* chore: add new test data to config

* tests: define single-end and paired-end cases

* refactor: choose specific output

* tests: do not expect single FASTQ for paired-end

* feat: add compression

* Apply suggestions from code review

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

* tests: revert the test data name

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-12 14:20:58 +01:00
Sébastien Guizard
3a4935d21b
New module: bamtools/split (#798)
* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 📦 NEW: Add galgal6 chr30 test data

* 📦 NEW: Add bamtools module

* 👌 IMPROVE: Ignore test data

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 📦 NEW: Add galgal6 chr30 test data

* 📦 NEW: Add bamtools module

* 👌 IMPROVE: Ignore test data

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Update with new versions.yml file

* 🐛 FIX: Update meta.yml + correct typos

* Update modules/bamtools/split/meta.yml

Add bam, split, chunk tags

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

* 🐛 FIX: Correct meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-10-12 14:43:08 +02:00
Moritz E. Beber
07c0830057
Add a module for sra-tools prefetch (#714)
* chore: apply module template

* refactor: add NCBI settings to options

* docs: complete meta information

* feat: add prefetch process

* fix: correct bash commands

* tests: define the right tests

* style: move option definition to satisfy linting

* fix: extract version correctly

* fix: correct newline issues

* refactor: address review comments

* Apply suggestions from code review

* chore: add retrying via nf-core label

* refactor: validate download thoroughly

* refactor: remove vdb-config input

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-11 22:30:41 +01:00
Edmund Miller
c19671dca9
Subworkflow Infrastructure (#662)
* feat(subworkflows): Add align_bowtie2 subworkflow

For testing CI setup

* test(align_bowtie2): Add initial list of changes to test

* test(align_bowtie2): Add initial test

* refactor: Use tags to run subworkflows ci

For every underlying module used by workflow and allow the modules
pytest-modules definition be the source of truth.

* refactor: Use individual directories for subworkflows

* docs(align_bowtie2): Add initial meta.yml

Copied most of it from the bowtie2/align module.

* fix(align_bowtie2): Fix module include paths

* test(bam_sort_samtools): Add initial test

* ci(bam_sort_samtools): Add modules that trigger the tag

* test(bam_stats_samtools): Add initial test

* ci(bam_stats_samtools): Add keys to pick up changes

* docs(bam_samtools): Add initial meta.yml

* test(align_bowtie2): Fix path to subworkflow

* test(align_bowtie2): Update entry point

* fix(bam_sort_samtools): Update include paths

* test(bam_sort_samtools): Fix path

* style: Clean up addParams

* test(samtools_sort): Add suffix for test

* test(align_bowtie2): Add samtools_options for suffix

* test(bam_stats_samtools): Update path

* test(bam_stats_samtools): Use stats input

Otherwise it's just an example of how it's used in the bam_sort_samtools subworkflow

* ci(linting): Skip module linting of subworkflows

* ci(linting): Clean up startsWith statement

* test(bam_stats_samtools): Use single end test data for single end test

* test(bam_stats_samtools): Add expected files

* test(align_bowtie2): Add paired-end test

* test(align_bowtie2): Sort order of output

* test(align_bowtie2): Update hashes

* docs(align_bowtie2): Fix typo

* test(align_bowtie2): Update samtools output names

* test(align_bowtie2): Remove md5sums for bam/bai

* feat(subworkflows): Add nextflow.configs

These can be used for default settings in the future. They can then be
included in the conf/modules.config so that the params don't have to be
duplicated in the root nextflow.config.

* docs(subworkflows): Include modules instead of tools

* fix: Update to versions

* chore(align_bowtie2): Remove duplicate tag

* style: Format yamls

* test(subworkflows): Only check versions for modules

* chore: Update subworkflows to match rnaseq dev

* fix(subworkflows): Update paths

* fix(bam_sort_samtools): Fix sort parameters for testing

* Apply suggestions from code review

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

* docs: Update TODOs with a message

* ci: Try using a matrix for strategy

* ci: Try passing an array

* Revert "ci: Try passing an array"

This reverts commit d3611fcd8332bbb9a8501e8dd299d0a623aaecaa.

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-08 16:02:42 +01:00
GCJMackenzie
f479d4fb8d
Learnreadorientationmodel (#794)
* files for learnreadorientationmodel initialised for first commit

* finished scripts and yml files. test working locally but needs an f1r2 test data on nf-core before it can be submitted

* updated test data location

* versions file updated, test data added

* updated versions file, edited test file

* small formatting update to main.nf

* Update main.nf

* Update test_data.config

* updated tests main.nf

* Update test_data.config

* Apply suggestions from code review

* Update modules/gatk4/learnreadorientationmodel/main.nf

* Update modules/gatk4/learnreadorientationmodel/meta.yml

* fixed tests failing

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-07 13:55:06 +01:00
Sébastien Guizard
5a49d2c1bf
New module: isoseq3/cluster (#801)
* 📦 NEW: Add isoseq3/cluster module

* 🐛FIX: Fix reports channel and add .pbi to it

* 🐛FIX: Fix report channel definition

* 👌IMPROVE: Move .pbi file into reports channel

* 👌IMPROVE: remove --use_qvs option from command line

* 👌 IMPROVE: Add in addParams removed options from command line

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 👌 IMPROVE: The module accept one channel (primers moved into the first channel)

* 📦 NEW: Add galgal6 chr30 test data

* 📦 NEW: Add bamtools module

* 👌 IMPROVE: Ignore test data

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: add singletons parameter and improve outputs

* 🐛 FIX: Update test with last module model

* 👌 IMPROVE: Add test tag

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Update test data config

* 👌 IMPROVE: Remove pbi from input files

* 👌 IMPROVE: Remove unused index

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Fill contains args

* 📦 NEW: Add isoseq3/cluster module

* 🐛FIX: Fix reports channel and add .pbi to it

* 🐛FIX: Fix report channel definition

* 👌IMPROVE: Move .pbi file into reports channel

* 👌IMPROVE: remove --use_qvs option from command line

* 👌 IMPROVE: Add in addParams removed options from command line

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 👌 IMPROVE: The module accept one channel (primers moved into the first channel)

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: add singletons parameter and improve outputs

* 🐛 FIX: Update test with last module model

* 👌 IMPROVE: Add test tag

* 👌 IMPROVE: Update test data config

* 👌 IMPROVE: Remove pbi from input files

* 👌 IMPROVE: Remove unused index

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Fill contains args

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 📦 NEW: Add galgal6 chr30 test data

* 📦 NEW: Add bamtools module

* 👌 IMPROVE: Ignore test data

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Update code to new versions capture + better output channels

* 👌 IMPROVE: Update with new versions.yml file

* 🐛 FIX: Update meta.yml + correct typos

* 👌 IMPROVE: Clean output file names + correct typo

* 🐛 FIX: Remove bamtools/split module from isoseq3/cluster
2021-10-07 10:06:02 +01:00
Sébastien Guizard
79d38a306b
New module: isoseq3/refine (#748)
* 📦 NEW: Add isoseq3/refine module

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add parallelization

* 🐛 FIX: Correct Typo

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 👌 IMPROVE: The module accept one channel (primers moved into the first channel)

* 👌 IMPROVE: Assign a value channel to primers input 

Improve workflow code readability

* 👌 IMPROVE: Update to the version of templates

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Remove pbi from input files

* 👌 IMPROVE: Update test file

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Fill contains args

* 📦 NEW: Add isoseq3/refine module

* 👌 IMPROVE: Add parallelization

* 🐛 FIX: Correct Typo

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 👌 IMPROVE: The module accept one channel (primers moved into the first channel)

* 👌 IMPROVE: Assign a value channel to primers input 

Improve workflow code readability

* 👌 IMPROVE: Update to the version of templates

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Remove pbi from input files

* 👌 IMPROVE: Update test file

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Fill contains args

* 👌 IMPROVE: Add one channel per output file

* 👌 IMPROVE: Minor updates

* 👌 IMPROVE: Minors Update

- Remove TODO from test.yml
- Remove useless piece of code

* 📦 NEW: Add isoseq3/refine module

* 👌 IMPROVE: Add parallelization

* 🐛 FIX: Correct Typo

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 👌 IMPROVE: The module accept one channel (primers moved into the first channel)

* 👌 IMPROVE: Assign a value channel to primers input 

Improve workflow code readability

* 👌 IMPROVE: Update to the version of templates

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Remove pbi from input files

* 👌 IMPROVE: Update test file

* 👌 IMPROVE: Fill contains args

* 📦 NEW: Add isoseq3/refine module

* 👌 IMPROVE: Add parallelization

* 🐛 FIX: Correct Typo

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 👌 IMPROVE: The module accept one channel (primers moved into the first channel)

* 👌 IMPROVE: Assign a value channel to primers input 

Improve workflow code readability

* 👌 IMPROVE: Update to the version of templates

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Remove pbi from input files

* 👌 IMPROVE: Update test file

* 👌 IMPROVE: Add one channel per output file

* 👌 IMPROVE: Minor updates

* 👌 IMPROVE: Minors Update

- Remove TODO from test.yml
- Remove useless piece of code

* 🐛 FIX: Remove unwanted files

* 🐛 FIX: Protect \

* 🐛 FIX: Remove test files

* Apply suggestions from code review

* Apply suggestions from code review

* Update tests/modules/isoseq3/refine/test.yml

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-06 11:13:48 +01:00
Jose Espinosa-Carrasco
84f2302920
Correct parsing versions with trailing zeros (#795)
* Correct parsing versions with trailing zeros

* Fix test

* Update modules/custom/dumpsoftwareversions/main.nf

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

* Fix tests and go back to output versions.yml

* Update tests/test_versions_yml.py to use BaseLoader

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-10-06 08:16:36 +02:00
Sébastien Guizard
bcf2681b03
New module: pbbam/pbmerge (#752)
* 👌 IMPROVE: Add some pacbio test files

* 📦 NEW: Add pbbam/pbmerge module

* 🐛 FIX: Add optional arguments to command line

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Update test data config and test script

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Add some pacbio test files

* 📦 NEW: Add pbbam/pbmerge module

* 🐛 FIX: Add optional arguments to command line

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Update test data config and test script

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Update and clean code

* 🐛 FIX: Update module path in test

* 🐛 FIX: Add missing () + correct module path in test

* 👌 IMPROVE: Update pbmerge from version 1.6.0 to 1.7.0

* 👌 IMPROVE: Change output filename suffix for something more generic

* 🐛 Update test.yml

* Apply suggestions from code review

* Update tests/modules/pbbam/pbmerge/test.yml

* Update tests/modules/pbbam/pbmerge/main.nf

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 23:16:45 +01:00
GCJMackenzie
aa32a8a72e
new module: gatk4/calculatecontamination (#778)
* initiated files for calculate contamination

* pushing local repo to remote

* created script, filled in meta yml, created tests and test yml. local checks passing, needs repo side test data

* added option and tests for outputting optional segmentation file

* saving for test push

* versions updated, test data added

* Update main.nf

* fixed versions info, should report correctly now

* small update to main.nf outputs formatting

* Apply suggestions from code review

* Update test_data.config

* Apply suggestions from code review

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 22:52:00 +01:00
Robert A. Petit III
053797510d
add pirate module (#777)
* new module pirate

* remove md5 check for non reproducible binary files

* get those to-dos out

* Update main.nf

* Update meta.yml

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 22:28:25 +01:00
Robert A. Petit III
e77b3d72f3
add spatyper module (#784)
* add spatyper module

* lint fix

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 22:21:35 +01:00
Robert A. Petit III
0ba88fb869
add roary module (#776)
* add module roary

* Update meta.yml

* Update meta.yml

* Update meta.yml

* Update meta.yml

* Update main.nf

* Update meta.yml

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 22:08:47 +01:00
Robert A. Petit III
8d04c34934
add ismapper module (#773)
* add ismapper module

* Update main.nf

* Update main.nf

* Update meta.yml

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 21:55:41 +01:00
Robert A. Petit III
8179bab819
add csvtk/concat module (#785)
* add csvtk/concat module

* Update modules/csvtk/concat/main.nf

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

* allow alternate delimiters

* Update main.nf

* Update modules/csvtk/concat/main.nf

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

* Update modules/csvtk/concat/main.nf

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

* Update modules/csvtk/concat/main.nf

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

* Update modules/csvtk/concat/main.nf

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

* Update modules/csvtk/concat/main.nf

* Apply suggestions from code review

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 21:48:47 +01:00
Robert A. Petit III
bb7beff497
add hicap module (#772)
* add hicap module

* add info on optional inputs

* fix typo

* Update meta.yml

* Update main.nf

* Update meta.yml

* Update modules/hicap/main.nf

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

* Update modules/hicap/main.nf

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

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 21:42:09 +01:00
Robert A. Petit III
7d98bf1d7d
add mashtree module (#767)
* add mashtree module

* remove todo

* whitespace adjustment

* remove un-reproducible md5sum

* Update main.nf

* Update main.nf

* Update meta.yml

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 21:27:30 +01:00
Abhinav Sharma
3868c3ab4b
Add gtdbtk/classifywf module (#765)
* initial commit [ci skip]

* reuse the modules code from nf-core/mag [ci skip]

* add contextual information for the module [ci skip]

* add stubs to avoid downloading db [ci skip]

* trigger test

* iterate on tests [ci skip]

* itereate tests [ci skip]

* add bins [ci skip]

* fix stubs [ci skip]

* interation on tests with stubs [ci skip]

* use the existing pattern and fasta for input

* accomodate the new version file format

* use variable for the stub [ci skip]

* update the versions file in meta.yml

* Accomodate code review regarding publishDir function [ci skip]

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

* remove extra newline

* use bioconda channel

* update the description for filtered file

* Apply suggestions from code review

* Update main.nf

* Update main.nf

* Update modules/gtdbtk/classifywf/meta.yml

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

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 21:23:01 +01:00
Lee Katz
f20c427339
added classic mlst module (#742)
* added classic mlst module

* removed nf-core TODO comments

* included drpatelh suggestions

* adjust version capture identation

* update main to pass lint

* follow output expected by test.yml

* suggested prefix change from rpetit3

* Apply suggestions from code review

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 20:49:46 +01:00
Jose Espinosa-Carrasco
5b1cea7f7f
Add bbmap/bbsplit module (#771)
* Add bbmap/bbsplit module

* Conda complains about md5sum

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-30 13:37:35 +01:00
James A. Fellows Yates
01cc326c23
add Amps (#768)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Start work, continue once on non-mobile internet

* finished and working on conda

* Update modules/amps/main.nf

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

* Apply suggestions from code review

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

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-09-30 12:54:16 +02:00
Harshil Patel
b2c2d4deb4
Add custom/dumpsoftwareversions modules for nf-core pipeline template (#761)
* Add custom/dumpsoftwareversions modules for nf-core pipeline template

* Remove md5sums due to differing NF versions
2021-09-29 14:27:00 +01:00
Harshil Patel
b932210f27
Fix flash and cat/fastq modules (#759)
* Fix version commands: round 3

* Fix seqkit/split2 modules

* Fix flash and cat/fastq modules

* Remove md5sums on gz files
2021-09-28 21:14:11 +01:00
Robert A. Petit III
5c463ca6b4
few version and test data config fixes (#758)
* update kleborate version info

* fix stderr capture

* few more version fixes

* fix version info on more tools
2021-09-28 20:42:04 +01:00
Gregor Sturm
c3687ef54b
fix more ver yml (#757)
* Fix featurecounts

* whitespace change to trigger CI on yara/mapper

* update test yaml
2021-09-28 20:25:10 +01:00
Jose Espinosa-Carrasco
cde1d827f9
Fix yml ver (#756)
* Fix kallisto index tests

* Fix nanoplot

* Fix kallistobustools

* Fix pairix

* Fix plasmidid

* Fix pbccs

* Fix raxmlng

* Fix prokka

* Fix shovill

* Fix typo

* Deleted workflow by mistake added again
2021-09-28 18:33:07 +02:00
Harshil Patel
9c31cf1566
Fix version commands: round 3 (#754)
* Fix version commands: round 3

* Fix seqkit/split2 modules
2021-09-28 14:37:47 +01:00
James A. Fellows Yates
e971f538a9
Module new version reporting fixes (#753)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Fix IQ tree

* Fix picard markdup and merge sam

* Fix plink/vcf version

* Fix plink version output

* Fix prokka version command

* Fix pydamage

* Try fixing markduplicates

* Fix snpEff

* Fix vcftools version

* Fix pydamage and filtersamreads test run

* Fix MarkDuplicates tests

* Add missing unsorted checks

* Remove MD5 sym due to stochasicity in BAM file
2021-09-28 10:51:19 +01:00
Harshil Patel
3c5492b4a3
Fix more version commands (#750)
* Fix outstanding tests

* Fix more version commands

* Fix remaining modules
2021-09-28 06:56:27 +01:00
Harshil Patel
43c2779258
Fix version commands (#749)
* Fix version commands

* Fix version commands: again
2021-09-27 22:10:37 +01:00
Sébastien Guizard
4ec8b025bd
New module: LIMA (#719)
* 📦 NEW: Add module lima

* 👌 IMPROVE: Move .pbi output to reports channel

* 🐛 FIX: Fix report channel definition

* 👌IMPROVE; Remove options from command line

update test script with removed options

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 🐛 FIX: Add pbi input

* 👌 IMPROVE: Add parallelization to lima

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 👌 IMPROVE: The accept one channel (primers move into the first channel)

* 👌 IMPROVE: Assign a value channel for pimers 

Improve code workflow readability

* 👌 IMPROVE: Update .gitignore

* 👌 IMPROVE: Update module to last template version

* 🐛 FIX: Correct Singularity and Docker URL

* 👌 IMPROVE: Update to the last version of modules template

* 👌 IMPROVE: Update test_data.config

* 👌 IMPROVE: Remove pbi from input files

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 🐛 FIX: Fill contains args

* 📦 NEW: Add module lima

* 👌 IMPROVE: Move .pbi output to reports channel

* 🐛 FIX: Fix report channel definition

* 👌IMPROVE; Remove options from command line

update test script with removed options

* 🐛 FIX: Add pbi input

* 👌 IMPROVE: Add parallelization to lima

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 👌 IMPROVE: The accept one channel (primers move into the first channel)

* 👌 IMPROVE: Assign a value channel for pimers 

Improve code workflow readability

* 👌 IMPROVE: Update .gitignore

* 👌 IMPROVE: Update module to last template version

* 🐛 FIX: Correct Singularity and Docker URL

* 👌 IMPROVE: Update to the last version of modules template

* 👌 IMPROVE: Update test_data.config

* 👌 IMPROVE: Remove pbi from input files

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 🐛 FIX: Fill contains args

* 👌 IMPROVE: Add channel for each output

* 👌 IMPROVE: Remove comments

* 📦 NEW: Add module lima

* 👌 IMPROVE: Move .pbi output to reports channel

* 🐛 FIX: Fix report channel definition

* 👌IMPROVE; Remove options from command line

update test script with removed options

* 🐛 FIX: Add pbi input

* 👌 IMPROVE: Add parallelization to lima

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 👌 IMPROVE: The accept one channel (primers move into the first channel)

* 👌 IMPROVE: Assign a value channel for pimers 

Improve code workflow readability

* 👌 IMPROVE: Update module to last template version

* 🐛 FIX: Correct Singularity and Docker URL

* 👌 IMPROVE: Update to the last version of modules template

* 👌 IMPROVE: Update test_data.config

* 👌 IMPROVE: Remove pbi from input files

* 🐛 FIX: Fill contains args

* 📦 NEW: Add module lima

* 👌 IMPROVE: Move .pbi output to reports channel

* 🐛 FIX: Fix report channel definition

* 👌IMPROVE; Remove options from command line

update test script with removed options

* 🐛 FIX: Add pbi input

* 👌 IMPROVE: Add parallelization to lima

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 👌 IMPROVE: The accept one channel (primers move into the first channel)

* 👌 IMPROVE: Assign a value channel for pimers 

Improve code workflow readability

* 👌 IMPROVE: Update module to last template version

* 🐛 FIX: Correct Singularity and Docker URL

* 👌 IMPROVE: Update to the last version of modules template

* 👌 IMPROVE: Update test_data.config

* 👌 IMPROVE: Remove pbi from input files

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 🐛 FIX: Fill contains args

* 👌 IMPROVE: Add channel for each output

* 👌 IMPROVE: Remove comments

* 🐛 FIX: Clean test_data.config

* Update modules/lima/main.nf

Add meta to each output

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

* Update modules/lima/main.nf

Remove useless parenthesis

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

* 🐛 FIX: Keep version number only

* 🐛 FIX: Reintegrate prefix variable and use it to define output file name

* 👌 IMPROVE: add suffix arg to check output files names

* 👌 IMPROVE: Use prefix for output filename

* 🐛 FIX: Set optional output

Allow usage of different input formats

* 👌 IMPROVE: Update meta file

* 👌 IMPROVE: Update test

One test for each input file type

* 👌 IMPROVE: add fasta, fastq.gz, fastq, fastq.gz test files

* 👌 IMPROVE: Update with last templates / Follow new version.yaml rule

* 🐛 FIX: Fix typos and include getProcessName function

* 👌 IMPROVE: Update .gitignore

* 👌 IMPROVE: Using suffix to manage output was not a my best idea

Add a bash code to detect extension and update output file name

* 👌 IMPROVE: clean code

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
2021-09-27 16:14:35 +01:00
Stephen Ficklin
ca53f7525b
Diamond (#710)
* Added diamond

* minor tweaks & yml fix

* Fixed spacing issues due to failing lint

* Update modules/diamond/blastp/main.nf

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

* Update modules/diamond/blastp/main.nf

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

* Update modules/diamond/blastp/main.nf

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

* Update modules/diamond/blastp/main.nf

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

* Update modules/diamond/blastp/main.nf

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

* Update modules/diamond/blastx/main.nf

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

* Update modules/diamond/blastx/main.nf

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

* Update modules/diamond/blastx/main.nf

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

* Update modules/diamond/blastx/main.nf

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

* Update modules/diamond/makedb/main.nf

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

* Update modules/diamond/makedb/main.nf

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

* Update tests/modules/diamond/blastp/main.nf

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

* Update tests/modules/diamond/blastx/main.nf

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

* Update tests/modules/diamond/blastx/main.nf

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

* Update tests/modules/diamond/blastp/main.nf

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

* Update modules/diamond/blastp/meta.yml

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

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-23 09:13:04 +01:00
Ramprasad Neethiraj
25943a4c23
Add glnexus (#729)
* Add glnexus

* Fix lint error

* Refactor

* Suggested changes

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-22 13:31:01 +01:00
James A. Fellows Yates
5758e9f451
Unzip update (#730)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Change test dataset
2021-09-22 11:02:32 +01:00
Abhinav Sharma
77a2895785
Add module kleborate (#711)
* initial commit [ci skip]

* remove todo from the module files [ci skip]

* add a sample test case [ci skip]

* push the latest work [ci skip]

* bump kleborate build

* test passing with the new build for kleborate [ci skip]

* ready for review

* Apply suggestions from code review

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-21 20:45:42 +01:00
Abhinav Sharma
0d53a34eed
module fastani (#695)
* initiate agrvate module

* remove todos [ci skip]

* initiate fastani draft [ci skip]

* clean stubs [ci skip]

* interim commit [ci skip]

* accomodate the batch/per-sample processing [ci skip]

* use the meta map [ci skip]

* run first test [ci skip]

* remove extra spaces [ci skip]

* change output file name [ci skip]

* update the expected output [ci skip]

* update the files used for test [ci skip]

* fix typo [ci skip]

* test passing [ci skip]

* update the description

* remove extra files

* accomodate CR suggestions [ci skip]

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

* accomodate CR suggestions [ci skip]

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

* accomodate CR suggestions [ci skip]

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

* use meta map for batch analysis

* fix the tests

* rely upon tuples

* Apply suggestions from code review

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-21 20:20:26 +01:00
James A. Fellows Yates
7830a4a80c
add: MALTEXTRACT (#725)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Start maltextract module

* start tests

* Get tests working now we have test data

* Apply suggestions from code review

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

* Changes after review

* Update tests/modules/maltextract/main.nf

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

* Update tests/modules/maltextract/main.nf

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

* Update tests/modules/maltextract/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-09-21 19:57:27 +01:00
Harshil Patel
1d6f47ce54
Refactor cat/cat module (#723)
* Refactor cat/cat module

* Change gzip terminology
2021-09-21 11:17:00 +01:00
Daniel Lundin
b32c46c6a2
CAT CAT (#722)
* bbmap/align done

* Tests for single end and prebuilt index

* Write bam file directly

* Forgot to use all cpus for bbmap

* Test md5sums

* Added pigz support

* Update modules/bbmap/align/meta.yml

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

* process_medium and fastq

* cat/cat module

* Remove filter from CAT_CAT

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-20 21:02:22 +01:00
Michael L Heuer
60d8bd7c04
Update pangolin to 3.1.11 (#721)
* Update pangolin to 3.1.11.

* Update md5sum for test.pangolin.csv.
2021-09-20 19:59:05 +01:00
Daniel Lundin
97b803a8a7
Module to map reads with BBMap (#717) 2021-09-20 11:27:34 +02:00
GCJMackenzie
3c4eaec52b
Update for mutect2: add output channel for stats file (#716)
* added output channel for stats file, updated meta yml with description and test yml with check for stats file

* Update modules/gatk4/mutect2/main.nf

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-17 09:56:56 +01:00
Maxime Borry
7e45cbf4d1
Add PyDamage filter (#713)
* add pydamage module

* remove TODOs

* split module by subcommands

* update version parsing

* remove forgotten TODOs

* update module names

* remove old holistic module

* Update modules/pydamage/analyze/main.nf

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

* add keywords

* update resource requirement

* Update modules/pydamage/filter/main.nf

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

* Update modules/pydamage/filter/meta.yml

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-09-16 15:05:49 +02:00
Maxime Borry
d9dfbe9d9d
Add pydamage analyze module (#705)
* add pydamage module

* remove TODOs

* split module by subcommands

* update version parsing

* remove forgotten TODOs

* update module names

* remove old holistic module

* Update modules/pydamage/analyze/main.nf

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

* add keywords

* simplify PR to analyze subcommand

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-09-16 14:03:51 +02:00
Sébastien Guizard
bbf268c5d3
new module: pbccs (#688)
* 📦 NEW: First commit of pbccs module

* 👌 IMPROVE: Remove option from command + rename output (ccs -> bam)

* 👌 IMPROVE: Move .pbi output  into report channel

* 🐛FIX: Correct code after --rq option removal from command line module

- module main.nf: Remove ramaining rq input channel
- Test main.nf: Transfert rq into addParams
- Test test.yml: Update md5sums

* 🐛FIX: Repair additionnal option usage

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: CCS is run in parallel with --chunk option

* 👌 IMPROVE: Add Pbindex in bam ouput channel

* 👌 IMPROVE: Change label to process_low

* 👌 IMPROVE: Define reports files names + add json version of txt report

* 🐛 FIX: Add missing backslashes

* 🐛 FIX: Add missing gz extension

* 🐛 FIX: update ouput channel

* 🐛 FIX: output file name

* 👌 IMPROVE: .gitignore

* 👌 IMPROVE: Update function.nf to last version

* 👌 IMPROVE: Update saveAs in main.nf

* 👌 IMPROVE: Add pbccs module

* 🐛 FIX: Fix Broken test

* 👌 IMPROVE: Update test_data.config

* 🐛 FIX: Fix test

* 👌 IMPROVE: Update path of test dataset files

* 👌 IMPROVE: Remove useless index + Fix Typos

* 📦 NEW: First commit of pbccs module

* 👌 IMPROVE: Remove option from command + rename output (ccs -> bam)

* 👌 IMPROVE: Move .pbi output  into report channel

* 🐛FIX: Correct code after --rq option removal from command line module

- module main.nf: Remove ramaining rq input channel
- Test main.nf: Transfert rq into addParams
- Test test.yml: Update md5sums

* 🐛FIX: Repair additionnal option usage

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: CCS is run in parallel with --chunk option

* 👌 IMPROVE: Add Pbindex in bam ouput channel

* 👌 IMPROVE: Change label to process_low

* 👌 IMPROVE: Define reports files names + add json version of txt report

* 🐛 FIX: Add missing backslashes

* 🐛 FIX: Add missing gz extension

* 🐛 FIX: update ouput channel

* 🐛 FIX: output file name

* 👌 IMPROVE: .gitignore

* 👌 IMPROVE: Update function.nf to last version

* 👌 IMPROVE: Update saveAs in main.nf

* 👌 IMPROVE: Add pbccs module

* 🐛 FIX: Fix Broken test

* 👌 IMPROVE: Update test_data.config

* 🐛 FIX: Fix test

* 👌 IMPROVE: Update path of test dataset files

* 👌 IMPROVE: Remove useless index + Fix Typos

* 🐛 FIX: fill contains args

* 👌 IMPROVE: One output => One Channel

* 👌 IMPROVE: One input => One channel

* 🐛 FIX: Update tests

* 🐛 FIX: Remove TODOs from test.yaml

* 👌 IMPROVE: Revert and keep bam and pbi together

* 🐛 FIX: Remove old rq input from meta.yml

* 👌 IMPROVE: Update test to match input channels

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-09-16 11:48:18 +01:00
Abhinav Sharma
1840289068
module for agrvate (#693)
* initiate agrvate module

* remove todos [ci skip]

* remove todos and fix containers [ci skip]

* ready for testing


Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-16 12:42:23 +02:00
José Fernández Navarro
e9c57083a0
Fix bug in gffread (#686)
* Fix bug in gffread that would cause it to fail if the input has .gtf as extension

* Update test.yml

* Update meta file

* Update main.nf

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-15 19:55:08 +01:00
Robert A. Petit III
073bbf1b26
add staphopia-sccmec module (#702)
* add staphopia-sccmec module

* add additional test

* change output name

* Update main.nf

* Update test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-15 17:24:11 +01:00
Mahesh Binzer-Panchal
58134cb929
Chromap Module (#659)
* Initialise chromap module

* Revert "Initialise chromap module"

This reverts commit 47c67ae231a6f221ef5b9b7b444b583b5406852b.

* Remake chromap base files with new layout

* Copy chromap

* Copy index

* Add compression

* Update padding

* Update container

* Update chromap input test data

* Add chromap chromap tests

* Add padding

* Update comment

* update yaml file

* Remove TODOs

* Add fasta input to yaml

* Update YAML

* Remove comment, update container

* Remove comments

* Import Chromap index

* Update test.yml

* Fix read input

* Update test.yml

* Add bcftools/concat module. (#641)

* draft for bcftools modules [ci skip]

* initial test for bcftools concat

* Update the params for testing

* fix tests

* Accomodate code review [ci skip]

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

* Update the meta file and open PR for review

* Update the keyword

* Update the tags for module [ci skip[

* add threads

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

* add module for dragonflye (#633)

* add module for dragonflye

* fix tests for dragonflye

* Update test.yml

* Update meta.yml

* Update main.nf

* Update main.nf

* Update modules/dragonflye/meta.yml

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

* update typos. change quote from ' to ". (#652)

* Add bcftools/norm module (#655)

* Initial draft [ci skip]

* trigger first test

* update output file path

* Tests passing

* finishing touches for meta.yml and update checksum

* tweak checksum

* add threads to the module

* skip version info for matching test md5sum [ci skip]

* Add ref fasta and finalize the module

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

* Expansionhunter (#666)


Please enter the commit message for your changes. Lines starting

* adds expansionhunter module

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

* Update test.yml (#668)

* Specify in guidelines one should split CPUs when module has n > 1 tool (#660)

* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Describe CPU splitting

* Update README.md

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

* More CPU examples

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

* Add dsh-bio export-segments module (#631)

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

* update: `BWA/ALN` (#653)

* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Remove reads from output channel following module guidelines. Should do a .join() based on $meta, to reassociate.

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

* Update seqwish reported version to match bioconda version. (#678)

* Bbmap index (#683)

BBMap index module

* Initialise chromap module

* Revert "Initialise chromap module"

This reverts commit 47c67ae231a6f221ef5b9b7b444b583b5406852b.

* Remove unnecessary files

* Remove unnecessary files

* Update modules/chromap/index/main.nf

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

* Update modules/chromap/index/main.nf

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

* Update modules/chromap/chromap/main.nf

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

* Update tests/modules/chromap/chromap/main.nf

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

* Update tests/modules/chromap/chromap/main.nf

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

* Update tests/modules/chromap/chromap/main.nf

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

* Update modules/chromap/index/main.nf

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

* Remove pytest_software.yml

* Apply suggestions from code review

Co-authored-by: Abhinav Sharma <abhi18av@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: JIANHONG OU <jianhong@users.noreply.github.com>
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Michael L Heuer <heuermh@acm.org>
Co-authored-by: Daniel Lundin <daniel.lundin@lnu.se>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-15 17:20:55 +01:00
James A. Fellows Yates
561f16fe74
update: MALT build version bump (#699)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Bump versions

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-15 16:46:29 +01:00
Abhinav Sharma
1bc3f6cf39
module: snp-dists (#697)
* initial commit for draft [ci skip]

* baseline code [ci skip]

* update the test [ci skip]

* finalize the description and all tests passing

* accomodate optional args [ci skip]

* fix the leftover todo statement

* Update modules/snpdists/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-15 16:36:49 +01:00
Daniel Lundin
3a8bfc1d33
Get rid of meta map from bbmap/index (#700)
Got rid of meta map from bbmap/index
2021-09-15 12:38:56 +02:00
Mei Wu
b2a6f5409e
modify markduplicates module (#681)
* tested

* updated meta config and test config
2021-09-15 11:02:28 +02:00
James A. Fellows Yates
c485109d9b
Add module: bamaligncleaner (#676)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Add bamAlignCleaner module

* Add container tags

* Update modules/bamaligncleaner/main.nf
2021-09-15 10:31:49 +02:00
Abhinav Sharma
6ff995e93d
Add bcftools/query module (#670)
* initial commit [ci skip]

* add basic structure [ci skip]

* finalized the bcftools/query module

* add optional files [ci skip]

* Add the vcf index file as param [ci skip]

* update the md5sum for output file [ci skip]

* all tests passing
2021-09-14 09:19:01 +02:00
Davi Marcon
59ca7444cf
Adding plink/vcf module (#656)
* adding plink module using nf-core tool [ci skip]

* Restructures the project for plink/vcf (#1)

* Add version string for plink
* Create a plink/vcf module

* small tweaks on main.nf and started to test [ci skip]

* small changes on test args, local test with docker passed!

* Update plink/vcf module listing

* Update tag

* fix tags as per linting guidelines

* revert to the original state of tags

* adding --threads to `main.nf` and `meta.yml` information

Co-authored-by: Abhinav Sharma <abhi18av@users.noreply.github.com>
2021-09-14 08:51:40 +02:00
GCJMackenzie
bd68797ffb
Mutect2 (#682)
* mutect2 files added, first draft of module code entered

* removing comment from main.nf

* removing comment from main.nf

* test added, commit made before editing yaml

* tests added, still needs final check and info/comments added

* gatk4 version changed to gatk4=4.2.0.0

* multiple sample support added, information added to module yaml file

* Update meta.yml

fixed linting error

* add keywords to meta.yml

* Corrections made to meta.yml

* removed whitespace from meta.yml

Co-authored-by: Gavin.Mackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-09-13 16:16:23 +01:00
GCJMackenzie
1023a98b51
Getpileupsummaries (#689)
* first commit, added template files for new module

* created getpileupsummaries script, tests and both yml files

* fixed typo in meta.yml

* Update modules/gatk4/getpileupsummaries/meta.yml

changed gz_tbi to gz.tbi as suggested

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

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-09-13 16:04:14 +01:00
Abhinav Sharma
c5634ba99b
Add bcftools/view module (#669)
* initial commit [ci skip]

* add stubs [ci skip]

* Finalize the bcftools/view module

* accomodate optional files

* add optional region file

* refer the targets file in the tests

* all tests passing

* documen the optional parameters
2021-09-12 19:51:40 +02:00
Edmund Miller
669fb5caed
Homer Modules (#75)
* feat(homer): Add initial makeTagDirectory

* feat(homer): Add initial findPeaks module

* feat(homer): Update with new options

See 1d30e2c21a

* fix(homer): Correct findpeaks process name

* fix(homer): Takes a bam file instead of bed

* feat(homer): Add initial makeTagDirectory test

* fix(homer): Hardcode genome and configureHomer

I'd like to modularize configureHomer, but I need to figure out how
exactly the genomes work.

* fix(homer): bam => bed

Bam requires samtools to be present, which it's not in this docker image

* feat(homer): Add initial configureHomer script

* ci(homer): Add initial test

* test(homer): Reproducible configuration workaround

- I can't run both tests(one file and two files) at the same time because it breaks
- I can't copy the genome stuff from the configurehomer module because it's read only
- So I can't make the makeTagDirectory module depend on configureHomer

* test(homer): Add placeholder annotatepeaks

The required inputs are necessarily required for all workflows from what
I've used, but I'll need to look at the actual docs

* test(homer): Add missing B.bed

* test(homer): Rename two => groseq

Then all of the various workflows that homer provides can be e2e tested

* feat(homer): Add initial makeUCSCfile module

* test(homer): Add start to makeUCSCfile testing

* chore(homer): Add various cleanups

* test(homer): Rewrite annotatepeaks

Not passing yet

* test(homer): Rewrite configurehomer

* test(homer): Rewrite findpeaks

Still failing

* test(homer): Rewrite makeucscfile

Not passing yet

* test(homer): Rewrite maketagdirectory

All homer modules now follow the new structure. Time to make them pass.

* test(homer): Fix typo for workflow name

* fix(homer): Use correct container

* fix(homer): Accept fasta in maketagdirectory

Apparently all of the homer stuff can just take any old fasta and you
don't need to configure the genome ahead of time with configureHomer

* test(homer): makeTagDirectory passes now

* fix(homer): Update containers in makeucscfile

* test(homer): Rewrite makeucscfile

Takes input from maketagdirectory which is how the module should be used

* fix(homer): Update makeUCSCFile bedgraph path

* test(homer): Update makeucscfile expected output

* fix(homer): Update containers in findpeaks

* fix(homer): Change findpeaks args

The user is just going to have to know what they're doing for now

* test(homer): findPeaks rewrite with tagDir input

* test(homer): Update expected files for findPeaks

And bump filters

* style: Appease editorconfig

* ci: Remove old workflow

* tests(homer): Add md5sums

* test(homer): Add meta test

* style(homer): Capitalize HOMER

* docs(homer): Add maketagdirectory meta.yml

* docs(homer): Add makeucscfile meta.yml

* docs(homer): Add findpeaks meta.yml

* test(homer): Update to new test data standards

* chore: Remove stuff that got revived in the rebase

* chore: software => modules

* test(homer): Update tags

* test(homer): Update annotatepeaks

* ci: Fix uploading of artifacts

GitHub actions doesn't like the / in the tags

* test(homer): Remove annotate md5sum

This is failing and breaking new tests

* test(homer): Use bams instead of beds

* test(homer): Fix meta maketagdirectory

* test(homer): Fix input in all tests

* test(homer): Move back to bed files

Forgot samtools isn't present

* chore(homer): Add TODOs for tests

* test(homer): Add bed format arg

* test(homer): Update md5sums

* test(homer): Fix tags tsvs

* style(homer): Appease nf-core linting

* docs(homer): Be in line with what is in the main.nf file

Co-authored-by: Kevin Menden <kevin.menden@live.com>

Co-authored-by: Kevin Menden <kevin.menden@live.com>
2021-09-08 15:40:34 +00:00
Kevin Brick
0732028e15
Add bedtools/makewindows module (#658)
* Add bedtools/makewindows module
2021-09-07 14:36:06 -04:00
Daniel Lundin
0f59b07945
Bbmap index (#683)
BBMap index module
2021-09-03 09:28:28 +02:00
Michael L Heuer
bc7b5b3a12
Add dsh-bio export-segments module (#631)
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-08-17 15:53:41 +02:00
James A. Fellows Yates
69b21f0dc0
Update test.yml (#668) 2021-08-17 15:08:21 +02:00
Anders Jemt
b261c1f549
Expansionhunter (#666)
Please enter the commit message for your changes. Lines starting

* adds expansionhunter module

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-08-16 17:47:42 +02:00
Abhinav Sharma
0954204f9e
Add bcftools/norm module (#655)
* Initial draft [ci skip]

* trigger first test

* update output file path

* Tests passing

* finishing touches for meta.yml and update checksum

* tweak checksum

* add threads to the module

* skip version info for matching test md5sum [ci skip]

* Add ref fasta and finalize the module

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-08-16 17:40:03 +02:00
Robert A. Petit III
653e9e05b1
add module for dragonflye (#633)
* add module for dragonflye

* fix tests for dragonflye

* Update test.yml

* Update meta.yml

* Update main.nf

* Update main.nf

* Update modules/dragonflye/meta.yml

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-08-16 11:51:30 +02:00
Abhinav Sharma
67cc3bd116
Add bcftools/concat module. (#641)
* draft for bcftools modules [ci skip]

* initial test for bcftools concat

* Update the params for testing

* fix tests

* Accomodate code review [ci skip]

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

* Update the meta file and open PR for review

* Update the keyword

* Update the tags for module [ci skip[

* add threads

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-08-10 15:10:27 +02:00
praveenraj2018
5de3f2c50e
Added PL tag in read group information for downstream analysis (#649)
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-08-04 11:16:51 +02:00
James A. Fellows Yates
292e8eceb9
module: MALT/RUN (#646)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Add MALT with incomplete tests

* Parameter typo fix

* Clean up test yaml

* Finish MALT module prior UNZIP and MALT_BUILD modiules

* Add required modules for tests

* Sync test out with malt-build

* Fix input parameters in tests based on final build module

* Update modules/malt/run/meta.yml

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

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-08-04 11:06:08 +02:00
James A. Fellows Yates
6913da9d2d
module: MALT/BUILD (#645)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Start MALT-build

* Start MALT build (missing meta files and outputs specS)

* Local tests

* Correct test map_type

* Finished module, just waiting for UNZIP module to finalise tests

* Correct tests in preparation for Unzip

* Ouptut log file too

* Update meta.yml

* Rename log file

* Rename log file

* Remove debugging stuff

* Add Unzip module

* Linting update

* Linting update

* Fix input db

* Fix db file in cmd

* Update modules/malt/build/main.nf

* Update modules/malt/build/main.nf

* Update main.nf
2021-08-03 16:24:19 +02:00
James A. Fellows Yates
4f1c1601cf
module: bwa/sampe (#625)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Add bwa/aln module

* Also output reads as required with SAI

* Add sampe

* Fix container paths

* Update based on code review from @grst

* Update input docs
2021-08-02 15:37:48 +02:00
James A. Fellows Yates
8a2f01c416
module: bwa/samse (#626)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Add bwa/aln module

* Also output reads as required with SAI

* Add bwa samse

* Fix container paths

* remove TODO comment

* Updated based on code from from @grst on bwa/sampe

* Clarify output docs
2021-08-02 15:21:23 +02:00
James A. Fellows Yates
e01a98a704
module: unzip (#642)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Add unzip module

* Remove missing TODOs update mtea

* Apply changes after code-review from @grst

* Account for user trying to supply two input archives

* Remove debugging test

* Update modules/unzip/main.nf

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

* Correct output path

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-08-02 09:40:57 +02:00
Harshil Patel
29c8474240
Update Nextclade to output all files by default (#638) 2021-07-28 19:49:50 +01:00
Harshil Patel
c5235a983d
nf-core modules bump-versions for all modules (#630)
* Add blacklist of modules that shouldn't be updated to .nf-core.yml

* nf-core modules bump-versions for all modules

* Remove TODO statements identified by linting

* Fix md5sums for failing tests

* Fix more tests
2021-07-28 09:10:44 +01:00
James A. Fellows Yates
45dee96bdf
module: bwa/aln (#624)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Add bwa/aln module

* Also output reads as required with SAI

* fix container paths

* Sync bwa version samese/sampe

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-27 08:13:48 +01:00
Johnathan D
a21cc95c69
Add variantbam (#618)
* template created for variantbam (#616)

* Add bcftools reheader (#585) (#608)

* local tests and linting passing (#585)

* fix: picard filtersamreads input (#610)

* Move readlist into same input channel as bam

* Update test reflecting input restructuring

* Update tests/modules/picard/filtersamreads/main.nf

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

* fix test

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

* Added module arriba (#611)

* Updated the version of STAR in align and genomegenerate modules

* Changes in test.yml

* Changes in test.yml

* Added module arriba

* Changes in test configs

* Added module Arriba for fusion detection

* Fixed review comments

* Added an output option for discarded fusions

* Resolved some conflits

* conflicts

* Apply suggestions from code review

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

* added test for new header

* enhance module fastp: add `save_merged` (#598) (#614)

* enhance module fastp: add `save_merged` (#598)

* removed md5sum checks from log and json

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: praveenraj2018 <43108054+praveenraj2018@users.noreply.github.com>

* fixed autogenerated biocontainter links

* variantbam module passing all tests/lints (#616)

* Added an optional output junction channel in STAR (#621)

* Added an optional output channel for chimeric junctions

* Fix in test.yml

* Apply suggestions from code review

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

* removed qcreport output

fixes #616

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: praveenraj2018 <43108054+praveenraj2018@users.noreply.github.com>
2021-07-26 19:07:29 +01:00
praveenraj2018
df909015b6
Added an optional output junction channel in STAR (#621)
* Added an optional output channel for chimeric junctions

* Fix in test.yml

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-26 19:03:30 +02:00
Johnathan D
a813e2e3a6
Add bcftools reheader (#585) (#608)
* local tests and linting passing (#585)

* fix: picard filtersamreads input (#610)

* Move readlist into same input channel as bam

* Update test reflecting input restructuring

* Update tests/modules/picard/filtersamreads/main.nf

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

* fix test

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

* Added module arriba (#611)

* Updated the version of STAR in align and genomegenerate modules

* Changes in test.yml

* Changes in test.yml

* Added module arriba

* Changes in test configs

* Added module Arriba for fusion detection

* Fixed review comments

* Added an output option for discarded fusions

* Resolved some conflits

* conflicts

* Apply suggestions from code review

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

* added test for new header

* enhance module fastp: add `save_merged` (#598) (#614)

* enhance module fastp: add `save_merged` (#598)

* removed md5sum checks from log and json

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: praveenraj2018 <43108054+praveenraj2018@users.noreply.github.com>
2021-07-23 22:24:19 +01:00
Johnathan D
6f561b3b41
enhance module fastp: add save_merged (#598) (#614)
* enhance module fastp: add `save_merged` (#598)

* removed md5sum checks from log and json
2021-07-23 10:44:00 +01:00
praveenraj2018
3cabc95d0e
Added module arriba (#611)
* Updated the version of STAR in align and genomegenerate modules

* Changes in test.yml

* Changes in test.yml

* Added module arriba

* Changes in test configs

* Added module Arriba for fusion detection

* Fixed review comments

* Added an output option for discarded fusions

* Resolved some conflits

* conflicts

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-22 15:19:42 +01:00
James A. Fellows Yates
553f51d6bf
fix: picard filtersamreads input (#610)
* Move readlist into same input channel as bam

* Update test reflecting input restructuring

* Update tests/modules/picard/filtersamreads/main.nf

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

* fix test

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-22 11:19:51 +01:00
James A. Fellows Yates
3cc43838e1
module: picard filtersamreads (#602)
* Start work filtersamreads

* Refactored to allow optional input

* Use proper readlist test data

* Remove typo

* Fix if else condition

* Remove debugging code

* Fix container URLs

* Add required input specification meta

* Cleanup

* Apply suggestions from code review

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

* Fix suffixing

* Additional formatting tweaks

* Update modules/picard/filtersamreads/main.nf

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

* Update modules/picard/filtersamreads/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-21 15:22:19 +01:00
Jose Espinosa-Carrasco
217303f5c1
Add option -p to set the # of cpus on stringtie (#601)
* Add option -p  to set  the # of cpus on stringtie

* Bump version 2.1.7 to stringtie modules

* Output stringtie/merge version

* Fix padding

* Apply suggestions from code review

* Defining software variable

* Fix test, gff can't be md5 check, contains instead

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-21 15:38:40 +02:00
James A. Fellows Yates
a0019d4175
fix: picard sortsam (#605)
* Add picard/sortsam module

* Fix container links

* Changes after code review

* Input meta in the right place

* Correct output file suffix

* Define only `bam` in output tuple
2021-07-21 14:34:21 +01:00
praveenraj2018
f43778b0e6
Updated the version of STAR in align and genomegenerate modules (#604)
* Updated the version of STAR in align and genomegenerate modules

* Changes in test.yml

* Changes in test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-21 13:30:52 +01:00
James A. Fellows Yates
1a26d48104
module: picard sortsam (#603)
* Add picard/sortsam module

* Fix container links

* Changes after code review

* Input meta in the right place
2021-07-21 13:48:07 +02:00
James A. Fellows Yates
10502399ad
Replaced param with input val channel (#595)
* Replaced param with input val channel

* Apply suggestions from code review

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Apply suggestions from code review

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

* Apply suggestions from code review (missed one)

* YAML lint

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-21 10:00:48 +02:00
Harshil Patel
e4df336294
Add hifiasm module (#596)
* Add hifiasm module

* Tidy up module

* Add pacbio files to test_data.config
2021-07-20 21:50:22 +01:00
Johnathan D
2e619add87
Add samtools ampliconclip (#590)
* created template for `samtools/ampliconclip` (#584)

* All tests passing (#584)

* Linting fixed (#584)

* Final linting fixed (#584)

* Optional output flags moved to `input` (#584)

* typo fix (#584)

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-20 21:31:31 +01:00
Harshil Patel
e7e30b6da6
Bump Pangolin to 3.1.7 (#593)
* Bump Pangolin to 3.1.7

* Update md5sum

* Update README

* Re-word

* Re-word again

* Use channels
2021-07-20 12:25:36 +01:00
Johnathan D
0b40798d1b
fix: lofreq/callparallel missing arg (#562) (#586)
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-19 09:19:27 +01:00
Johnathan D
8c294882d7
fix: lofreq/call test.yml md5sum (#587) 2021-07-19 08:53:27 +01:00
Maxime U. Garcia
adfb8a3d65
fix: update samtools_merge (#582)
* fix: update samtools_merge

* Update modules/samtools/merge/main.nf

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

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-16 14:32:17 +02:00
Maxime U. Garcia
b3c4667732
fix: update to gatk4.2.0.0 (#575)
* fix: update to gatk4.2.0.0

* fix: update md5sum
2021-07-16 11:26:28 +02:00
Harshil Patel
e937c7950a
Rename software/ directory to modules/ to re-organise module structure (#567)
* Update README

* Rename pytest_software.yml to pytest_modules.yml

* Rename main software directory to modules

* Remove deprecated modules

* Rename tests software to modules

* Replace paths for tests in pytest_modules.yml

* Replace software with modules in Github Actions

* Replace software with modules in main.nf tests

* Rename software to modules in test.yml
2021-07-07 10:10:18 +01:00