Commit graph

369 commits

Author SHA1 Message Date
Michael L Heuer
73aaecbc3a
Add BAM indexes as input for optitype module. (#1388) 2022-03-15 17:02:40 +01:00
Lasse Folkersen
d6244b42f5
ASCAT (#1332)
* First commit

* putting correct links for singularity and docker containers (just had to search for bioconda+ascat to find them, and then put them in like the rest of the nf-core tools had it

* adding first try of relevant commands (not working yet, just took their basic pipeline example

* test commit

* remove test

* starting up work with module after 3.0.0 upgrade

* add ascat.prepareHTS statemet

* add location of docker for new mulled alleleCounter+ASCAT container

* first full run with ASCAT on HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam

* add notes on dropbox download

* use a newer pytest_modules.yml

* add outpit

* trying to align with current Sarek output

* adding in FH comments

* busy clearing up arguments and testing. Still WIP

* first working run, in nextflow, with sarek-like output. Still needs more work on input arguments

* cleaning up before writing up findings

* testing with putting in arguments in args

* draft for solution 3 style for arguments

* one more test added

* adding FH map

* finished testing maps for args

* wrap-up cram/crai test successfully

* updates to address ability to put in ref.fasta argument for cram running

* adding remaining import-HTS commands in as args, and removing the chr21/chr22 only testing to test-nextflow.config

* first test with auto-downloading the s3-data (when not given as an argument)

* removing download-logic for supporting files, documenting in meta.yml, fixing ref_fasta bug

* adding mulled singularity container

* removing tests

* fix left padding lint issue

* lint failure in meta.yml

* more linting errors

* add when argument

* adding stub functionality

* add stub run

* correct md5sum for versions.yml

* more testing with -runstub

* stub code in pure bash - not mixed with R

* reformat version.yml

* get rid of absolute paths in test.yml

* correct wrong md5sum

* adding allelecount conda link

* rename normal_bam to input_bam etc

* let the pipeline dev worry about matching the right loci and allele files

* dont hardcode default genomebuild

* adding download instruction comment

* add doi

* fix conda addition bug

* add args documentation

* test new indent

* new test with meta.yml indentation

* retry with new meta.yml

* retry with new meta.yml - now with empty lines around

* retry with new meta.yml - remove trailing whitepsace

* trying to fix found quote character that cannot start any token error

* try with one empty line above triple-quote and no empty line below

* trying with pipe character

* checking if its the ending triple quote

* one more try with meta.yml

* test update bioconda versioning for linting failure

* test update bioconda versioning for linting failure 2

* testing allelecounter version error on conda

Co-authored-by: @lassefolkersen 
Co-authored-by: @FriederikeHanssen
2022-03-15 11:18:43 +01:00
Sima Rahimi
86ac223916
Cnvpytor (#1297)
* Added cnvpytor/importreaddepth module

* Corrected process name in meta.yml file

* added -chrom argument

* space correction

* Added complementary info

* fixed typo

* md5sum added

* modified the module to work on cram files as well

* Added cnvpytor/histogram module and test files

* Added cnvpytor/partition module and test files

* added cnvpytor/callcnvs module and tests

* modified by new modules

* Added test file and fixed input path in modules

* added when block

* little fixes

* skip tracking test.yml

* removed changes to test if conflicts get resolved

* updated outfile name

* corrected the version.yml content
2022-03-15 10:20:46 +01:00
Nathan Spix
801240a971
Add core Biscuit tools (#1354)
* create files with nf-core command

* update meta.yml files

* starting to work on index main.nf

* prelim test for index

* index test working; not finding all output files

* index passing tests

* index and align passing tests

* prototyping biscuitblaster and pileup

* update containers

* updates to pileup

* pileup passing tests

* template creation for more biscuit tools

* tests passing on blaster,bsconv,pupsom

* epiread passing tests, but need to update SNP bed file path

* vcf2bed working; change test file

* all biscuit commands passing tests

* biscuitblaster rename

* try to fix permissions

* more permission fixes

* trying a couple more permission changes

* hopefully last permission fixes

* really last permission changes

* few more permissions

* add when blocks

* Remove read group meta

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

* remove read group meta

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

* changes for first round of review

* update meta.yml with more specific links

* Update modules/biscuit/biscuitblaster/main.nf

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Apply new version reporting

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/biscuit/pileup/main.nf

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Update main.nf

* Update modules/biscuit/pileupsomatic/main.nf

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* update test file path

* Update modules/biscuit/align/main.nf

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/biscuit/align/main.nf

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* tests passing again

* Update modules/biscuit/align/main.nf

* Update modules/biscuit/bsconv/main.nf

* Update modules/biscuit/epiread/main.nf

* Update modules/biscuit/index/main.nf

* Update test.yml

* Update modules/biscuit/pileupsomatic/main.nf

* remove module-specific extension/prefix

* remove module-specific extension/prefix

* add missing args

* switch pileup strategy

* update test.yml

* remove debug

* whitespace cleanup

* add in newline escapes

* requested changes

* Update modules/biscuit/pileup/meta.yml

Co-authored-by: Spix <nathan.spix@submit.cm.cluster>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Spix <nathan.spix@node107.cm.cluster>
Co-authored-by: njspix <nathan.spix@vai.org>
2022-03-14 09:34:22 -04:00
Simon Pearce
79a9d5e1ea
New module: NGSCheckMate (#1290)
NGSCheckMate ncm mode, working on bam files and vcf files to check that (human) samples match as expected 

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
2022-03-11 09:02:10 +00:00
Michael J Cipriano
24f0bdd14e
added module seqkit replace (#1382)
* added module seqkit replace

* added when

* removed extra line

* Update modules/seqkit/replace/main.nf

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

* Updated meta

* updated indents

Co-authored-by: Cipriano <rrn8@cdc.gov>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-03-09 10:36:05 -07:00
Benjamin Wingfield
de0d57a562
implement plink2/score module (#1259)
* implement plink2/score module

* fix test yml

* fix typo :(

* set cpu

* set mem

* fix input process input block

* fix tests

Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
2022-03-07 13:02:40 -05:00
Ramprasad Neethiraj
d8028dc1c3
Add picard/sortvcf (#1370)
* sortvcf

* add files

* update meta

* update java mem

* update documentation link

* remove todo

* review suggestions

* fix test.yml

* fix conda error

* fix version code
2022-03-03 11:40:16 -05:00
James A. Fellows Yates
61c88c6233
Add hamronization/summarize (#1366)
* fix: remove left-over unnecessary code

* Add hamronizer/deeparg

* Add hamronisation/summarise

* Update test.yml

* Update modules/hamronization/summarize/meta.yml

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

* line up outputs

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
2022-03-03 08:02:04 +01:00
James A. Fellows Yates
4983f77796
Add hamronization/deeparg (#1364)
* fix: remove left-over unnecessary code

* Add hamronizer/deeparg

* Add when condition

* Apply suggestions from code review

* Update modules/hamronization/deeparg/meta.yml
2022-03-02 13:04:22 +01:00
Lauri Mesilaakso
fe4eb459fb
Add stranger (#1360)
* Add stranger

* Add when clause

* Update paths

* Update modules/stranger/main.nf

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

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
2022-03-01 14:29:46 +01:00
FriederikeHanssen
c189835b1b
add controlfreec (#1333)
* add drafty controlfreec

* get sofatware version

* use maps in map

* update paths to new and soon-to-be merged test files, add more input docu

* Stab at documenting args map

* Update syntax

* Bit more description

* Make the linter happy

* tests pass locally

* Add outputs & docu

* tests are failing locally now :/ but cpn file can also be added

* All tests passing, need to update test data again to add folder

* Clean up files

* Clean up files

* Clean up files

* Don't know how to get the test to run with the direcotry for now. they pass locally though

* Make linter happy

* Name process back

* Update to use tar folder

* fix the checksum
2022-02-28 19:08:58 +01:00
Mei Wu
38ffbfdb63
bcftools/annotate follow up corrections (#1359)
* bcf annotate ready2go

* edited output name

* fixed output

* updated bcftools ver

* changed contain output string

* removed contain key entirely

* fixed md5sum for test.yml

* using match instead of find

* bcftools/annotate refactored with complete test

* rm trailing white space

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-02-28 10:16:29 -05:00
Mei Wu
ef811d952b
bcftools/annotate ready2go (#1291)
* bcf annotate ready2go

* edited output name

* fixed output

* updated bcftools ver

* changed contain output string

* removed contain key entirely

* fixed md5sum for test.yml

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
2022-02-28 14:23:12 +01:00
841c661cad
Add MAFFT module (#1351)
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>

Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-02-28 00:40:24 -07:00
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
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
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
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
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
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
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
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
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