Patrick Hüther
8a44258548
remove params section from meta.yml ( #282 )
2021-03-19 13:16:50 +01:00
Kevin Menden
a90332906b
add mergebamalignment ( #259 )
...
* add mergebamalignment
* fix test.yml
* update to latest gatk4 version
* Update software/gatk4/mergebamalignment/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/data/README.md
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/gatk4/mergebamalignment/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/gatk4/mergebamalignment/meta.yml
* fixed unmapped/unaligned
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-17 15:56:56 +01:00
Kevin Menden
17dbff52f4
added gatk4 variantfiltration ( #265 )
...
* added gatk4 variantfiltration
* replace merge with filter
* Update software/gatk4/variantfiltration/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* updated input
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-17 09:42:35 +01:00
Jose Espinosa-Carrasco
572abb00b3
Remove def from module options definition in main ( #270 )
...
* Remove def from module options definition in main
* Fix bismark_deduplicate tests
* Fix bwameth_align tests
* Fixing gatk4 conda tests ("=" instead of ':' in build id)
* Same as previous commit (Fix gatk4 test)
* Fix qualimap bamqc test (no md5 check for pngs)
* Fix seqkit split2 tests. Changed to new test data
* Fix samtools tests. Some were missing initOptions include
* Removing TOOL SUBTOOL template module since now it is included on tools repo
2021-03-15 12:16:43 +00:00
Maxime Garcia
05cbbbaded
Rename gatk/createsequencedictionary -> gatk4/createsequencedictionary ( #260 )
...
* fix: update and sort filters
* fix: rename gatk/createsequencedictionary -> gatk4/createsequencedictionary
2021-03-08 14:45:46 +01:00
kevinmenden
3fee38ee2d
added gatk4 revertsam
2021-02-22 15:21:39 +01:00
kevinmenden
efd60d94ee
adding revertsam/ fix typo in mergevcfs
2021-02-22 15:10:20 +01:00
kevinmenden
69d7bb4fca
reformatted input to tuple
2021-02-22 13:31:54 +01:00
kevinmenden
bb5c0ceca5
adding SplitNCigarReads
2021-02-19 14:59:29 +01:00
Kevin Menden
0202162b17
Merge branch 'master' into gatk4-mergevcfs
2021-02-19 14:11:30 +01:00
kevinmenden
02abe106ec
added optional reference dictionary as input
2021-02-19 14:09:32 +01:00
kevinmenden
c288e081b4
initial commit adding mergevcfs
2021-02-19 13:29:08 +01:00
Kevin Menden
5c325f2942
Merge branch 'master' into master
2021-02-19 13:08:43 +01:00
kevinmenden
bd8ba42a8d
added gatk4 SamToFastq
2021-02-19 12:41:29 +01:00
kevinmenden
6dcaf5ffc8
add gatk4 bedtointervallist
2021-02-19 11:26:31 +01:00
