Jose Espinosa-Carrasco
|
313241749c
|
Add kraken2 run module (#266)
* Add kraken2 run module
* Add kraken2 run module
* Add coronavirus kraken2 db
* Adding kraken2 run tests
* Update software/kraken2/run/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Fixing files commited by mistake
* Remove params for meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
|
2021-03-18 13:08:06 +00:00 |
|
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
|
3c4d9466f4
|
Adding minia for viralrecon (#267)
* initial 'modules create' of minia
* fixed tests
* finished meta.yml
* fixed filters.yml
* resolved issues in pytest_software.yml
* add newline
* Update software/minia/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
|
2021-03-17 12:54:15 +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
|
74ff11b07b
|
Fix bowtie builds (#273)
* Fix bowtie build test
* Forgot to delete old bowtie_build
* Fix bowtie2 build tests
* Add initOptions include on hisat2 extractsplicesites
|
2021-03-15 15:39:42 +01:00 |
|
Harshil Patel
|
9b99b33401
|
Rename .github/filters.yml -> tests/config/pytest_software.yml (#271)
* Rename pytest filters.yml
* Change filters.yml name
* Update resoures for ivar trim
|
2021-03-15 12:51:30 +00:00 |
|