Anthony Underwood
4422454ba5
Snpsites ( #480 )
...
* output constant sites as a val as well as a file so it can be passed into iqtree
* Using an env variable because that's far safer!
* Update software/snpsites/main.nf
* remove hardcoded param that should be a user option
* Update software/snpsites/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-06 16:05:07 +01:00
Anthony Underwood
212177d479
output constant sites as a val so it can be passed into iqtree ( #429 )
...
* output constant sites as a val as well as a file so it can be passed into iqtree
* Using an env variable because that's far safer!
* Update software/snpsites/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-10 18:49:35 +01:00
Harshil Patel
dce27b8102
Update functions.nf to be more flexible for publishing by meta keys ( #423 )
...
* Update functions.nf
* Replace saveAs line in module main script
* Add spacing for ECLint
2021-04-09 17:23:56 +01:00
Anthony Underwood
6927f1d086
New Snpsites module ( #416 )
...
* new gubbins module
* new gubbins module
* new gubbins module
* Update software/gubbins/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/gubbins/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/gubbins/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/gubbins/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* new gubbins module
* new gubbins module
* new gubbins module
* new gubbins module
* new gubbins module
* new gubbins module
* new gubbins module
* Update tests/config/test_data.config
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/software/gubbins/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* new gubbins module
* new gubbins module
* new snpsites module
* new snpsites module
* new snpsites module
* new snpsites module
* adding fasttree module
* correct trailing whitespace
* using sarscov2 as a test dir
* use sars-cov-2 alignment
* remove old test alignment
* new snpsites module
* new snpsites module
* new snpsites module
* updated test file names
* new snpsites module
* revert to gubbins test on upstream
* add new lines
* renove whitespace
* Apply suggestions from code review
Co-authored-by: avantonder <avt@sanger.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: avantonder <ajv37@cam.ac.uk>
2021-04-09 08:00:33 +01:00
