2 commits

Author	SHA1	Message	Date
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	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