nf-core_modules/tests/software/gubbins/test.yml
Anthony Underwood 63b3975292
Update gubbins module to use new files (#417)
* 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

* remove snpsites from gubbins branch

* remove redundant test_fas alignment

* update md5 sums

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 07:54:11 +01:00

23 lines
1.1 KiB
YAML

- name: gubbins
command: nextflow run ./tests/software/gubbins -entry test_gubbins -c tests/config/nextflow.config
tags:
- gubbins
files:
- path: output/gubbins/all_sites.filtered_polymorphic_sites.fasta
md5sum: 4cbfd93868d8ed7d4d8b099eba137134
- path: output/gubbins/all_sites.recombination_predictions.embl
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/gubbins/all_sites.recombination_predictions.gff
md5sum: f95871e79968340cb82532e2c9b0c92b
- path: output/gubbins/all_sites.branch_base_reconstruction.embl
md5sum: 02e6fb268f7422bfe34b27ecd3b2c245
- path: output/gubbins/all_sites.summary_of_snp_distribution.vcf
md5sum: 276e62e888ea811577c8ffb2da0b3aff
- path: output/gubbins/all_sites.per_branch_statistics.csv
md5sum: 94b09b25d10504b56aa0307beae98a98
- path: output/gubbins/all_sites.filtered_polymorphic_sites.phylip
md5sum: 0a77f397a7797c5c3386832745b0c97a
- path: output/gubbins/all_sites.final_tree.tre
md5sum: e3c7ea18e2c5c49774c0e2ff78bd1818
- path: output/gubbins/all_sites.node_labelled.final_tree.tre
md5sum: 7727b4c4111ebf49cc8a4f1fdd25092c