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Update gubbins module to use new files (#417)

Browse source 
* 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>
This commit is contained in:
Anthony Underwood 2021-04-09 07:54:11 +01:00 committed by GitHub
parent f90dde0d88
commit 63b3975292
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GPG key ID: 4AEE18F83AFDEB23
4 changed files with 18 additions and 27 deletions
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1
tests/config/test_data.config
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@ -26,7 +26,6 @@ params {
test_wig_gz = "${test_data_dir}/genomics/sarscov2/genome/gcwiggle/test.wig.gz" test_wig_gz = "${test_data_dir}/genomics/sarscov2/genome/gcwiggle/test.wig.gz"
test_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/test.fas"
all_sites_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/all_sites.fas" all_sites_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/all_sites.fas"
informative_sites_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/informative_sites.fas" informative_sites_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/informative_sites.fas"

8
tests/data/genomics/sarscov2/genome/alignment/test.fas
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File diff suppressed because one or more lines are too long

2
tests/software/gubbins/main.nf
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@ -5,7 +5,7 @@ nextflow.enable.dsl = 2
include { GUBBINS } from '../../../software/gubbins/main.nf' addParams( options: [:] ) include { GUBBINS } from '../../../software/gubbins/main.nf' addParams( options: [:] )
workflow test_gubbins { workflow test_gubbins {
input = file(params.test_data['sarscov2']['genome']['test_fas'], checkIfExists: true) input = file(params.test_data['sarscov2']['genome']['all_sites_fas'], checkIfExists: true)
GUBBINS ( input ) GUBBINS ( input )
} }

34
tests/software/gubbins/test.yml
View file

@ -3,21 +3,21 @@
tags: tags:
- gubbins - gubbins
files: files:
- path: output/gubbins/test.filtered_polymorphic_sites.fasta - path: output/gubbins/all_sites.filtered_polymorphic_sites.fasta
md5sum: c9dff2294307eb2200a6e19efce47796 md5sum: 4cbfd93868d8ed7d4d8b099eba137134
- path: output/gubbins/test.recombination_predictions.embl - path: output/gubbins/all_sites.recombination_predictions.embl
md5sum: d41d8cd98f00b204e9800998ecf8427e md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/gubbins/test.recombination_predictions.gff - path: output/gubbins/all_sites.recombination_predictions.gff
md5sum: a2ca9c119674f4d121a8f78e4078fe05 md5sum: f95871e79968340cb82532e2c9b0c92b
- path: output/gubbins/test.branch_base_reconstruction.embl - path: output/gubbins/all_sites.branch_base_reconstruction.embl
md5sum: d41d8cd98f00b204e9800998ecf8427e md5sum: 02e6fb268f7422bfe34b27ecd3b2c245
- path: output/gubbins/test.summary_of_snp_distribution.vcf - path: output/gubbins/all_sites.summary_of_snp_distribution.vcf
md5sum: afee50e92fb919a5df487fbda0b9dbb5 md5sum: 276e62e888ea811577c8ffb2da0b3aff
- path: output/gubbins/test.per_branch_statistics.csv - path: output/gubbins/all_sites.per_branch_statistics.csv
md5sum: 0f364b5e0b01a6be9b6a4407658ab25f md5sum: 94b09b25d10504b56aa0307beae98a98
- path: output/gubbins/test.filtered_polymorphic_sites.phylip - path: output/gubbins/all_sites.filtered_polymorphic_sites.phylip
md5sum: 85db9d0896cfec34a73641496b7498bb md5sum: 0a77f397a7797c5c3386832745b0c97a
- path: output/gubbins/test.final_tree.tre - path: output/gubbins/all_sites.final_tree.tre
md5sum: dce7164a0c69bb3d642a419907364aa3 md5sum: e3c7ea18e2c5c49774c0e2ff78bd1818
- path: output/gubbins/test.node_labelled.final_tree.tre - path: output/gubbins/all_sites.node_labelled.final_tree.tre
md5sum: beef5ce05aca4598bb3f42caf126e045 md5sum: 7727b4c4111ebf49cc8a4f1fdd25092c