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>

tests/config/test_data.config

@@ -26,7 +26,6 @@ params {
 
                 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"
                 informative_sites_fas                     = "${test_data_dir}/genomics/sarscov2/genome/alignment/informative_sites.fas"
                 

tests/software/gubbins/main.nf

@@ -5,7 +5,7 @@ nextflow.enable.dsl = 2
 include { GUBBINS } from '../../../software/gubbins/main.nf' addParams( options: [:] )
 
 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 )
 }

tests/software/gubbins/test.yml

@@ -3,21 +3,21 @@
   tags:
     - gubbins
   files:
-    - path: output/gubbins/test.filtered_polymorphic_sites.fasta
-      md5sum: c9dff2294307eb2200a6e19efce47796
-    - path: output/gubbins/test.recombination_predictions.embl
+    - path: output/gubbins/all_sites.filtered_polymorphic_sites.fasta
+      md5sum: 4cbfd93868d8ed7d4d8b099eba137134
+    - path: output/gubbins/all_sites.recombination_predictions.embl
       md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/gubbins/test.recombination_predictions.gff
-      md5sum: a2ca9c119674f4d121a8f78e4078fe05
-    - path: output/gubbins/test.branch_base_reconstruction.embl
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/gubbins/test.summary_of_snp_distribution.vcf
-      md5sum: afee50e92fb919a5df487fbda0b9dbb5
-    - path: output/gubbins/test.per_branch_statistics.csv
-      md5sum: 0f364b5e0b01a6be9b6a4407658ab25f
-    - path: output/gubbins/test.filtered_polymorphic_sites.phylip
-      md5sum: 85db9d0896cfec34a73641496b7498bb
-    - path: output/gubbins/test.final_tree.tre
-      md5sum: dce7164a0c69bb3d642a419907364aa3
-    - path: output/gubbins/test.node_labelled.final_tree.tre
-      md5sum: beef5ce05aca4598bb3f42caf126e045
+    - 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