2012 bug related to species input in goattaxonsearch module (#2099)

* updated input for taxon

* updated test_single_species

* updated test file

* run prettier on test.yml

* updated label process_low

* restored lable process_single

Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>

modules/goat/taxonsearch/main.nf

@@ -20,7 +20,7 @@ process GOAT_TAXONSEARCH {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    input = taxa_file ? "-f ${taxa_file}" : "-t ${taxon}"
+    input = taxa_file ? "-f ${taxa_file}" : "-t \"${taxon}\""
     if (!taxon && !taxa_file) error "No input. Valid input: single taxon identifier or a .txt file with identifiers"
     if (taxon && taxa_file ) error "Only one input is required: a single taxon identifier or a .txt file with identifiers"
     """

tests/modules/goat/taxonsearch/main.nf

@@ -7,11 +7,11 @@ include { GOAT_TAXONSEARCH } from '../../../../modules/goat/taxonsearch/main.nf'
 //
 // Test with genus name (Canis)
 //
-workflow test_goat_taxonsearch_genus_name {
+workflow test_goat_taxonsearch_single_species {
 
     input = [
-      [ id:'test_genus_name' ], // meta map
-      taxon = 'Canis',
+      [ id:'test_single_species' ], // meta map
+      taxon = 'Meles meles',
       []
   ]
     GOAT_TAXONSEARCH ( input )

tests/modules/goat/taxonsearch/test.yml

@@ -1,17 +1,17 @@
-- name: goat taxonsearch test_goat_taxonsearch_genus_name
-  command: nextflow run ./tests/modules/goat/taxonsearch -entry test_goat_taxonsearch_genus_name -c ./tests/config/nextflow.config  -c ./tests/modules/goat/taxonsearch/nextflow.config
+- name: goat taxonsearch test_goat_taxonsearch_single_species
+  command: nextflow run ./tests/modules/goat/taxonsearch -entry test_goat_taxonsearch_single_species -c ./tests/config/nextflow.config  -c ./tests/modules/goat/taxonsearch/nextflow.config
   tags:
-    - goat
     - goat/taxonsearch
+    - goat
   files:
-    - path: output/goat/test_genus_name.tsv
-      md5sum: e3de63a2bc2e16038aabeb325452bd16
+    - path: output/goat/test_single_species.tsv
+      md5sum: ed5b0afc7a6cf2f4b558882c10b35ef7
 
 - name: goat taxonsearch test_goat_taxonsearch_genus_id
   command: nextflow run ./tests/modules/goat/taxonsearch -entry test_goat_taxonsearch_genus_id -c ./tests/config/nextflow.config  -c ./tests/modules/goat/taxonsearch/nextflow.config
   tags:
-    - goat
     - goat/taxonsearch
+    - goat
   files:
     - path: output/goat/test_genus_id.tsv
       md5sum: 2cc41abbbc21b4b66f4d5126cfbba2bc
@@ -19,8 +19,8 @@
 - name: goat taxonsearch test_goat_taxonsearch_species
   command: nextflow run ./tests/modules/goat/taxonsearch -entry test_goat_taxonsearch_species -c ./tests/config/nextflow.config  -c ./tests/modules/goat/taxonsearch/nextflow.config
   tags:
-    - goat
     - goat/taxonsearch
+    - goat
   files:
     - path: output/goat/test_species.tsv
       md5sum: 7f5b36414820bd3ce2bfda06d98e479c