refactor: require settings input always

modules/sratools/prefetch/meta.yml

@@ -25,9 +25,8 @@ input:
   - ncbi_settings:
       type: file
       description: >
-        Either a proper NCBI settings file or in case an existing file should be used,
+        An NCBI user settings file.
-        a file with name EXISTS.
+      pattern: "*.mkfg"
-      pattern: "*.mkfg | EXISTS"
 
 output:
   - meta:

modules/sratools/prefetch/templates/retry_with_backoff.sh

@@ -40,9 +40,7 @@ retry_with_backoff() {
     echo "${output}"
 }
 
-if [[ "!{ncbi_settings.name}" != "EXISTS" ]]; then
+export NCBI_SETTINGS="$PWD/!{ncbi_settings}"
-    export NCBI_SETTINGS="$PWD/!{ncbi_settings}"
-fi
 
 retry_with_backoff !{args2} \
     prefetch \

tests/modules/sratools/prefetch/main.nf

@@ -4,31 +4,12 @@ nextflow.enable.dsl = 2
 
 include { SRATOOLS_PREFETCH } from '../../../../modules/sratools/prefetch/main.nf'
 
-workflow test_sratools_prefetch_with_settings_input {
+workflow test_sratools_prefetch {
-
-    file(params.settings_path).mkdirs()
-    def settings = file(params.settings_file)
-    settings.text = "/LIBS/GUID = \"5b0d4b7d-88c7-4802-98fd-e3afd06feb32\"\n/libs/cloud/report_instance_identity = \"true\"\n"
 
     input = [
         [ id:'test', single_end:false ], // meta map
         'DRR000774'
     ]
 
-    SRATOOLS_PREFETCH(input, settings)
+    SRATOOLS_PREFETCH(input, file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true))
 }
-
-workflow test_sratools_prefetch_without_settings_input {
-
-    file(params.settings_path).mkdirs()
-    def settings = file(params.settings_file)
-    settings.text = "/LIBS/GUID = \"5b0d4b7d-88c7-4802-98fd-e3afd06feb32\"\n/libs/cloud/report_instance_identity = \"true\"\n"
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        'DRR000774'
-    ]
-
-    SRATOOLS_PREFETCH(input, file('EXISTS'))
-}
-

tests/modules/sratools/prefetch/nextflow.config

@@ -1,6 +1,3 @@
-params.settings_path = '/tmp/.ncbi'
-params.settings_file = "${params.settings_path}/user-settings.mkfg"
-
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }

tests/modules/sratools/prefetch/nextflow_mount.config

@@ -1,17 +0,0 @@
-params.settings_path = '/tmp/.ncbi'
-params.settings_file = "${params.settings_path}/user-settings.mkfg"
-
-env.NCBI_SETTINGS = params.settings_file
-
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName: SRATOOLS_PREFETCH {
-        containerOptions = {
-            (workflow.containerEngine == 'singularity') ?
-            "-B ${params.settings_path}:${params.settings_path}" :
-            "-v ${params.settings_path}:${params.settings_path}"
-        }
-    }
-}

tests/modules/sratools/prefetch/test.yml

@@ -1,17 +1,5 @@
-- name: sratools prefetch test_sratools_prefetch_with_settings_input
+- name: sratools prefetch test_sratools_prefetch
-  command: nextflow run ./tests/modules/sratools/prefetch -entry test_sratools_prefetch_with_settings_input -c ./tests/config/nextflow.config -c ./tests/modules/sratools/prefetch/nextflow.config
+  command: nextflow run ./tests/modules/sratools/prefetch -entry test_sratools_prefetch -c ./tests/config/nextflow.config -c ./tests/modules/sratools/prefetch/nextflow.config
-  tags:
-    - sratools/prefetch
-    - sratools
-  files:
-    - path: output/sratools/DRR000774/DRR000774.sra
-      md5sum: 7647dba20c89c0e3d7ad13842f060eb0
-    - path: output/sratools/versions.yml
-      contains:
-        - "sratools: 2.11.0"
-
-- name: sratools prefetch test_sratools_prefetch_without_settings_input
-  command: nextflow run ./tests/modules/sratools/prefetch -entry test_sratools_prefetch_without_settings_input -c ./tests/config/nextflow.config -c ./tests/modules/sratools/prefetch/nextflow_mount.config
   tags:
     - sratools/prefetch
     - sratools