Merge pull request #1631 from nf-core/refactor-prefetch

Refactor prefetch

modules/sratools/prefetch/main.nf

@@ -9,10 +9,11 @@ process SRATOOLS_PREFETCH {
 
     input:
     tuple val(meta), val(id)
+    path ncbi_settings
 
     output:
     tuple val(meta), path(id), emit: sra
-    path "versions.yml"         , emit: versions
+    path 'versions.yml'      , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -20,7 +21,5 @@ process SRATOOLS_PREFETCH {
     shell:
     args = task.ext.args ?: ''
     args2 = task.ext.args2 ?: '5 1 100'  // <num retries> <base delay in seconds> <max delay in seconds>
-    config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
-
     template 'retry_with_backoff.sh'
 }

modules/sratools/prefetch/meta.yml

@@ -10,7 +10,7 @@ tools:
       homepage: https://github.com/ncbi/sra-tools
       documentation: https://github.com/ncbi/sra-tools/wiki
       tool_dev_url: https://github.com/ncbi/sra-tools
-      licence: ["US-Government-Work"]
+      licence: ["Public Domain"]
 
 input:
   - meta:
@@ -22,6 +22,11 @@ input:
       type: val
       description: >
         A string denoting an SRA id.
+  - ncbi_settings:
+      type: file
+      description: >
+        An NCBI user settings file.
+      pattern: "*.mkfg"
 
 output:
   - meta:

modules/sratools/prefetch/templates/retry_with_backoff.sh

@@ -40,11 +40,7 @@ retry_with_backoff() {
     echo "${output}"
 }
 
-eval "$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
+export NCBI_SETTINGS="$PWD/!{ncbi_settings}"
-if [[ ! -f "${NCBI_SETTINGS}" ]]; then
-    mkdir -p "$(dirname "${NCBI_SETTINGS}")"
-    printf '!{config}' > "${NCBI_SETTINGS}"
-fi
 
 retry_with_backoff !{args2} \
     prefetch \

tests/config/test_data.config

@@ -426,6 +426,9 @@ params {
                 test_merge_cool_cp2             = "${test_data_dir}/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cp2.cool"
 
             }
+            'config' {
+                ncbi_user_settings              = "${test_data_dir}/generic/config/ncbi_user_settings.mkfg"
+            }
         }
     }
 }

tests/modules/sratools/prefetch/main.nf

@@ -8,8 +8,8 @@ workflow test_sratools_prefetch {
 
     input = [
         [ id:'test', single_end:false ], // meta map
-        'ERR2815334'
+        'DRR000774'
     ]
 
-    SRATOOLS_PREFETCH ( input )
+    SRATOOLS_PREFETCH(input, file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true))
 }

tests/modules/sratools/prefetch/test.yml

@@ -4,5 +4,8 @@
     - sratools/prefetch
     - sratools
   files:
-    - path: output/sratools/ERR2815334/ERR2815334.sra
+    - path: output/sratools/DRR000774/DRR000774.sra
-      md5sum: 9a98c7f6f4774b7ef94aa915b92a54ea
+      md5sum: 7647dba20c89c0e3d7ad13842f060eb0
+    - path: output/sratools/versions.yml
+      contains:
+        - "sratools: 2.11.0"