Merge pull request #1632 from nf-core/refactor-fasterq-dump

Refactor fasterq dump

modules/sratools/fasterqdump/main.nf

@@ -9,6 +9,7 @@ process SRATOOLS_FASTERQDUMP {
 
     input:
     tuple val(meta), path(sra)
+    path ncbi_settings
 
     output:
     tuple val(meta), path(output), emit: reads
@@ -20,17 +21,12 @@ process SRATOOLS_FASTERQDUMP {
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
-    def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
     // Paired-end data extracted by fasterq-dump (--split-3 the default) always creates
     // *_1.fastq *_2.fastq files but sometimes also an additional *.fastq file
     // for unpaired reads which we ignore here.
     output = meta.single_end ? '*.fastq.gz' : '*_{1,2}.fastq.gz'
     """
-    eval "\$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
-    if [[ ! -f "\${NCBI_SETTINGS}" ]]; then
-        mkdir -p "\$(dirname "\${NCBI_SETTINGS}")"
-        printf '${config}' > "\${NCBI_SETTINGS}"
-    fi
+    export NCBI_SETTINGS="\$PWD/${ncbi_settings}"
 
     fasterq-dump \\
         $args \\

modules/sratools/fasterqdump/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: directory
       description: Directory containing ETL data for the given SRA.
       pattern: "*/*.sra"
+  - ncbi_settings:
+      type: file
+      description: >
+        An NCBI user settings file.
+      pattern: "*.mkfg"
 
 output:
   - meta:

tests/modules/sratools/fasterqdump/main.nf

@@ -13,7 +13,7 @@ workflow test_sratools_fasterqdump_single_end {
     def input = Channel.of([ id:'test_single_end', single_end:true ])
         .combine(UNTAR.out.untar.map{ it[1] })
 
-    SRATOOLS_FASTERQDUMP ( input )
+    SRATOOLS_FASTERQDUMP(input, file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true))
 }
 
 workflow test_sratools_fasterqdump_paired_end {
@@ -24,5 +24,5 @@ workflow test_sratools_fasterqdump_paired_end {
     def input = Channel.of([ id:'test_paired_end', single_end:false ])
         .combine(UNTAR.out.untar.map{ it[1] })
 
-    SRATOOLS_FASTERQDUMP ( input )
+    SRATOOLS_FASTERQDUMP(input, file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true))
 }

tests/modules/sratools/fasterqdump/test.yml

@@ -8,6 +8,9 @@
       md5sum: 1054c7b71884acdb5eed8a378f18be82
     - path: output/untar/SRR13255544/SRR13255544.sra
       md5sum: 466d05dafb2eec672150754168010b4d
+    - path: output/sratools/versions.yml
+      contains:
+        - "sratools: 2.11.0"
 
 - name: sratools fasterqdump test_sratools_fasterqdump_paired_end
   command: nextflow run ./tests/modules/sratools/fasterqdump -entry test_sratools_fasterqdump_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/sratools/fasterqdump/nextflow.config
@@ -21,3 +24,6 @@
       md5sum: 3e3b3af3413f50a1685fd7b3f1456d4e
     - path: output/untar/SRR11140744/SRR11140744.sra
       md5sum: 065666caf5b2d5dfb0cb25d5f3abe659
+    - path: output/sratools/versions.yml
+      contains:
+        - "sratools: 2.11.0"