refactor: require NCBI user settings always

modules/sratools/fasterqdump/main.nf

@@ -9,7 +9,7 @@ process SRATOOLS_FASTERQDUMP {
 
     input:
     tuple val(meta), path(sra)
-    path(ncbi_settings)
+    path ncbi_settings
 
     output:
     tuple val(meta), path(output), emit: reads
@@ -26,9 +26,7 @@ process SRATOOLS_FASTERQDUMP {
     // for unpaired reads which we ignore here.
     output = meta.single_end ? '*.fastq.gz' : '*_{1,2}.fastq.gz'
     """
-    if [[ "${ncbi_settings.name}" != "EXISTS" ]]; then
     export NCBI_SETTINGS="\$PWD/${ncbi_settings}"
-    fi
 
     fasterq-dump \\
         $args \\

modules/sratools/fasterqdump/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,
-        a file with name EXISTS.
-      pattern: "*.mkfg | EXISTS"
+        An NCBI user settings file.
+      pattern: "*.mkfg"
 
 output:
   - meta:

tests/modules/sratools/fasterqdump/main.nf

@@ -5,11 +5,7 @@ nextflow.enable.dsl = 2
 include { UNTAR } from '../../../../modules/untar/main.nf'
 include { SRATOOLS_FASTERQDUMP } from '../../../../modules/sratools/fasterqdump/main.nf'
 
-workflow test_sratools_fasterqdump_single_end_with_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"
+workflow test_sratools_fasterqdump_single_end {
 
     archive = [ [], file(params.test_data['sarscov2']['illumina']['SRR13255544_tar_gz'], checkIfExists: true) ]
     UNTAR ( archive )
@@ -17,14 +13,10 @@ workflow test_sratools_fasterqdump_single_end_with_input {
     def input = Channel.of([ id:'test_single_end', single_end:true ])
         .combine(UNTAR.out.untar.map{ it[1] })
 
-    SRATOOLS_FASTERQDUMP(input, settings)
+    SRATOOLS_FASTERQDUMP(input, file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true))
 }
 
-workflow test_sratools_fasterqdump_paired_end_with_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"
+workflow test_sratools_fasterqdump_paired_end {
 
     archive = [ [], file(params.test_data['sarscov2']['illumina']['SRR11140744_tar_gz'], checkIfExists: true) ]
     UNTAR ( archive )
@@ -32,35 +24,5 @@ workflow test_sratools_fasterqdump_paired_end_with_input {
     def input = Channel.of([ id:'test_paired_end', single_end:false ])
         .combine(UNTAR.out.untar.map{ it[1] })
 
-    SRATOOLS_FASTERQDUMP(input, settings)
-}
-
-workflow test_sratools_fasterqdump_single_end_without_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"
-
-    archive = [ [], file(params.test_data['sarscov2']['illumina']['SRR13255544_tar_gz'], checkIfExists: true) ]
-    UNTAR ( archive )
-
-    def input = Channel.of([ id:'test_single_end', single_end:true ])
-        .combine(UNTAR.out.untar.map{ it[1] })
-
-    SRATOOLS_FASTERQDUMP(input, file('EXISTS'))
-}
-
-workflow test_sratools_fasterqdump_paired_end_without_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"
-
-    archive = [ [], file(params.test_data['sarscov2']['illumina']['SRR11140744_tar_gz'], checkIfExists: true) ]
-    UNTAR ( archive )
-
-    def input = Channel.of([ id:'test_paired_end', single_end:false ])
-        .combine(UNTAR.out.untar.map{ it[1] })
-
-    SRATOOLS_FASTERQDUMP(input, file('EXISTS'))
+    SRATOOLS_FASTERQDUMP(input, file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true))
 }

tests/modules/sratools/fasterqdump/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/fasterqdump/nextflow_mount.config

@@ -1,18 +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_FASTERQDUMP {
-        containerOptions = {
-            (workflow.containerEngine == 'singularity') ?
-            "-B ${params.settings_path}:${params.settings_path}" :
-            "-v ${params.settings_path}:${params.settings_path}"
-        }
-    }
-}

tests/modules/sratools/fasterqdump/test.yml

@@ -1,5 +1,5 @@
-- name: sratools fasterqdump test_sratools_fasterqdump_single_end_with_input
-  command: nextflow run ./tests/modules/sratools/fasterqdump -entry test_sratools_fasterqdump_single_end_with_input -c ./tests/config/nextflow.config -c ./tests/modules/sratools/fasterqdump/nextflow.config
+- name: sratools fasterqdump test_sratools_fasterqdump_single_end
+  command: nextflow run ./tests/modules/sratools/fasterqdump -entry test_sratools_fasterqdump_single_end -c ./tests/config/nextflow.config -c ./tests/modules/sratools/fasterqdump/nextflow.config
   tags:
     - sratools
     - sratools/fasterqdump
@@ -12,38 +12,8 @@
       contains:
         - "sratools: 2.11.0"
 
-- name: sratools fasterqdump test_sratools_fasterqdump_paired_end_with_input
-  command: nextflow run ./tests/modules/sratools/fasterqdump -entry test_sratools_fasterqdump_paired_end_with_input -c ./tests/config/nextflow.config -c ./tests/modules/sratools/fasterqdump/nextflow.config
-  tags:
-    - sratools
-    - sratools/fasterqdump
-  files:
-    - path: output/sratools/SRR11140744_1.fastq.gz
-      md5sum: 193809c784a4ea132ab2a253fa4f55b6
-    - path: output/sratools/SRR11140744_2.fastq.gz
-      md5sum: 3e3b3af3413f50a1685fd7b3f1456d4e
-    - path: output/untar/SRR11140744/SRR11140744.sra
-      md5sum: 065666caf5b2d5dfb0cb25d5f3abe659
-    - path: output/sratools/versions.yml
-      contains:
-        - "sratools: 2.11.0"
-
-- name: sratools fasterqdump test_sratools_fasterqdump_single_end_without_input
-  command: nextflow run ./tests/modules/sratools/fasterqdump -entry test_sratools_fasterqdump_single_end_without_input -c ./tests/config/nextflow.config -c ./tests/modules/sratools/fasterqdump/nextflow_mount.config
-  tags:
-    - sratools
-    - sratools/fasterqdump
-  files:
-    - path: output/sratools/SRR13255544.fastq.gz
-      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_without_input
-  command: nextflow run ./tests/modules/sratools/fasterqdump -entry test_sratools_fasterqdump_paired_end_without_input -c ./tests/config/nextflow.config -c ./tests/modules/sratools/fasterqdump/nextflow_mount.config
+- 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
   tags:
     - sratools
     - sratools/fasterqdump