refactor: rename module

modules/custom/sratoolsncbisettings/main.nf

@@ -1,4 +1,4 @@
-process SRATOOLS_NCBISETTINGS {
+process CUSTOM_SRATOOLSNCBISETTINGS {
     tag 'ncbi-settings'
     label 'process_low'
 

modules/custom/sratoolsncbisettings/meta.yml

@@ -1,4 +1,4 @@
-name: "sratools_ncbisettings"
+name: "sratoolsncbisettings"
 description: Test for the presence of suitable NCBI settings or create them on the fly.
 keywords:
   - NCBI

tests/config/pytest_modules.yml

@@ -495,6 +495,10 @@ custom/getchromsizes:
   - modules/custom/getchromsizes/**
   - tests/modules/custom/getchromsizes/**
 
+custom/sratoolsncbisettings:
+  - modules/custom/sratoolsncbisettings/**
+  - tests/modules/custom/sratoolsncbisettings/**
+
 cutadapt:
   - modules/cutadapt/**
   - tests/modules/cutadapt/**
@@ -1819,10 +1823,6 @@ sratools/fasterqdump:
   - modules/sratools/fasterqdump/**
   - tests/modules/sratools/fasterqdump/**
 
-sratools/ncbisettings:
-  - modules/sratools/ncbisettings/**
-  - tests/modules/sratools/ncbisettings/**
-
 sratools/prefetch:
   - modules/sratools/prefetch/**
   - tests/modules/sratools/prefetch/**

tests/modules/custom/ncbisettings/test.yml

@@ -1,44 +0,0 @@
-- name: "sratools ncbisettings test_sratools_ncbisettings_with_good_existing"
-  command: nextflow run ./tests/modules/sratools/ncbisettings -entry test_sratools_ncbisettings_with_good_existing -c ./tests/config/nextflow.config -c ./tests/modules/sratools/ncbisettings/nextflow_mount.config
-  tags:
-    - "sratools"
-    - "sratools/ncbisettings"
-  files:
-    - path: "output/sratools/user-settings.mkfg"
-      md5sum: 955e27aff2c277c2f1f0943a098888c1
-    - path: output/sratools/versions.yml
-      contains:
-        - "sratools: 2.11.0"
-
-- name: "sratools ncbisettings test_sratools_ncbisettings_with_bad_existing"
-  command: nextflow run ./tests/modules/sratools/ncbisettings -entry test_sratools_ncbisettings_with_bad_existing -c ./tests/config/nextflow.config -c ./tests/modules/sratools/ncbisettings/nextflow_mount.config
-  tags:
-    - "sratools"
-    - "sratools/ncbisettings"
-  exit_code: 1
-  stdout:
-    contains:
-      - "Command error:"
-      - "missing the required entries"
-      - "/LIBS/GUID"
-      - "/libs/cloud/report_instance_identity"
-      - "Feel free to add the following"
-  files:
-    - path: "output/sratools/user-settings.mkfg"
-      should_exist: false
-    - path: output/sratools/versions.yml
-      should_exist: false
-
-- name: "sratools ncbisettings test_sratools_ncbisettings_with_nonexisting"
-  command: nextflow run ./tests/modules/sratools/ncbisettings -entry test_sratools_ncbisettings_with_nonexisting -c ./tests/config/nextflow.config -c ./tests/modules/sratools/ncbisettings/nextflow.config
-  tags:
-    - "sratools"
-    - "sratools/ncbisettings"
-  files:
-    - path: "output/sratools/user-settings.mkfg"
-      contains:
-        - "/LIBS/GUID"
-        - "/libs/cloud/report_instance_identity"
-    - path: output/sratools/versions.yml
-      contains:
-        - "sratools: 2.11.0"

tests/modules/custom/sratoolsncbisettings/main.nf

@@ -2,18 +2,18 @@
 
 nextflow.enable.dsl = 2
 
-include { SRATOOLS_NCBISETTINGS } from '../../../../modules/sratools/ncbisettings/main.nf'
+include { CUSTOM_SRATOOLSNCBISETTINGS } from '../../../../modules/custom/sratoolsncbisettings/main.nf'
 
-workflow test_sratools_ncbisettings_with_good_existing {
+workflow test_sratoolsncbisettings_with_good_existing {
 
     file(params.settings_path).mkdirs()
     def settings = file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true)
     settings.copyTo(params.settings_file)
 
-    SRATOOLS_NCBISETTINGS()
+    CUSTOM_SRATOOLSNCBISETTINGS()
 }
 
-workflow test_sratools_ncbisettings_with_bad_existing {
+workflow test_sratoolsncbisettings_with_bad_existing {
 
     file(params.settings_path).mkdirs()
     def settings = file(params.settings_file)
@@ -33,9 +33,9 @@ workflow test_sratools_ncbisettings_with_bad_existing {
     /repository/user/default-path = "/root/ncbi"
     '''.stripIndent()
 
-    SRATOOLS_NCBISETTINGS()
+    CUSTOM_SRATOOLSNCBISETTINGS()
 }
 
-workflow test_sratools_ncbisettings_with_nonexisting {
-    SRATOOLS_NCBISETTINGS()
+workflow test_sratoolsncbisettings_with_nonexisting {
+    CUSTOM_SRATOOLSNCBISETTINGS()
 }

tests/modules/custom/sratoolsncbisettings/nextflow_mount.config

@@ -7,7 +7,7 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
-    withName: SRATOOLS_NCBISETTINGS {
+    withName: CUSTOM_SRATOOLSNCBISETTINGS {
         containerOptions = {
             (workflow.containerEngine == 'singularity') ?
             "-B ${params.settings_path}:${params.settings_path}" :

tests/modules/custom/sratoolsncbisettings/test.yml

@@ -0,0 +1,44 @@
+- name: "custom sratoolsncbisettings test_sratoolsncbisettings_with_good_existing"
+  command: nextflow run ./tests/modules/custom/sratoolsncbisettings -entry test_sratoolsncbisettings_with_good_existing -c ./tests/config/nextflow.config -c ./tests/modules/custom/sratoolsncbisettings/nextflow_mount.config
+  tags:
+    - "custom"
+    - "custom/sratoolsncbisettings"
+  files:
+    - path: "output/custom/user-settings.mkfg"
+      md5sum: 955e27aff2c277c2f1f0943a098888c1
+    - path: output/custom/versions.yml
+      contains:
+        - "sratools: 2.11.0"
+
+- name: "custom sratoolsncbisettings test_sratoolsncbisettings_with_bad_existing"
+  command: nextflow run ./tests/modules/custom/sratoolsncbisettings -entry test_sratoolsncbisettings_with_bad_existing -c ./tests/config/nextflow.config -c ./tests/modules/custom/sratoolsncbisettings/nextflow_mount.config
+  tags:
+    - "custom"
+    - "custom/sratoolsncbisettings"
+  exit_code: 1
+  stdout:
+    contains:
+      - "Command error:"
+      - "missing the required entries"
+      - "/LIBS/GUID"
+      - "/libs/cloud/report_instance_identity"
+      - "Feel free to add the following"
+  files:
+    - path: "output/custom/user-settings.mkfg"
+      should_exist: false
+    - path: output/custom/versions.yml
+      should_exist: false
+
+- name: "custom sratoolsncbisettings test_sratoolsncbisettings_with_nonexisting"
+  command: nextflow run ./tests/modules/custom/sratoolsncbisettings -entry test_sratoolsncbisettings_with_nonexisting -c ./tests/config/nextflow.config -c ./tests/modules/custom/sratoolsncbisettings/nextflow.config
+  tags:
+    - "custom"
+    - "custom/sratoolsncbisettings"
+  files:
+    - path: "output/custom/user-settings.mkfg"
+      contains:
+        - "/LIBS/GUID"
+        - "/libs/cloud/report_instance_identity"
+    - path: output/custom/versions.yml
+      contains:
+        - "sratools: 2.11.0"