From e4551a9ab3bf4317a485ddfe0cd867b1a9baabb0 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Wed, 11 May 2022 14:07:18 +0200
Subject: [PATCH] refactor: always output settings

---
 modules/sratools/ncbisettings/main.nf           |  4 ++--
 modules/sratools/ncbisettings/meta.yml          |  4 ++--
 .../templates/detect_ncbi_settings.sh           |  6 ++++++
 tests/modules/sratools/ncbisettings/main.nf     |  5 -----
 .../sratools/ncbisettings/nextflow.config       | 12 ------------
 .../sratools/ncbisettings/nextflow_mount.config | 17 +++++++++++++++++
 tests/modules/sratools/ncbisettings/test.yml    |  6 +++---
 7 files changed, 30 insertions(+), 24 deletions(-)
 create mode 100644 tests/modules/sratools/ncbisettings/nextflow_mount.config

diff --git a/modules/sratools/ncbisettings/main.nf b/modules/sratools/ncbisettings/main.nf
index 9d905f8b..f3015c74 100644
--- a/modules/sratools/ncbisettings/main.nf
+++ b/modules/sratools/ncbisettings/main.nf
@@ -8,8 +8,8 @@ process SRATOOLS_NCBISETTINGS {
         'quay.io/biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"
 
     output:
-    path('user-settings.mkfg'), optional: true, emit: ncbi_settings
-    path 'versions.yml'       , emit: versions
+    path('*.mkfg')     , emit: ncbi_settings
+    path 'versions.yml', emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/sratools/ncbisettings/meta.yml b/modules/sratools/ncbisettings/meta.yml
index 29bcfe34..6043ece4 100644
--- a/modules/sratools/ncbisettings/meta.yml
+++ b/modules/sratools/ncbisettings/meta.yml
@@ -21,8 +21,8 @@ output:
       pattern: "versions.yml"
   - ncbi_settings:
       type: file
-      description: An optional, minimal NCBI settings file.
-      pattern: "user-settings.mkfg"
+      description: An NCBI user settings file.
+      pattern: "*.mkfg"
 
 authors:
   - "@Midnighter"
diff --git a/modules/sratools/ncbisettings/templates/detect_ncbi_settings.sh b/modules/sratools/ncbisettings/templates/detect_ncbi_settings.sh
index b1b51c1f..cfe3a324 100644
--- a/modules/sratools/ncbisettings/templates/detect_ncbi_settings.sh
+++ b/modules/sratools/ncbisettings/templates/detect_ncbi_settings.sh
@@ -31,6 +31,12 @@ else
         echo "$(printf '!{config}')" >&2
         exit 1
     fi
+    if [[ "${NCBI_SETTINGS}" != *.mkfg ]]; then
+        echo "The detected settings '${NCBI_SETTINGS}' do not have the required"\
+        "file extension '.mkfg'." >&2
+        exit 1
+    fi
+    cp "${NCBI_SETTINGS}" ./
 fi
 
 cat <<-END_VERSIONS > versions.yml
diff --git a/tests/modules/sratools/ncbisettings/main.nf b/tests/modules/sratools/ncbisettings/main.nf
index 08968bb9..e52c993e 100644
--- a/tests/modules/sratools/ncbisettings/main.nf
+++ b/tests/modules/sratools/ncbisettings/main.nf
@@ -37,10 +37,5 @@ workflow test_sratools_ncbisettings_with_bad_existing {
 }
 
 workflow test_sratools_ncbisettings_with_nonexisting {
-
-    file(params.settings_path).mkdirs()
-    def settings = file(params.settings_file)
-    settings.delete()
-
     SRATOOLS_NCBISETTINGS()
 }
diff --git a/tests/modules/sratools/ncbisettings/nextflow.config b/tests/modules/sratools/ncbisettings/nextflow.config
index 823082c0..8730f1c4 100644
--- a/tests/modules/sratools/ncbisettings/nextflow.config
+++ b/tests/modules/sratools/ncbisettings/nextflow.config
@@ -1,17 +1,5 @@
-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_NCBISETTINGS {
-        containerOptions = {
-            (workflow.containerEngine == 'singularity') ?
-            "-B ${params.settings_path}:${params.settings_path}" :
-            "-v ${params.settings_path}:${params.settings_path}"
-        }
-    }
 }
diff --git a/tests/modules/sratools/ncbisettings/nextflow_mount.config b/tests/modules/sratools/ncbisettings/nextflow_mount.config
new file mode 100644
index 00000000..823082c0
--- /dev/null
+++ b/tests/modules/sratools/ncbisettings/nextflow_mount.config
@@ -0,0 +1,17 @@
+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_NCBISETTINGS {
+        containerOptions = {
+            (workflow.containerEngine == 'singularity') ?
+            "-B ${params.settings_path}:${params.settings_path}" :
+            "-v ${params.settings_path}:${params.settings_path}"
+        }
+    }
+}
diff --git a/tests/modules/sratools/ncbisettings/test.yml b/tests/modules/sratools/ncbisettings/test.yml
index 07c45dc7..891ebb58 100644
--- a/tests/modules/sratools/ncbisettings/test.yml
+++ b/tests/modules/sratools/ncbisettings/test.yml
@@ -1,17 +1,17 @@
 - 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.config
+  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"
-      should_exist: false
+      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.config
+  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"