From eae7161a3213117c3ec6dfb37ee071cbbf896fc8 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Sun, 8 May 2022 17:00:28 +0200
Subject: [PATCH] tests: add settings input or not and test all branches

---
 tests/modules/sratools/fasterqdump/main.nf    | 46 +++++++++++++++++--
 .../sratools/fasterqdump/nextflow.config      |  3 ++
 .../fasterqdump/nextflow_mount.config         | 18 ++++++++
 tests/modules/sratools/fasterqdump/test.yml   | 44 ++++++++++++++++--
 4 files changed, 103 insertions(+), 8 deletions(-)
 create mode 100644 tests/modules/sratools/fasterqdump/nextflow_mount.config

diff --git a/tests/modules/sratools/fasterqdump/main.nf b/tests/modules/sratools/fasterqdump/main.nf
index c2b98526..2bf9daed 100644
--- a/tests/modules/sratools/fasterqdump/main.nf
+++ b/tests/modules/sratools/fasterqdump/main.nf
@@ -5,7 +5,11 @@ 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 {
+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"
 
     archive = [ [], file(params.test_data['sarscov2']['illumina']['SRR13255544_tar_gz'], checkIfExists: true) ]
     UNTAR ( archive )
@@ -13,10 +17,14 @@ 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, settings)
 }
 
-workflow test_sratools_fasterqdump_paired_end {
+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"
 
     archive = [ [], file(params.test_data['sarscov2']['illumina']['SRR11140744_tar_gz'], checkIfExists: true) ]
     UNTAR ( archive )
@@ -24,5 +32,35 @@ 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, 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'))
 }
diff --git a/tests/modules/sratools/fasterqdump/nextflow.config b/tests/modules/sratools/fasterqdump/nextflow.config
index 8730f1c4..a6c70bd3 100644
--- a/tests/modules/sratools/fasterqdump/nextflow.config
+++ b/tests/modules/sratools/fasterqdump/nextflow.config
@@ -1,3 +1,6 @@
+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()}" }
diff --git a/tests/modules/sratools/fasterqdump/nextflow_mount.config b/tests/modules/sratools/fasterqdump/nextflow_mount.config
new file mode 100644
index 00000000..b79d1a82
--- /dev/null
+++ b/tests/modules/sratools/fasterqdump/nextflow_mount.config
@@ -0,0 +1,18 @@
+
+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}"
+        }
+    }
+}
diff --git a/tests/modules/sratools/fasterqdump/test.yml b/tests/modules/sratools/fasterqdump/test.yml
index 64cf2404..73f9a0aa 100644
--- a/tests/modules/sratools/fasterqdump/test.yml
+++ b/tests/modules/sratools/fasterqdump/test.yml
@@ -1,5 +1,5 @@
-- 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
+- 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
   tags:
     - sratools
     - sratools/fasterqdump
@@ -8,9 +8,12 @@
       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
+- 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
@@ -21,3 +24,36 @@
       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
+  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"