From 5d593bdb45eb241e65c9c7b1a4ffb2cf48ce695d Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Sun, 8 May 2022 16:44:33 +0200
Subject: [PATCH 01/24] docs: correct license and input description

---
 modules/sratools/fasterqdump/meta.yml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/modules/sratools/fasterqdump/meta.yml b/modules/sratools/fasterqdump/meta.yml
index ec5f69a5..ac62bc61 100644
--- a/modules/sratools/fasterqdump/meta.yml
+++ b/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 +22,12 @@ input:
       type: directory
       description: Directory containing ETL data for the given SRA.
       pattern: "*/*.sra"
+  - 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"
 
 output:
   - meta:

From d4f13ebfff9b421bd36dbc6001669078adc2369a Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Sun, 8 May 2022 16:46:52 +0200
Subject: [PATCH 02/24] refactor: create new settings input

---
 modules/sratools/fasterqdump/main.nf | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/modules/sratools/fasterqdump/main.nf b/modules/sratools/fasterqdump/main.nf
index 1980ffeb..6351efd2 100644
--- a/modules/sratools/fasterqdump/main.nf
+++ b/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
@@ -20,16 +21,13 @@ 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}"
+    if [[ "${ncbi_settings.name}" != "EXISTS" ]]; then
+        export NCBI_SETTINGS="\$PWD/${ncbi_settings}"
     fi
 
     fasterq-dump \\

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 03/24] 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"

From 0cdf7767a79faf424645beeff83ecfa5528b6a7c Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Wed, 11 May 2022 13:02:52 +0200
Subject: [PATCH 04/24] refactor: require NCBI user settings always

---
 modules/sratools/fasterqdump/main.nf          |  6 +--
 modules/sratools/fasterqdump/meta.yml         |  5 +-
 tests/modules/sratools/fasterqdump/main.nf    | 46 ++-----------------
 .../sratools/fasterqdump/nextflow.config      |  3 --
 .../fasterqdump/nextflow_mount.config         | 18 --------
 tests/modules/sratools/fasterqdump/test.yml   | 38 ++-------------
 6 files changed, 12 insertions(+), 104 deletions(-)
 delete mode 100644 tests/modules/sratools/fasterqdump/nextflow_mount.config

diff --git a/modules/sratools/fasterqdump/main.nf b/modules/sratools/fasterqdump/main.nf
index 6351efd2..18f46e51 100644
--- a/modules/sratools/fasterqdump/main.nf
+++ b/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
+    export NCBI_SETTINGS="\$PWD/${ncbi_settings}"
 
     fasterq-dump \\
         $args \\
diff --git a/modules/sratools/fasterqdump/meta.yml b/modules/sratools/fasterqdump/meta.yml
index ac62bc61..d6fbd444 100644
--- a/modules/sratools/fasterqdump/meta.yml
+++ b/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:
diff --git a/tests/modules/sratools/fasterqdump/main.nf b/tests/modules/sratools/fasterqdump/main.nf
index 2bf9daed..daa7a5ae 100644
--- a/tests/modules/sratools/fasterqdump/main.nf
+++ b/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))
 }
diff --git a/tests/modules/sratools/fasterqdump/nextflow.config b/tests/modules/sratools/fasterqdump/nextflow.config
index a6c70bd3..8730f1c4 100644
--- a/tests/modules/sratools/fasterqdump/nextflow.config
+++ b/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()}" }
diff --git a/tests/modules/sratools/fasterqdump/nextflow_mount.config b/tests/modules/sratools/fasterqdump/nextflow_mount.config
deleted file mode 100644
index b79d1a82..00000000
--- a/tests/modules/sratools/fasterqdump/nextflow_mount.config
+++ /dev/null
@@ -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}"
-        }
-    }
-}
diff --git a/tests/modules/sratools/fasterqdump/test.yml b/tests/modules/sratools/fasterqdump/test.yml
index 73f9a0aa..6fbf608c 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_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

From 3ae8cbfad754dc45cae7fb42315f2873a7e9e417 Mon Sep 17 00:00:00 2001
From: CMGG ICT Team <ict@cmgg.be>
Date: Wed, 11 May 2022 13:32:56 +0200
Subject: [PATCH 05/24] bowtie2: remove code duplication

---
 modules/bowtie2/align/main.nf        | 112 +++++++++++++--------------
 tests/modules/bowtie2/align/test.yml |  88 ++++-----------------
 2 files changed, 65 insertions(+), 135 deletions(-)

diff --git a/modules/bowtie2/align/main.nf b/modules/bowtie2/align/main.nf
index c233f955..18209bdf 100644
--- a/modules/bowtie2/align/main.nf
+++ b/modules/bowtie2/align/main.nf
@@ -1,11 +1,11 @@
 process BOWTIE2_ALIGN {
     tag "$meta.id"
-    label 'process_high'
+    label "process_high"
 
-    conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6' : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0' :
-        'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0' }"
+    conda (params.enable_conda ? "bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6" : null)
+    container "${ workflow.containerEngine == "singularity" && !task.ext.singularity_pull_docker_container ?
+        "https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" :
+        "quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" }"
 
     input:
     tuple val(meta), path(reads)
@@ -13,69 +13,61 @@ process BOWTIE2_ALIGN {
     val   save_unaligned
 
     output:
-    tuple val(meta), path('*.bam')    , emit: bam
-    tuple val(meta), path('*.log')    , emit: log
-    tuple val(meta), path('*fastq.gz'), emit: fastq, optional:true
+    tuple val(meta), path("*.bam")    , emit: bam
+    tuple val(meta), path("*.log")    , emit: log
+    tuple val(meta), path("*fastq.gz"), emit: fastq, optional:true
     path  "versions.yml"              , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def args2 = task.ext.args2 ?: ''
+    def args = task.ext.args ?: ""
+    def args2 = task.ext.args2 ?: ""
     def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def unaligned = ""
+    def reads_args = ""
+
     if (meta.single_end) {
-        def unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
-        """
-        INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
-        [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed 's/.rev.1.bt2l//'`
-        [ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1
-        bowtie2 \\
-            -x \$INDEX \\
-            -U $reads \\
-            --threads $task.cpus \\
-            $unaligned \\
-            $args \\
-            2> ${prefix}.bowtie2.log \\
-            | samtools view -@ $task.cpus $args2 -bhS -o ${prefix}.bam -
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
-            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-            pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
-        END_VERSIONS
-        """
+        unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ""
+        reads_args = "-U ${reads}"
     } else {
-        def unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
-        """
-        INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
-        [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed 's/.rev.1.bt2l//'`
-        [ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1
-        bowtie2 \\
-            -x \$INDEX \\
-            -1 ${reads[0]} \\
-            -2 ${reads[1]} \\
-            --threads $task.cpus \\
-            $unaligned \\
-            $args \\
-            2> ${prefix}.bowtie2.log \\
-            | samtools view -@ $task.cpus $args2 -bhS -o ${prefix}.bam -
-
-        if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
-            mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
-        fi
-        if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
-            mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
-        fi
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
-            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-            pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
-        END_VERSIONS
-        """
+        unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ""
+        reads_args = "-1 ${reads[0]} -2 ${reads[1]}"
     }
+
+    def samtools = "samtools view -@ $task.cpus --fast --with-header ${args2} > ${prefix}.bam"
+
+
+    """
+    INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/.rev.1.bt2//"`
+    [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed "s/.rev.1.bt2l//"`
+    [ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1
+
+    bowtie2 \\
+        -x \$INDEX \\
+        ${reads_args} \\
+        --threads $task.cpus \\
+        ${unaligned} \\
+        $args \\
+        2> ${prefix}.bowtie2.log \\
+        | ${samtools}
+
+    if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
+        mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
+    fi
+
+    if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
+        mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
+    fi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+        pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
+    END_VERSIONS
+    """
 }
+
diff --git a/tests/modules/bowtie2/align/test.yml b/tests/modules/bowtie2/align/test.yml
index ea9aa72a..b3cb8330 100644
--- a/tests/modules/bowtie2/align/test.yml
+++ b/tests/modules/bowtie2/align/test.yml
@@ -1,83 +1,21 @@
-- name: bowtie2 align single-end
-  command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config
+- name: bowtie2 align test_bowtie2_align_single_end
+  command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c tests/config/nextflow.config
   tags:
-    - bowtie2
     - bowtie2/align
+    - bowtie2
   files:
-    - path: ./output/bowtie2/test.bam
-    - path: ./output/bowtie2/test.bowtie2.log
-    - path: ./output/bowtie2/bowtie2/genome.3.bt2
-      md5sum: 4ed93abba181d8dfab2e303e33114777
-    - path: ./output/bowtie2/bowtie2/genome.2.bt2
-      md5sum: 47b153cd1319abc88dda532462651fcf
-    - path: ./output/bowtie2/bowtie2/genome.1.bt2
-      md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf
-    - path: ./output/bowtie2/bowtie2/genome.4.bt2
-      md5sum: c25be5f8b0378abf7a58c8a880b87626
-    - path: ./output/bowtie2/bowtie2/genome.rev.1.bt2
-      md5sum: 52be6950579598a990570fbcf5372184
-    - path: ./output/bowtie2/bowtie2/genome.rev.2.bt2
-      md5sum: e3b4ef343dea4dd571642010a7d09597
+    - path: output/bowtie2/test.bam
+    - path: output/bowtie2/test.bowtie2.log
+      md5sum: 7b8a9e61b7646da1089b041333c41a87
+    - path: output/bowtie2/versions.yml
 
-- name: bowtie2 align paired-end
-  command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config
+- name: bowtie2 align test_bowtie2_align_paired_end
+  command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config
   tags:
-    - bowtie2
     - bowtie2/align
-  files:
-    - path: ./output/bowtie2/test.bam
-    - path: ./output/bowtie2/test.bowtie2.log
-    - path: ./output/bowtie2/bowtie2/genome.3.bt2
-      md5sum: 4ed93abba181d8dfab2e303e33114777
-    - path: ./output/bowtie2/bowtie2/genome.2.bt2
-      md5sum: 47b153cd1319abc88dda532462651fcf
-    - path: ./output/bowtie2/bowtie2/genome.1.bt2
-      md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf
-    - path: ./output/bowtie2/bowtie2/genome.4.bt2
-      md5sum: c25be5f8b0378abf7a58c8a880b87626
-    - path: ./output/bowtie2/bowtie2/genome.rev.1.bt2
-      md5sum: 52be6950579598a990570fbcf5372184
-    - path: ./output/bowtie2/bowtie2/genome.rev.2.bt2
-      md5sum: e3b4ef343dea4dd571642010a7d09597
-
-- name: bowtie2 align single-end large-index
-  command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config --force_large_index
-  tags:
     - bowtie2
-    - bowtie2/align
   files:
-    - path: ./output/bowtie2/test.bam
-    - path: ./output/bowtie2/test.bowtie2.log
-    - path: ./output/bowtie2/bowtie2/genome.3.bt2l
-      md5sum: 8952b3e0b1ce9a7a5916f2e147180853
-    - path: ./output/bowtie2/bowtie2/genome.2.bt2l
-      md5sum: 22c284084784a0720989595e0c9461fd
-    - path: ./output/bowtie2/bowtie2/genome.1.bt2l
-      md5sum: 07d811cd4e350d56267183d2ac7023a5
-    - path: ./output/bowtie2/bowtie2/genome.4.bt2l
-      md5sum: c25be5f8b0378abf7a58c8a880b87626
-    - path: ./output/bowtie2/bowtie2/genome.rev.1.bt2l
-      md5sum: fda48e35925fb24d1c0785f021981e25
-    - path: ./output/bowtie2/bowtie2/genome.rev.2.bt2l
-      md5sum: 802c26d32b970e1b105032b7ce7348b4
-
-- name: bowtie2 align paired-end large-index
-  command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config --force_large_index
-  tags:
-    - bowtie2
-    - bowtie2/align
-  files:
-    - path: ./output/bowtie2/test.bam
-    - path: ./output/bowtie2/test.bowtie2.log
-    - path: ./output/bowtie2/bowtie2/genome.3.bt2l
-      md5sum: 8952b3e0b1ce9a7a5916f2e147180853
-    - path: ./output/bowtie2/bowtie2/genome.2.bt2l
-      md5sum: 22c284084784a0720989595e0c9461fd
-    - path: ./output/bowtie2/bowtie2/genome.1.bt2l
-      md5sum: 07d811cd4e350d56267183d2ac7023a5
-    - path: ./output/bowtie2/bowtie2/genome.4.bt2l
-      md5sum: c25be5f8b0378abf7a58c8a880b87626
-    - path: ./output/bowtie2/bowtie2/genome.rev.1.bt2l
-      md5sum: fda48e35925fb24d1c0785f021981e25
-    - path: ./output/bowtie2/bowtie2/genome.rev.2.bt2l
-      md5sum: 802c26d32b970e1b105032b7ce7348b4
+    - path: output/bowtie2/test.bam
+    - path: output/bowtie2/test.bowtie2.log
+      md5sum: bd89ce1b28c93bf822bae391ffcedd19
+    - path: output/bowtie2/versions.yml

From 0d00452ecaff35d83ce931f57be9ab6244245c36 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Wed, 11 May 2022 13:55:45 +0200
Subject: [PATCH 06/24] Update tests/modules/bowtie2/align/test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 tests/modules/bowtie2/align/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/modules/bowtie2/align/test.yml b/tests/modules/bowtie2/align/test.yml
index b3cb8330..9aec709c 100644
--- a/tests/modules/bowtie2/align/test.yml
+++ b/tests/modules/bowtie2/align/test.yml
@@ -1,5 +1,5 @@
 - name: bowtie2 align test_bowtie2_align_single_end
-  command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config
   tags:
     - bowtie2/align
     - bowtie2

From 9dd083fa9480fd03b4995e364d2634e78b572049 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Wed, 11 May 2022 13:55:55 +0200
Subject: [PATCH 07/24] Update modules/bowtie2/align/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 modules/bowtie2/align/main.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/bowtie2/align/main.nf b/modules/bowtie2/align/main.nf
index 18209bdf..605aae34 100644
--- a/modules/bowtie2/align/main.nf
+++ b/modules/bowtie2/align/main.nf
@@ -28,7 +28,6 @@ process BOWTIE2_ALIGN {
 
     def unaligned = ""
     def reads_args = ""
-
     if (meta.single_end) {
         unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ""
         reads_args = "-U ${reads}"

From 94e8c3a882b7c03e7c24ee9a710a28511e31611f Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Wed, 11 May 2022 13:56:03 +0200
Subject: [PATCH 08/24] Update tests/modules/bowtie2/align/test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 tests/modules/bowtie2/align/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/modules/bowtie2/align/test.yml b/tests/modules/bowtie2/align/test.yml
index 9aec709c..ef05d70d 100644
--- a/tests/modules/bowtie2/align/test.yml
+++ b/tests/modules/bowtie2/align/test.yml
@@ -10,7 +10,7 @@
     - path: output/bowtie2/versions.yml
 
 - name: bowtie2 align test_bowtie2_align_paired_end
-  command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config
   tags:
     - bowtie2/align
     - bowtie2

From ff4b297827d3a78ea66172241a4ed414ea1148da Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Wed, 11 May 2022 13:57:11 +0200
Subject: [PATCH 09/24] Update modules/bowtie2/align/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 modules/bowtie2/align/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/bowtie2/align/main.nf b/modules/bowtie2/align/main.nf
index 605aae34..8ee198bb 100644
--- a/modules/bowtie2/align/main.nf
+++ b/modules/bowtie2/align/main.nf
@@ -48,7 +48,7 @@ process BOWTIE2_ALIGN {
         -x \$INDEX \\
         ${reads_args} \\
         --threads $task.cpus \\
-        ${unaligned} \\
+        $unaligned \\
         $args \\
         2> ${prefix}.bowtie2.log \\
         | ${samtools}

From b456d8fa0aa797258ea9a308120be45e5b7b9667 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Wed, 11 May 2022 13:57:19 +0200
Subject: [PATCH 10/24] Update modules/bowtie2/align/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 modules/bowtie2/align/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/bowtie2/align/main.nf b/modules/bowtie2/align/main.nf
index 8ee198bb..b7334614 100644
--- a/modules/bowtie2/align/main.nf
+++ b/modules/bowtie2/align/main.nf
@@ -46,7 +46,7 @@ process BOWTIE2_ALIGN {
 
     bowtie2 \\
         -x \$INDEX \\
-        ${reads_args} \\
+        $reads_args \\
         --threads $task.cpus \\
         $unaligned \\
         $args \\

From 971a889e2a8adce2c8831f296ac37d335c5f93c7 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Wed, 11 May 2022 13:57:27 +0200
Subject: [PATCH 11/24] Update modules/bowtie2/align/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 modules/bowtie2/align/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/bowtie2/align/main.nf b/modules/bowtie2/align/main.nf
index b7334614..6d65aa50 100644
--- a/modules/bowtie2/align/main.nf
+++ b/modules/bowtie2/align/main.nf
@@ -42,7 +42,7 @@ process BOWTIE2_ALIGN {
     """
     INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/.rev.1.bt2//"`
     [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed "s/.rev.1.bt2l//"`
-    [ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1
+    [ -z "\$INDEX" ] && echo "Bowtie2 index files not found" 1>&2 && exit 1
 
     bowtie2 \\
         -x \$INDEX \\

From 9097abf277f25b34bd41480c35bd7deac6f9a7c2 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Wed, 11 May 2022 13:58:58 +0200
Subject: [PATCH 12/24] Update modules/bowtie2/align/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 modules/bowtie2/align/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/bowtie2/align/main.nf b/modules/bowtie2/align/main.nf
index 6d65aa50..126c93ae 100644
--- a/modules/bowtie2/align/main.nf
+++ b/modules/bowtie2/align/main.nf
@@ -36,7 +36,7 @@ process BOWTIE2_ALIGN {
         reads_args = "-1 ${reads[0]} -2 ${reads[1]}"
     }
 
-    def samtools = "samtools view -@ $task.cpus --fast --with-header ${args2} > ${prefix}.bam"
+    def samtools_command = "samtools view -@ $task.cpus --fast --with-header ${args2} > ${prefix}.bam"
 
 
     """

From bcd7fe55b171e4532cd19312c091258ee7ccc26a Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Wed, 11 May 2022 13:59:03 +0200
Subject: [PATCH 13/24] Update modules/bowtie2/align/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 modules/bowtie2/align/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/bowtie2/align/main.nf b/modules/bowtie2/align/main.nf
index 126c93ae..9fd19469 100644
--- a/modules/bowtie2/align/main.nf
+++ b/modules/bowtie2/align/main.nf
@@ -51,7 +51,7 @@ process BOWTIE2_ALIGN {
         $unaligned \\
         $args \\
         2> ${prefix}.bowtie2.log \\
-        | ${samtools}
+        | $samtools_command
 
     if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
         mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz

From fbe2f85e7b9a047c6deed6155c145422524959ee Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Wed, 11 May 2022 13:53:38 +0000
Subject: [PATCH 14/24] Fix path

---
 tests/config/test_data.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index 63c3ac16..aaab2243 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -382,7 +382,7 @@ params {
                 test3_gff                       = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test3.gff"
             }
             'illumina' {
-                test_1_fastq_gz                 = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fasta/test_1.fastq.gz"
+                test_1_fastq_gz                 = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_1.fastq.gz"
                 test_2_fastq_gz                 = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_2.fastq.gz"
                 test_se_fastq_gz                = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_se.fastq.gz"
             }

From c8d3de2ad965bfd8e165f6f6d91249eea3436854 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Wed, 11 May 2022 16:17:30 +0200
Subject: [PATCH 15/24] restore samtools cmd to defaults

---
 modules/bowtie2/align/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/bowtie2/align/main.nf b/modules/bowtie2/align/main.nf
index 9fd19469..38242fcb 100644
--- a/modules/bowtie2/align/main.nf
+++ b/modules/bowtie2/align/main.nf
@@ -36,7 +36,7 @@ process BOWTIE2_ALIGN {
         reads_args = "-1 ${reads[0]} -2 ${reads[1]}"
     }
 
-    def samtools_command = "samtools view -@ $task.cpus --fast --with-header ${args2} > ${prefix}.bam"
+    def samtools_command = "samtools view -@ $task.cpus --bam --with-header ${args2} > ${prefix}.bam"
 
 
     """

From 64ff23f3c1d26e22742e13e93da29b52a82da8d2 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Sun, 8 May 2022 15:44:13 +0200
Subject: [PATCH 16/24] feat: add module that verifies NCBI settings

---
 modules/sratools/ncbisettings/main.nf         | 20 ++++++++
 modules/sratools/ncbisettings/meta.yml        | 28 +++++++++++
 .../templates/detect_ncbi_settings.sh         | 39 ++++++++++++++++
 tests/config/pytest_modules.yml               |  4 ++
 tests/modules/sratools/ncbisettings/main.nf   | 46 +++++++++++++++++++
 .../sratools/ncbisettings/nextflow.config     | 17 +++++++
 tests/modules/sratools/ncbisettings/test.yml  | 44 ++++++++++++++++++
 7 files changed, 198 insertions(+)
 create mode 100644 modules/sratools/ncbisettings/main.nf
 create mode 100644 modules/sratools/ncbisettings/meta.yml
 create mode 100644 modules/sratools/ncbisettings/templates/detect_ncbi_settings.sh
 create mode 100644 tests/modules/sratools/ncbisettings/main.nf
 create mode 100644 tests/modules/sratools/ncbisettings/nextflow.config
 create mode 100644 tests/modules/sratools/ncbisettings/test.yml

diff --git a/modules/sratools/ncbisettings/main.nf b/modules/sratools/ncbisettings/main.nf
new file mode 100644
index 00000000..9d905f8b
--- /dev/null
+++ b/modules/sratools/ncbisettings/main.nf
@@ -0,0 +1,20 @@
+process SRATOOLS_NCBISETTINGS {
+    tag 'ncbi-settings'
+    label 'process_low'
+
+    conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' :
+        'quay.io/biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"
+
+    output:
+    path('user-settings.mkfg'), optional: true, emit: ncbi_settings
+    path 'versions.yml'       , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    shell:
+    config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
+    template 'detect_ncbi_settings.sh'
+}
diff --git a/modules/sratools/ncbisettings/meta.yml b/modules/sratools/ncbisettings/meta.yml
new file mode 100644
index 00000000..29bcfe34
--- /dev/null
+++ b/modules/sratools/ncbisettings/meta.yml
@@ -0,0 +1,28 @@
+name: "sratools_ncbisettings"
+description: Test for the presence of suitable NCBI settings or create them on the fly.
+keywords:
+  - NCBI
+  - settings
+  - sra-tools
+  - prefetch
+  - fasterq-dump
+tools:
+  - "sratools":
+      description: "SRA Toolkit and SDK from NCBI"
+      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: "['Public Domain']"
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - ncbi_settings:
+      type: file
+      description: An optional, minimal NCBI settings file.
+      pattern: "user-settings.mkfg"
+
+authors:
+  - "@Midnighter"
diff --git a/modules/sratools/ncbisettings/templates/detect_ncbi_settings.sh b/modules/sratools/ncbisettings/templates/detect_ncbi_settings.sh
new file mode 100644
index 00000000..b1b51c1f
--- /dev/null
+++ b/modules/sratools/ncbisettings/templates/detect_ncbi_settings.sh
@@ -0,0 +1,39 @@
+#!/usr/bin/env bash
+
+set -u
+
+
+# Get the expected NCBI settings path and define the environment variable
+# `NCBI_SETTINGS`.
+eval "$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
+
+# If the user settings do not exist yet, create a file suitable for `prefetch`
+# and `fasterq-dump`. If an existing settings file does not contain the required
+# values, error out with a helpful message.
+if [[ ! -f "${NCBI_SETTINGS}" ]]; then
+    printf '!{config}' > 'user-settings.mkfg'
+else
+    prefetch --help &> /dev/null
+    if [[ $? = 78 ]]; then
+        echo "You have an existing vdb-config at '${NCBI_SETTINGS}' but it is"\
+        "missing the required entries for /LIBS/GUID and"\
+        "/libs/cloud/report_instance_identity."\
+        "Feel free to add the following to your settings file:" >&2
+        echo "$(printf '!{config}')" >&2
+        exit 1
+    fi
+    fasterq-dump --help &> /dev/null
+    if [[ $? = 78 ]]; then
+        echo "You have an existing vdb-config at '${NCBI_SETTINGS}' but it is"\
+        "missing the required entries for /LIBS/GUID and"\
+        "/libs/cloud/report_instance_identity."\
+        "Feel free to add the following to your settings file:" >&2
+        echo "$(printf '!{config}')" >&2
+        exit 1
+    fi
+fi
+
+cat <<-END_VERSIONS > versions.yml
+"!{task.process}":
+    sratools: $(vdb-config --version 2>&1 | grep -Eo '[0-9.]+')
+END_VERSIONS
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 9afe83fd..4a922a4d 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1819,6 +1819,10 @@ 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/**
diff --git a/tests/modules/sratools/ncbisettings/main.nf b/tests/modules/sratools/ncbisettings/main.nf
new file mode 100644
index 00000000..08968bb9
--- /dev/null
+++ b/tests/modules/sratools/ncbisettings/main.nf
@@ -0,0 +1,46 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SRATOOLS_NCBISETTINGS } from '../../../../modules/sratools/ncbisettings/main.nf'
+
+workflow test_sratools_ncbisettings_with_good_existing {
+
+    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"
+
+    SRATOOLS_NCBISETTINGS()
+}
+
+workflow test_sratools_ncbisettings_with_bad_existing {
+
+    file(params.settings_path).mkdirs()
+    def settings = file(params.settings_file)
+    settings.text = '''
+    ## auto-generated configuration file - DO NOT EDIT ##
+
+    config/default = "false"
+    /repository/remote/main/CGI/resolver-cgi = "https://trace.ncbi.nlm.nih.gov/Traces/names/names.fcgi"
+    /repository/remote/protected/CGI/resolver-cgi = "https://trace.ncbi.nlm.nih.gov/Traces/names/names.fcgi"
+    /repository/user/ad/public/apps/file/volumes/flatAd = "."
+    /repository/user/ad/public/apps/refseq/volumes/refseqAd = "."
+    /repository/user/ad/public/apps/sra/volumes/sraAd = "."
+    /repository/user/ad/public/apps/sraPileup/volumes/ad = "."
+    /repository/user/ad/public/apps/sraRealign/volumes/ad = "."
+    /repository/user/ad/public/apps/wgs/volumes/wgsAd = "."
+    /repository/user/ad/public/root = "."
+    /repository/user/default-path = "/root/ncbi"
+    '''.stripIndent()
+
+    SRATOOLS_NCBISETTINGS()
+}
+
+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
new file mode 100644
index 00000000..823082c0
--- /dev/null
+++ b/tests/modules/sratools/ncbisettings/nextflow.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
new file mode 100644
index 00000000..07c45dc7
--- /dev/null
+++ b/tests/modules/sratools/ncbisettings/test.yml
@@ -0,0 +1,44 @@
+- 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
+  tags:
+    - "sratools"
+    - "sratools/ncbisettings"
+  files:
+    - path: "output/sratools/user-settings.mkfg"
+      should_exist: false
+    - 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
+  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"

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 17/24] 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"

From a83dd33a7ef63a362786c3943bb02d3cc43eb8d3 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Wed, 11 May 2022 14:13:50 +0200
Subject: [PATCH 18/24] tests: use remove settings file

---
 tests/modules/sratools/ncbisettings/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/modules/sratools/ncbisettings/main.nf b/tests/modules/sratools/ncbisettings/main.nf
index e52c993e..f4d1fcfd 100644
--- a/tests/modules/sratools/ncbisettings/main.nf
+++ b/tests/modules/sratools/ncbisettings/main.nf
@@ -7,8 +7,8 @@ include { SRATOOLS_NCBISETTINGS } from '../../../../modules/sratools/ncbisetting
 workflow test_sratools_ncbisettings_with_good_existing {
 
     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"
+    def settings = file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true)
+    settings.copyTo(params.settings_file)
 
     SRATOOLS_NCBISETTINGS()
 }

From 23091aabdaa8815ed86e57e7aa40dd4a44593745 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Wed, 11 May 2022 17:07:59 +0200
Subject: [PATCH 19/24] refactor: move files to custom section

---
 modules/{sratools => custom}/ncbisettings/main.nf                 | 0
 modules/{sratools => custom}/ncbisettings/meta.yml                | 0
 .../ncbisettings/templates/detect_ncbi_settings.sh                | 0
 tests/modules/{sratools => custom}/ncbisettings/main.nf           | 0
 tests/modules/{sratools => custom}/ncbisettings/nextflow.config   | 0
 .../{sratools => custom}/ncbisettings/nextflow_mount.config       | 0
 tests/modules/{sratools => custom}/ncbisettings/test.yml          | 0
 7 files changed, 0 insertions(+), 0 deletions(-)
 rename modules/{sratools => custom}/ncbisettings/main.nf (100%)
 rename modules/{sratools => custom}/ncbisettings/meta.yml (100%)
 rename modules/{sratools => custom}/ncbisettings/templates/detect_ncbi_settings.sh (100%)
 rename tests/modules/{sratools => custom}/ncbisettings/main.nf (100%)
 rename tests/modules/{sratools => custom}/ncbisettings/nextflow.config (100%)
 rename tests/modules/{sratools => custom}/ncbisettings/nextflow_mount.config (100%)
 rename tests/modules/{sratools => custom}/ncbisettings/test.yml (100%)

diff --git a/modules/sratools/ncbisettings/main.nf b/modules/custom/ncbisettings/main.nf
similarity index 100%
rename from modules/sratools/ncbisettings/main.nf
rename to modules/custom/ncbisettings/main.nf
diff --git a/modules/sratools/ncbisettings/meta.yml b/modules/custom/ncbisettings/meta.yml
similarity index 100%
rename from modules/sratools/ncbisettings/meta.yml
rename to modules/custom/ncbisettings/meta.yml
diff --git a/modules/sratools/ncbisettings/templates/detect_ncbi_settings.sh b/modules/custom/ncbisettings/templates/detect_ncbi_settings.sh
similarity index 100%
rename from modules/sratools/ncbisettings/templates/detect_ncbi_settings.sh
rename to modules/custom/ncbisettings/templates/detect_ncbi_settings.sh
diff --git a/tests/modules/sratools/ncbisettings/main.nf b/tests/modules/custom/ncbisettings/main.nf
similarity index 100%
rename from tests/modules/sratools/ncbisettings/main.nf
rename to tests/modules/custom/ncbisettings/main.nf
diff --git a/tests/modules/sratools/ncbisettings/nextflow.config b/tests/modules/custom/ncbisettings/nextflow.config
similarity index 100%
rename from tests/modules/sratools/ncbisettings/nextflow.config
rename to tests/modules/custom/ncbisettings/nextflow.config
diff --git a/tests/modules/sratools/ncbisettings/nextflow_mount.config b/tests/modules/custom/ncbisettings/nextflow_mount.config
similarity index 100%
rename from tests/modules/sratools/ncbisettings/nextflow_mount.config
rename to tests/modules/custom/ncbisettings/nextflow_mount.config
diff --git a/tests/modules/sratools/ncbisettings/test.yml b/tests/modules/custom/ncbisettings/test.yml
similarity index 100%
rename from tests/modules/sratools/ncbisettings/test.yml
rename to tests/modules/custom/ncbisettings/test.yml

From b2dbaa99309a2057efc32ef9d029ed91140068df Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Wed, 11 May 2022 17:32:50 +0200
Subject: [PATCH 20/24] refactor: rename module

---
 .../main.nf                                   |  2 +-
 .../meta.yml                                  |  2 +-
 .../templates/detect_ncbi_settings.sh         |  0
 tests/config/pytest_modules.yml               |  8 ++--
 tests/modules/custom/ncbisettings/test.yml    | 44 -------------------
 .../main.nf                                   | 14 +++---
 .../nextflow.config                           |  0
 .../nextflow_mount.config                     |  2 +-
 .../custom/sratoolsncbisettings/test.yml      | 44 +++++++++++++++++++
 9 files changed, 58 insertions(+), 58 deletions(-)
 rename modules/custom/{ncbisettings => sratoolsncbisettings}/main.nf (94%)
 rename modules/custom/{ncbisettings => sratoolsncbisettings}/meta.yml (95%)
 rename modules/custom/{ncbisettings => sratoolsncbisettings}/templates/detect_ncbi_settings.sh (100%)
 delete mode 100644 tests/modules/custom/ncbisettings/test.yml
 rename tests/modules/custom/{ncbisettings => sratoolsncbisettings}/main.nf (75%)
 rename tests/modules/custom/{ncbisettings => sratoolsncbisettings}/nextflow.config (100%)
 rename tests/modules/custom/{ncbisettings => sratoolsncbisettings}/nextflow_mount.config (91%)
 create mode 100644 tests/modules/custom/sratoolsncbisettings/test.yml

diff --git a/modules/custom/ncbisettings/main.nf b/modules/custom/sratoolsncbisettings/main.nf
similarity index 94%
rename from modules/custom/ncbisettings/main.nf
rename to modules/custom/sratoolsncbisettings/main.nf
index f3015c74..21bf3005 100644
--- a/modules/custom/ncbisettings/main.nf
+++ b/modules/custom/sratoolsncbisettings/main.nf
@@ -1,4 +1,4 @@
-process SRATOOLS_NCBISETTINGS {
+process CUSTOM_SRATOOLSNCBISETTINGS {
     tag 'ncbi-settings'
     label 'process_low'
 
diff --git a/modules/custom/ncbisettings/meta.yml b/modules/custom/sratoolsncbisettings/meta.yml
similarity index 95%
rename from modules/custom/ncbisettings/meta.yml
rename to modules/custom/sratoolsncbisettings/meta.yml
index 6043ece4..01e98856 100644
--- a/modules/custom/ncbisettings/meta.yml
+++ b/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
diff --git a/modules/custom/ncbisettings/templates/detect_ncbi_settings.sh b/modules/custom/sratoolsncbisettings/templates/detect_ncbi_settings.sh
similarity index 100%
rename from modules/custom/ncbisettings/templates/detect_ncbi_settings.sh
rename to modules/custom/sratoolsncbisettings/templates/detect_ncbi_settings.sh
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 4a922a4d..428c3652 100644
--- a/tests/config/pytest_modules.yml
+++ b/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/**
diff --git a/tests/modules/custom/ncbisettings/test.yml b/tests/modules/custom/ncbisettings/test.yml
deleted file mode 100644
index 891ebb58..00000000
--- a/tests/modules/custom/ncbisettings/test.yml
+++ /dev/null
@@ -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"
diff --git a/tests/modules/custom/ncbisettings/main.nf b/tests/modules/custom/sratoolsncbisettings/main.nf
similarity index 75%
rename from tests/modules/custom/ncbisettings/main.nf
rename to tests/modules/custom/sratoolsncbisettings/main.nf
index f4d1fcfd..be316a39 100644
--- a/tests/modules/custom/ncbisettings/main.nf
+++ b/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()
 }
diff --git a/tests/modules/custom/ncbisettings/nextflow.config b/tests/modules/custom/sratoolsncbisettings/nextflow.config
similarity index 100%
rename from tests/modules/custom/ncbisettings/nextflow.config
rename to tests/modules/custom/sratoolsncbisettings/nextflow.config
diff --git a/tests/modules/custom/ncbisettings/nextflow_mount.config b/tests/modules/custom/sratoolsncbisettings/nextflow_mount.config
similarity index 91%
rename from tests/modules/custom/ncbisettings/nextflow_mount.config
rename to tests/modules/custom/sratoolsncbisettings/nextflow_mount.config
index 823082c0..853844c5 100644
--- a/tests/modules/custom/ncbisettings/nextflow_mount.config
+++ b/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}" :
diff --git a/tests/modules/custom/sratoolsncbisettings/test.yml b/tests/modules/custom/sratoolsncbisettings/test.yml
new file mode 100644
index 00000000..df3cd936
--- /dev/null
+++ b/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"

From 888620063bb67a1645b54de1dba022a409f9a44f Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Wed, 11 May 2022 17:44:49 +0200
Subject: [PATCH 21/24] tests: delete settings for conda

---
 tests/modules/custom/sratoolsncbisettings/main.nf | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tests/modules/custom/sratoolsncbisettings/main.nf b/tests/modules/custom/sratoolsncbisettings/main.nf
index be316a39..9f49f20e 100644
--- a/tests/modules/custom/sratoolsncbisettings/main.nf
+++ b/tests/modules/custom/sratoolsncbisettings/main.nf
@@ -37,5 +37,8 @@ workflow test_sratoolsncbisettings_with_bad_existing {
 }
 
 workflow test_sratoolsncbisettings_with_nonexisting {
+    def settings = file(params.settings_file)
+    settings.delete()
+
     CUSTOM_SRATOOLSNCBISETTINGS()
 }

From 98d8a741ec574823a799e9c375ec2c62da654cf5 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Wed, 11 May 2022 18:17:27 +0200
Subject: [PATCH 22/24] tests: add missing paths to config

---
 tests/modules/custom/sratoolsncbisettings/nextflow.config | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tests/modules/custom/sratoolsncbisettings/nextflow.config b/tests/modules/custom/sratoolsncbisettings/nextflow.config
index 8730f1c4..a6c70bd3 100644
--- a/tests/modules/custom/sratoolsncbisettings/nextflow.config
+++ b/tests/modules/custom/sratoolsncbisettings/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()}" }

From 74b11ccc4431caf5bc2daffb52629799927fee86 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Wed, 11 May 2022 19:21:32 +0200
Subject: [PATCH 23/24] refactor: rename and update subworkflow

---
 subworkflows/nf-core/sra_fastq/main.nf        | 34 -----------------
 subworkflows/nf-core/srafastq/main.nf         | 38 +++++++++++++++++++
 .../nf-core/{sra_fastq => srafastq}/meta.yml  |  7 +++-
 .../{sra_fastq => srafastq}/nextflow.config   |  0
 tests/subworkflows/nf-core/sra_fastq/main.nf  | 23 -----------
 tests/subworkflows/nf-core/sra_fastq/test.yml | 27 -------------
 tests/subworkflows/nf-core/srafastq/main.nf   | 29 ++++++++++++++
 .../nf-core/srafastq/nextflow.config          |  5 +++
 tests/subworkflows/nf-core/srafastq/test.yml  | 29 ++++++++++++++
 9 files changed, 106 insertions(+), 86 deletions(-)
 delete mode 100644 subworkflows/nf-core/sra_fastq/main.nf
 create mode 100644 subworkflows/nf-core/srafastq/main.nf
 rename subworkflows/nf-core/{sra_fastq => srafastq}/meta.yml (90%)
 rename subworkflows/nf-core/{sra_fastq => srafastq}/nextflow.config (100%)
 delete mode 100644 tests/subworkflows/nf-core/sra_fastq/main.nf
 delete mode 100644 tests/subworkflows/nf-core/sra_fastq/test.yml
 create mode 100644 tests/subworkflows/nf-core/srafastq/main.nf
 create mode 100644 tests/subworkflows/nf-core/srafastq/nextflow.config
 create mode 100644 tests/subworkflows/nf-core/srafastq/test.yml

diff --git a/subworkflows/nf-core/sra_fastq/main.nf b/subworkflows/nf-core/sra_fastq/main.nf
deleted file mode 100644
index ffa380d9..00000000
--- a/subworkflows/nf-core/sra_fastq/main.nf
+++ /dev/null
@@ -1,34 +0,0 @@
-//
-// Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
-//
-
-params.prefetch_options    = [:]
-params.fasterqdump_options = [:]
-
-include { SRATOOLS_PREFETCH    } from '../../../modules/sratools/prefetch/main'    addParams( options: params.prefetch_options    )
-include { SRATOOLS_FASTERQDUMP } from '../../../modules/sratools/fasterqdump/main' addParams( options: params.fasterqdump_options )
-
-workflow SRA_FASTQ {
-    take:
-    sra_ids  // channel: [ val(meta), val(id) ]
-
-    main:
-
-    ch_versions = Channel.empty()
-
-    //
-    // Prefetch sequencing reads in SRA format.
-    //
-    SRATOOLS_PREFETCH ( sra_ids )
-    ch_versions = ch_versions.mix( SRATOOLS_PREFETCH.out.versions.first() )
-
-    //
-    // Convert the SRA format into one or more compressed FASTQ files.
-    //
-    SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra )
-    ch_versions = ch_versions.mix( SRATOOLS_FASTERQDUMP.out.versions.first() )
-
-    emit:
-    reads    = SRATOOLS_FASTERQDUMP.out.reads  // channel: [ val(meta), [ reads ] ]
-    versions = ch_versions                     // channel: [ versions.yml ]
-}
diff --git a/subworkflows/nf-core/srafastq/main.nf b/subworkflows/nf-core/srafastq/main.nf
new file mode 100644
index 00000000..26e8105e
--- /dev/null
+++ b/subworkflows/nf-core/srafastq/main.nf
@@ -0,0 +1,38 @@
+include { CUSTOM_SRATOOLSNCBISETTINGS } from '../../../modules/custom/sratoolsncbisettings/main'
+include { SRATOOLS_PREFETCH           } from '../../../modules/sratools/prefetch/main'
+include { SRATOOLS_FASTERQDUMP        } from '../../../modules/sratools/fasterqdump/main'
+
+/**
+ * Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
+ */
+workflow SRAFASTQ {
+    take:
+    sra_ids  // channel: [ val(meta), val(id) ]
+
+    main:
+
+    ch_versions = Channel.empty()
+
+    //
+    // Detect existing NCBI user settings or create new ones.
+    //
+    CUSTOM_SRATOOLSNCBISETTINGS()
+    def settings = CUSTOM_SRATOOLSNCBISETTINGS.out.ncbi_settings
+    ch_versions = ch_versions.mix( CUSTOM_SRATOOLSNCBISETTINGS.out.versions )
+
+    //
+    // Prefetch sequencing reads in SRA format.
+    //
+    SRATOOLS_PREFETCH ( sra_ids, settings )
+    ch_versions = ch_versions.mix( SRATOOLS_PREFETCH.out.versions.first() )
+
+    //
+    // Convert the SRA format into one or more compressed FASTQ files.
+    //
+    SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra, settings )
+    ch_versions = ch_versions.mix( SRATOOLS_FASTERQDUMP.out.versions.first() )
+
+    emit:
+    reads    = SRATOOLS_FASTERQDUMP.out.reads  // channel: [ val(meta), [ reads ] ]
+    versions = ch_versions                     // channel: [ versions.yml ]
+}
diff --git a/subworkflows/nf-core/sra_fastq/meta.yml b/subworkflows/nf-core/srafastq/meta.yml
similarity index 90%
rename from subworkflows/nf-core/sra_fastq/meta.yml
rename to subworkflows/nf-core/srafastq/meta.yml
index 5114bce5..873ccaca 100644
--- a/subworkflows/nf-core/sra_fastq/meta.yml
+++ b/subworkflows/nf-core/srafastq/meta.yml
@@ -1,11 +1,14 @@
 name: sra_fastq
 description: Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
 keywords:
+  - SRA
+  - NCBI
   - sequencing
   - FASTQ
   - prefetch
-  - dump
+  - fasterq-dump
 modules:
+  - custom/sratoolsncbisettings
   - sratools/prefetch
   - sratools/fasterqdump
 input:
@@ -17,7 +20,7 @@ input:
   - id:
       type: string
       description: >
-        SRA identifier.
+        SRA run identifier.
 # TODO Update when we decide on a standard for subworkflow docs
 output:
   - meta:
diff --git a/subworkflows/nf-core/sra_fastq/nextflow.config b/subworkflows/nf-core/srafastq/nextflow.config
similarity index 100%
rename from subworkflows/nf-core/sra_fastq/nextflow.config
rename to subworkflows/nf-core/srafastq/nextflow.config
diff --git a/tests/subworkflows/nf-core/sra_fastq/main.nf b/tests/subworkflows/nf-core/sra_fastq/main.nf
deleted file mode 100644
index 988758f3..00000000
--- a/tests/subworkflows/nf-core/sra_fastq/main.nf
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SRA_FASTQ } from '../../../../subworkflows/nf-core/sra_fastq/main.nf' addParams( [:] )
-
-workflow test_sra_fastq_single_end {
-    input = [
-        [ id:'test_single_end', single_end:true ], // meta map
-        'SRR13255544'
-    ]
-
-    SRA_FASTQ ( input )
-}
-
-workflow test_sra_fastq_paired_end {
-    input = [
-        [ id:'test_paired_end', single_end:false ], // meta map
-        'SRR11140744'
-    ]
-
-    SRA_FASTQ ( input )
-}
diff --git a/tests/subworkflows/nf-core/sra_fastq/test.yml b/tests/subworkflows/nf-core/sra_fastq/test.yml
deleted file mode 100644
index 4b75431f..00000000
--- a/tests/subworkflows/nf-core/sra_fastq/test.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-- name: sra fastq single-end
-  command: nextflow run ./tests/subworkflows/nf-core/sra_fastq -entry test_sra_fastq_single_end -c tests/config/nextflow.config
-  tags:
-    - subworkflows
-    # - subworkflows/sra_fastq
-    # Modules
-    # - sratools
-    # - sratools/prefetch
-    # - sratools/fasterqdump
-  files:
-    - path: output/sratools/SRR13255544.fastq.gz
-      md5sum: 1054c7b71884acdb5eed8a378f18be82
-
-- name: sra fastq paired-end
-  command: nextflow run ./tests/subworkflows/nf-core/sra_fastq -entry test_sra_fastq_paired_end -c tests/config/nextflow.config
-  tags:
-    - subworkflows
-    # - subworkflows/sra_fastq
-    # Modules
-    # - sratools
-    # - sratools/prefetch
-    # - sratools/fasterqdump
-  files:
-    - path: output/sratools/SRR11140744_1.fastq.gz
-      md5sum: 193809c784a4ea132ab2a253fa4f55b6
-    - path: output/sratools/SRR11140744_2.fastq.gz
-      md5sum: 3e3b3af3413f50a1685fd7b3f1456d4e
diff --git a/tests/subworkflows/nf-core/srafastq/main.nf b/tests/subworkflows/nf-core/srafastq/main.nf
new file mode 100644
index 00000000..82c8f29d
--- /dev/null
+++ b/tests/subworkflows/nf-core/srafastq/main.nf
@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SRAFASTQ } from '../../../../subworkflows/nf-core/srafastq/main.nf'
+
+workflow test_srafastq_single_end {
+    input = Channel.of(
+        [
+            [ id:'test_single_end1', single_end:true ], // meta map
+            'DRR000774'
+        ],
+        [
+            [ id:'test_single_end2', single_end:true ], // meta map
+            'DRR000775'
+        ]
+    )
+
+    SRAFASTQ ( input )
+}
+
+workflow test_srafastq_paired_end {
+    input = [
+        [ id:'test_paired_end', single_end:false ], // meta map
+        'SRR11140744'
+    ]
+
+    SRAFASTQ ( input )
+}
diff --git a/tests/subworkflows/nf-core/srafastq/nextflow.config b/tests/subworkflows/nf-core/srafastq/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/subworkflows/nf-core/srafastq/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/subworkflows/nf-core/srafastq/test.yml b/tests/subworkflows/nf-core/srafastq/test.yml
new file mode 100644
index 00000000..73424171
--- /dev/null
+++ b/tests/subworkflows/nf-core/srafastq/test.yml
@@ -0,0 +1,29 @@
+- name: srafastq single-end
+  command: nextflow run ./tests/subworkflows/nf-core/srafastq -entry test_srafastq_single_end -c tests/config/nextflow.config -c tests/subworkflows/nf-core/srafastq/nextflow.config
+  tags:
+    - subworkflows
+    # - subworkflows/srafastq
+    # Modules
+    # - sratools
+    # - sratools/prefetch
+    # - sratools/fasterqdump
+  files:
+    - path: output/sratools/DRR000774.fastq.gz
+      md5sum: 19029a1132115b55277a0d79ee089b49
+    - path: output/sratools/DRR000775.fastq.gz
+      md5sum: 59ff24c86ecb260752668c059c2a1eaf
+
+- name: srafastq paired-end
+  command: nextflow run ./tests/subworkflows/nf-core/srafastq -entry test_srafastq_paired_end -c tests/config/nextflow.config -c tests/subworkflows/nf-core/srafastq/nextflow.config
+  tags:
+    - subworkflows
+    # - subworkflows/srafastq
+    # Modules
+    # - sratools
+    # - sratools/prefetch
+    # - sratools/fasterqdump
+  files:
+    - path: output/sratools/SRR11140744_1.fastq.gz
+      md5sum: 193809c784a4ea132ab2a253fa4f55b6
+    - path: output/sratools/SRR11140744_2.fastq.gz
+      md5sum: 3e3b3af3413f50a1685fd7b3f1456d4e

From 6fa1c8089afe83e612dbc14e4b85f277166c4a2b Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Fri, 13 May 2022 10:03:20 +0200
Subject: [PATCH 24/24] Added memory allocation to VCFeval

---
 modules/rtgtools/vcfeval/main.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/rtgtools/vcfeval/main.nf b/modules/rtgtools/vcfeval/main.nf
index 1bad4231..27a488f7 100644
--- a/modules/rtgtools/vcfeval/main.nf
+++ b/modules/rtgtools/vcfeval/main.nf
@@ -35,12 +35,13 @@ process RTGTOOLS_VCFEVAL {
     def eval_regions = evaluation_regions ? "--evaluation-regions=$evaluation_regions" : ""
     def truth_index = truth_vcf_tbi ? "" : "rtg index $truth_vcf"
     def query_index = query_vcf_tbi ? "" : "rtg index $query_vcf"
+    def avail_mem = task.memory.toGiga() + "G"
 
     """
     $truth_index
     $query_index
 
-    rtg vcfeval \\
+    rtg RTG_MEM=$avail_mem vcfeval \\
         $args \\
         --baseline=$truth_vcf \\
         $bed_regions \\