sync nf-core modules and bump openms version

Author: jonasscheid

CHANGELOG.md

@@ -7,8 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
-- Migrate to topic channels  [#431](https://github.com/nf-core/mhcquant/pull/431)
- 
+- Migrate to topic channels [#431](https://github.com/nf-core/mhcquant/pull/431)
+
 ### `Dependencies`
 
 | Dependency | Old version | New version |

modules.json

@@ -17,52 +17,52 @@
                     },
                     "openms/decoydatabase": {
                         "branch": "master",
-                        "git_sha": "0c47e4193ddde2c5edbc206b5420cbcbee5c9797",
+                        "git_sha": "ca1cd2456f36c913fb3cfb6bdfbf9d1794fd493b",
                         "installed_by": ["modules"]
                     },
                     "openms/filefilter": {
                         "branch": "master",
-                        "git_sha": "0c47e4193ddde2c5edbc206b5420cbcbee5c9797",
+                        "git_sha": "ca1cd2456f36c913fb3cfb6bdfbf9d1794fd493b",
                         "installed_by": ["modules"]
                     },
                     "openms/idfilter": {
                         "branch": "master",
-                        "git_sha": "0c47e4193ddde2c5edbc206b5420cbcbee5c9797",
+                        "git_sha": "ca1cd2456f36c913fb3cfb6bdfbf9d1794fd493b",
                         "installed_by": ["modules"]
                     },
                     "openms/idmassaccuracy": {
                         "branch": "master",
-                        "git_sha": "0c47e4193ddde2c5edbc206b5420cbcbee5c9797",
+                        "git_sha": "ca1cd2456f36c913fb3cfb6bdfbf9d1794fd493b",
                         "installed_by": ["modules"]
                     },
                     "openms/idmerger": {
                         "branch": "master",
-                        "git_sha": "0c47e4193ddde2c5edbc206b5420cbcbee5c9797",
+                        "git_sha": "ca1cd2456f36c913fb3cfb6bdfbf9d1794fd493b",
                         "installed_by": ["modules"]
                     },
                     "openms/idripper": {
                         "branch": "master",
-                        "git_sha": "0c47e4193ddde2c5edbc206b5420cbcbee5c9797",
+                        "git_sha": "ca1cd2456f36c913fb3cfb6bdfbf9d1794fd493b",
                         "installed_by": ["modules"]
                     },
                     "openms/idscoreswitcher": {
                         "branch": "master",
-                        "git_sha": "0c47e4193ddde2c5edbc206b5420cbcbee5c9797",
+                        "git_sha": "ca1cd2456f36c913fb3cfb6bdfbf9d1794fd493b",
                         "installed_by": ["modules"]
                     },
                     "openms/peakpickerhires": {
                         "branch": "master",
-                        "git_sha": "0c47e4193ddde2c5edbc206b5420cbcbee5c9797",
+                        "git_sha": "ca1cd2456f36c913fb3cfb6bdfbf9d1794fd493b",
                         "installed_by": ["modules"]
                     },
                     "openms/peptideindexer": {
                         "branch": "master",
-                        "git_sha": "0c47e4193ddde2c5edbc206b5420cbcbee5c9797",
+                        "git_sha": "ca1cd2456f36c913fb3cfb6bdfbf9d1794fd493b",
                         "installed_by": ["modules"]
                     },
                     "openmsthirdparty/cometadapter": {
                         "branch": "master",
-                        "git_sha": "0c47e4193ddde2c5edbc206b5420cbcbee5c9797",
+                        "git_sha": "ca1cd2456f36c913fb3cfb6bdfbf9d1794fd493b",
                         "installed_by": ["modules"]
                     },
                     "thermorawfileparser": {

modules/local/openms/mapaligneridentification/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::openms=3.4.1
+  - bioconda::openms=3.5.0

modules/local/openms/mapaligneridentification/main.nf

@@ -4,15 +4,15 @@ process OPENMS_MAPALIGNERIDENTIFICATION {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:3.4.1--h81ffffe_1' :
-        'biocontainers/openms:3.4.1--h81ffffe_1' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.5.0--h78fb946_0' :
+        'biocontainers/openms:3.5.0--h78fb946_0' }"
 
     input:
     tuple val(meta), path(idxmls)
 
     output:
     tuple val(meta), path("*.trafoXML"), emit: trafoxml
-    tuple val("${task.process}"), val('openms'), eval("FileInfo --help 2>&1 | grep -E '^Version' | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//'"), emit: versions, topic: versions
+    tuple val("${task.process}"), val('openms'), eval("FileInfo --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\\1/p'"), emit: versions_openms, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/openms/maprttransformer/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::openms=3.4.1
+  - bioconda::openms=3.5.0

modules/local/openms/maprttransformer/main.nf

@@ -4,15 +4,15 @@ process OPENMS_MAPRTTRANSFORMER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:3.4.1--h81ffffe_1' :
-        'biocontainers/openms:3.4.1--h81ffffe_1' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.5.0--h78fb946_0' :
+        'biocontainers/openms:3.5.0--h78fb946_0' }"
 
     input:
     tuple val(meta), path(alignment_file), path(trafoxml)
 
     output:
     tuple val(meta), path("*_aligned.*"), emit: aligned
-    tuple val("${task.process}"), val('openms'), eval("FileInfo --help 2>&1 | grep -E '^Version' | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//'"), emit: versions, topic: versions
+    tuple val("${task.process}"), val('openms'), eval("FileInfo --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\\1/p'"), emit: versions_openms, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/openms/mztabexporter/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::openms=3.4.1
+  - bioconda::openms=3.5.0

modules/local/openms/mztabexporter/main.nf

@@ -4,15 +4,15 @@ process OPENMS_MZTABEXPORTER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:3.4.1--h81ffffe_1' :
-        'biocontainers/openms:3.4.1--h81ffffe_1' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.5.0--h78fb946_0' :
+        'biocontainers/openms:3.5.0--h78fb946_0' }"
 
     input:
     tuple val(meta), path(in_file)
 
     output:
     tuple val(meta), path("*.mzTab"), emit: mztab
-    tuple val("${task.process}"), val('openms'), eval("FileInfo --help 2>&1 | grep -E '^Version' | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//'"), emit: versions, topic: versions
+    tuple val("${task.process}"), val('openms'), eval("FileInfo --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\\1/p'"), emit: versions_openms, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/openms/psmfeatureextractor/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::openms=3.4.1
+  - bioconda::openms=3.5.0

modules/local/openms/psmfeatureextractor/main.nf

@@ -4,15 +4,15 @@ process OPENMS_PSMFEATUREEXTRACTOR {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:3.4.1--h81ffffe_1' :
-        'biocontainers/openms:3.4.1--h81ffffe_1' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.5.0--h78fb946_0' :
+        'biocontainers/openms:3.5.0--h78fb946_0' }"
 
     input:
     tuple val(meta), path(idxml), path(feature_file)
 
     output:
     tuple val(meta), path("*.idXML"), emit: idxml
-    tuple val("${task.process}"), val('openms'), eval("FileInfo --help 2>&1 | grep -E '^Version' | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//'"), emit: versions, topic: versions
+    tuple val("${task.process}"), val('openms'), eval("FileInfo --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\\1/p'"), emit: versions_openms, topic: versions
 
     when:
     task.ext.when == null || task.ext.when