Merge pull request #198 from nf-core/dev

Release 2.2.1 bugfix

CHANGELOG.md

@@ -3,6 +3,12 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v2.2.1 - WaldhaeuserOst Hotfix - 2023-03-16
+
+### `Fixed`
+
+- [#196](https://github.com/nf-core/epitopeprediction/pull/196) - Revert versions changes that caused bug with external tools predictions missing.
+
 ## v2.2.0 - WaldhaeuserOst - 2023-03-03
 
 ### `Added`

modules/local/cat_files.nf

@@ -10,7 +10,7 @@ process CAT_FILES {
     tuple val(meta), path(input)
 
     output:
-    tuple val(meta), path("*_prediction*"), emit: output
+    tuple val(meta), path("*_prediction{_result,_proteins}*"), emit: output
     path "versions.yml", emit: versions
 
     script:

modules/local/csvtk_concat.nf

@@ -10,7 +10,7 @@ process CSVTK_CONCAT {
     tuple val(meta), path(predicted)
 
     output:
-    tuple val(meta), path("*.tsv"), emit: predicted
+    tuple val(meta), path("*prediction_result.tsv"), emit: predicted
     path "versions.yml", emit: versions
 
     script:

modules/local/external_tools_import.nf

@@ -14,7 +14,7 @@ process EXTERNAL_TOOLS_IMPORT {
 
     output:
     path "${toolname}", emit: nonfree_tools
-    path  "versions.yml", emit: versions
+    path "versions.yml", emit: versions
 
     script:
     """
@@ -75,7 +75,9 @@ process EXTERNAL_TOOLS_IMPORT {
     #
     # CREATE VERSION FILE
     #
+
     cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
         ${toolname}: ${toolversion}
     END_VERSIONS
     """

modules/local/get_prediction_versions.nf

@@ -10,23 +10,22 @@ process GET_PREDICTION_VERSIONS {
     val external_tool_versions
 
     output:
-    path "versions.yml", emit: versions
+    path "versions.csv", emit: versions // this versions.csv is needed by a downstream process as well. TODO: fix to use versions.yml
 
     script:
     def external_tools = external_tool_versions.join(",")
 
     """
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        mhcflurry: \$(mhcflurry-predict --version 2>&1 | sed 's/^mhcflurry //; s/ .*\$//')
-        mhcnuggets: \$(python -c "import pkg_resources; print('mhcnuggets' + pkg_resources.get_distribution('mhcnuggets').version)" | sed 's/^mhcnuggets//; s/ .*\$//' )
-        epytope: \$(python -c "import pkg_resources; print('epytope' + pkg_resources.get_distribution('epytope').version)" | sed 's/^epytope//; s/ .*\$//')
+    cat <<-END_VERSIONS > versions.csv
+    mhcflurry: \$(mhcflurry-predict --version 2>&1 | sed 's/^mhcflurry //; s/ .*\$//')
+    mhcnuggets: \$(python -c "import pkg_resources; print('mhcnuggets' + pkg_resources.get_distribution('mhcnuggets').version)" | sed 's/^mhcnuggets//; s/ .*\$//' )
+    epytope: \$(python -c "import pkg_resources; print('epytope' + pkg_resources.get_distribution('epytope').version)" | sed 's/^epytope//; s/ .*\$//')
     END_VERSIONS
 
     IFS=',' read -r -a external_tools <<< \"$external_tools\"
     if ! [ -z "${external_tool_versions}" ]; then
         for TOOL in "\${external_tools[@]}"; do
-            echo "\$TOOL" >> versions.yml
+            echo "\$TOOL" >> versions.csv
         done
     fi
     """

nextflow.config

@@ -238,7 +238,7 @@ manifest {
     description     = """A fully reproducible and state of the art epitope prediction pipeline."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '2.2.0'
+    version = '2.2.1'
     doi             = ''
 }
 

workflows/epitopeprediction.nf

@@ -271,6 +271,7 @@ workflow EPITOPEPREDICTION {
     EXTERNAL_TOOLS_IMPORT(
         ch_nonfree_paths
     )
+    ch_versions = ch_versions.mix(EXTERNAL_TOOLS_IMPORT.out.versions.ifEmpty(null))
 
     /*
     ========================================================================================