fixed some parameter handling

Author: rwittler

.github/workflows/publish-container.yml

@@ -40,7 +40,7 @@ jobs:
           tags: |
             # set latest tag for default branch
             type=raw,value=latest
-            type=raw,value=v1.0.2
+            type=raw,value=v1.0.3
       # This step uses the `docker/build-push-action` action to build the image, based on your repository's `Dockerfile`. If the build succeeds, it pushes the image to GitHub Packages.
       # It uses the `context` parameter to define the build's context as the set of files located in the specified path. For more information, see "[Usage](https://github.com/docker/build-push-action#usage)" in the README of the `docker/build-push-action` repository.
       # It uses the `tags` and `labels` parameters to tag and label the image with the output from the "meta" step.

clowm/CHANGELOG.md

@@ -1,5 +1,13 @@
 # SANS Changelog
 
+
+## v1.0.3 [2025-02-07]
+
+### Fixed
+
+- consensus planar was missing in parameter definitions
+- some filtering combinations with tree/strict were not handled properly
+
 ## v1.0.2 [2025-02-0]
 
 ### Fixed

clowm/main.nf

@@ -8,7 +8,7 @@ params.file_of_files = "$projectDir/NO_FILE3"
 params.blacklist = "$projectDir/NO_FILE4"
 
 process sans {
-  container "ghcr.io/gi-bielefeld/sans:v1.0.2"
+  container "ghcr.io/gi-bielefeld/sans:v1.0.3"
   publishDir params.outdir, mode: 'symlink'
   debug false
   label 'highmemMedium'
@@ -79,7 +79,7 @@ process sans {
   ${ params.consensus == "none" && params.filter == 'strict' ? "--newick sans_tree.newick" : '' } \
   ${ params.consensus == "none" && params.filter == '2-tree' ? "--newick sans_tree.newick" : '' } \
   ${ params.consensus == "none" && params.filter == '3-tree' ? "--newick sans_tree.newick" : '' } \
-  ${ params.consensus == "tree" ? "--newick sans_tree.newick" : '' } \
+  ${ params.consensus == "strict" ? "--newick sans_tree.newick" : '' } \
   ${ params.consensus == "2-tree" ? "--newick sans_tree.newick" : '' } \
   ${ params.consensus == "3-tree" ? "--newick sans_tree.newick" : '' } \
   ${ params.consensus == "none" && params.filter == 'weakly' ? "--nexus sans_splitnetwork.nexus" : '' } \
@@ -101,15 +101,15 @@ process sans {
   ${ params.top != null ? "--top ${ params.top }" : "" } \
   ${ params.pdf  && params.consensus == "none" && params.filter == 'strict' ? "--svg sans_tree.svg" : "" } \
   ${ params.pdf  && params.consensus == "none" && params.filter != 'strict' ? "--svg sans_splitnetwork.svg" : "" } \
-  ${ params.pdf  && params.consensus == "tree" ? "--svg sans_tree.svg" : "" } \
+  ${ params.pdf  && params.consensus == "strict" ? "--svg sans_tree.svg" : "" } \
   ${ params.pdf  && params.consensus != "none" && params.consensus != "strict" ? "--svg sans_splitnetwork.svg" : "" } \
   ${ params.svg  && params.consensus == "none" && params.filter == 'strict' ? "--svg sans_tree.svg" : "" } \
   ${ params.svg  && params.consensus == "none" && params.filter != 'strict' ? "--svg sans_splitnetwork.svg" : "" } \
-  ${ params.svg  && params.consensus == "tree" ? "--svg sans_tree.svg" : "" } \
+  ${ params.svg  && params.consensus == "strict" ? "--svg sans_tree.svg" : "" } \
   ${ params.svg  && params.consensus != "none" && params.consensus != "strict" ? "--svg sans_splitnetwork.svg" : "" } \
   ${ params.filter == 'strict' ? "--filter strict" : '' } \
   ${ params.filter == 'weakly' ? "--filter weakly" : '' } \
-  ${ params.filter == 'planar' ? "--filter weakly" : '' } \
+  ${ params.filter == 'planar' ? "--filter planar" : '' } \
   ${ params.filter == '2-tree' ? "--filter 2-tree" : '' } \
   ${ params.filter == '3-tree' ? "--filter 3-tree" : '' } \
   ${ params.filter == 'default' ? "--filter weakly" : '' } \

clowm/nextflow_schema.json

@@ -158,6 +158,7 @@
                     "enum": [
                         "strict",
                         "weakly",
+                        "planar",
                         "2-tree",
                         "3-tree",
                         "none"