Merge branch 'viash-hub:main' into samtools_collate

_viash.yaml

@@ -7,4 +7,7 @@ links:
   issue_tracker: https://github.com/viash-hub/biobase/issues
   repository: https://github.com/viash-hub/biobase
 
-viash_version: 0.9.0-RC2
+viash_version: 0.9.0-RC2
+
+config_mods: |
+  .requirements.commands := ['ps']

src/falco/config.vsh.yaml

@@ -177,7 +177,7 @@ engines:
     image: debian:trixie-slim
     setup:
       - type: apt
-        packages: [wget, build-essential, g++, zlib1g-dev]
+        packages: [wget, build-essential, g++, zlib1g-dev, procps]
       - type: docker
         run: |
           wget https://github.com/smithlabcode/falco/releases/download/v1.2.2/falco-1.2.2.tar.gz -O /tmp/falco.tar.gz && \

src/multiqc/config.vsh.yaml

@@ -161,6 +161,12 @@ argument_groups:
         type: boolean_true
         description: |
           Disable coloured log output.
+      - name: "--cl_config"
+        type: string
+        required: false
+        description: |
+          YAML formatted string that allows to customize MultiQC behaviour like input file detection.
+        example: "qualimap_config: { general_stats_coverage: [20,40,200] }"
 
   - name: "Output format"
     arguments:

src/multiqc/script.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # disable flags
-[[ "$par_ignore_symlinks" == "false" ]] && unset ignore_symlinks
+[[ "$par_ignore_symlinks" == "false" ]] && unset par_ignore_symlinks
 [[ "$par_dirs" == "false" ]] && unset par_dirs
 [[ "$par_full_names" == "false" ]] && unset par_full_names
 [[ "$par_fn_as_s_name" == "false" ]] && unset par_fn_as_s_name
@@ -99,6 +99,7 @@ multiqc \
     ${include_modules} \
     ${par_include_modules:+--include-modules "$par_include_modules"} \
     ${par_data_format:+--data-format "$par_data_format"} \
+    ${par_cl_config:+--cl-config "$par_cl_config"} \
     ${par_zip_data_dir:+--zip-data-dir} \
     ${par_pdf:+--pdf} \
     ${par_interactive:+--interactive} \