From 954a6d03e358d710c86c2a29eb3bfb17f06f33e4 Mon Sep 17 00:00:00 2001
From: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
Date: Mon, 6 May 2024 11:32:44 +0200
Subject: [PATCH 1/3] FEAT: require 'ps' command to be available. (#45)

* FEAT: require 'ps' command to be available.

* Move to root of config

* Add 'ps' to falco.
---
 _viash.yaml               | 5 ++++-
 src/falco/config.vsh.yaml | 2 +-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/_viash.yaml b/_viash.yaml
index a72a1ab7..6d658e2d 100644
--- a/_viash.yaml
+++ b/_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
\ No newline at end of file
+viash_version: 0.9.0-RC2
+
+config_mods: |
+  .requirements.commands := ['ps']
diff --git a/src/falco/config.vsh.yaml b/src/falco/config.vsh.yaml
index 61cbb0d5..4d9cf656 100644
--- a/src/falco/config.vsh.yaml
+++ b/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 && \

From ce27c3e41be1dd12433dcf1406509908ea76c26a Mon Sep 17 00:00:00 2001
From: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
Date: Mon, 6 May 2024 16:10:32 +0200
Subject: [PATCH 2/3] FEAT: Add --cl_config to MultiQC (#46)

---
 src/multiqc/config.vsh.yaml | 6 ++++++
 src/multiqc/script.sh       | 1 +
 2 files changed, 7 insertions(+)

diff --git a/src/multiqc/config.vsh.yaml b/src/multiqc/config.vsh.yaml
index 7f29d109..0a3a784b 100644
--- a/src/multiqc/config.vsh.yaml
+++ b/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:
diff --git a/src/multiqc/script.sh b/src/multiqc/script.sh
index 6b04ff5b..b765520b 100755
--- a/src/multiqc/script.sh
+++ b/src/multiqc/script.sh
@@ -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} \

From fe8ffc238a2a93b60abf8a6aab2e0fce2116da19 Mon Sep 17 00:00:00 2001
From: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
Date: Tue, 7 May 2024 08:42:20 +0200
Subject: [PATCH 3/3] BUG: multiqc always ignores symlinked directories. (#47)

---
 src/multiqc/script.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/multiqc/script.sh b/src/multiqc/script.sh
index b765520b..6353eb11 100755
--- a/src/multiqc/script.sh
+++ b/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