Build branch main with version main (da414e7)

Build pipeline: viash-hub.biobox.main-7dwhr Source commit: da414e72c6 Source message: Add star solo component (#62) * add star solo component * change arguments from camelCase to snake_case * get rid of multiple_sep * drop star_solo component and just add arguments to star_align_reads * Update src/star/star_align_reads/script.py Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com> --------- Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
2024-07-29 08:14:56 +00:00
parent ae3fef8eec
commit 02c1c9ebea
309 changed files with 58822 additions and 4148 deletions
--- a/target/executable/multiqc/.config.vsh.yaml
+++ b/target/executable/multiqc/.config.vsh.yaml
@@ -1,5 +1,19 @@
 name: "multiqc"
 version: "main"
+authors:
+- name: "Dorien Roosen"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "dorien@data-intuitive.com"
+      github: "dorien-er"
+      linkedin: "dorien-roosen"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
 argument_groups:
 - name: "Input"
  arguments:
@@ -63,39 +77,43 @@ argument_groups:
    description: "Use only these module"
    info: null
    example:
-    - "fastqc,cutadapt"
+    - "fastqc"
+    - "cutadapt"
    required: false
    direction: "input"
    multiple: true
-    multiple_sep: ","
+    multiple_sep: ";"
  - type: "string"
    name: "--exclude_modules"
    description: "Do not use only these modules"
    info: null
    example:
-    - "fastqc,cutadapt"
+    - "fastqc"
+    - "cutadapt"
    required: false
    direction: "input"
    multiple: true
-    multiple_sep: ","
+    multiple_sep: ";"
  - type: "string"
    name: "--ignore_analysis"
    info: null
    example:
-    - "run_one/*,run_two/*"
+    - "run_one/*"
+    - "run_two/*"
    required: false
    direction: "input"
    multiple: true
-    multiple_sep: ","
+    multiple_sep: ";"
  - type: "string"
    name: "--ignore_samples"
    info: null
    example:
-    - "sample_1*,sample_3*"
+    - "sample_1*"
+    - "sample_3*"
    required: false
    direction: "input"
    multiple: true
-    multiple_sep: ","
+    multiple_sep: ";"
  - type: "boolean_true"
    name: "--ignore_symlinks"
    description: "Ignore symlinked directories and files"
@@ -438,7 +456,7 @@ build_info:
  output: "target/executable/multiqc"
  executable: "target/executable/multiqc/multiqc"
  viash_version: "0.9.0-RC6"
-  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
+  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/multiqc/multiqc
+++ b/target/executable/multiqc/multiqc
@@ -10,6 +10,9 @@
 # authors of this component should specify the license in the header of such
 # files, or include a separate license file detailing the licenses of all included
 # files.
+# 
+# Component authors:
+#  * Dorien Roosen (author, maintainer)

 set -e

@@ -207,21 +210,21 @@ function ViashHelp {
  echo "Modules and analyses to run:"
  echo "    --include_modules"
  echo "        type: string, multiple values allowed"
-  echo "        example: fastqc,cutadapt"
+  echo "        example: fastqc;cutadapt"
  echo "        Use only these module"
  echo ""
  echo "    --exclude_modules"
  echo "        type: string, multiple values allowed"
-  echo "        example: fastqc,cutadapt"
+  echo "        example: fastqc;cutadapt"
  echo "        Do not use only these modules"
  echo ""
  echo "    --ignore_analysis"
  echo "        type: string, multiple values allowed"
-  echo "        example: run_one/*,run_two/*"
+  echo "        example: run_one/*;run_two/*"
  echo ""
  echo "    --ignore_samples"
  echo "        type: string, multiple values allowed"
-  echo "        example: sample_1*,sample_3*"
+  echo "        example: sample_1*;sample_3*"
  echo ""
  echo "    --ignore_symlinks"
  echo "        type: boolean_true"
@@ -631,10 +634,11 @@ FROM quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0
 ENTRYPOINT []
 RUN multiqc --version | sed 's/multiqc, version\s\(.*\)/multiqc: "\1"/' > /var/software_versions.txt

+LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component multiqc"
-LABEL org.opencontainers.image.created="2024-07-01T20:00:27Z"
+LABEL org.opencontainers.image.created="2024-07-29T07:58:02Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
+LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
@@ -815,7 +819,7 @@ while [[ $# -gt 0 ]]; do
            if [ -z "$VIASH_PAR_INCLUDE_MODULES" ]; then
              VIASH_PAR_INCLUDE_MODULES="$2"
            else
-              VIASH_PAR_INCLUDE_MODULES="$VIASH_PAR_INCLUDE_MODULES,""$2"
+              VIASH_PAR_INCLUDE_MODULES="$VIASH_PAR_INCLUDE_MODULES;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --include_modules. Use "--help" to get more information on the parameters. && exit 1
            shift 2
@@ -824,7 +828,7 @@ while [[ $# -gt 0 ]]; do
            if [ -z "$VIASH_PAR_INCLUDE_MODULES" ]; then
              VIASH_PAR_INCLUDE_MODULES=$(ViashRemoveFlags "$1")
            else
-              VIASH_PAR_INCLUDE_MODULES="$VIASH_PAR_INCLUDE_MODULES,"$(ViashRemoveFlags "$1")
+              VIASH_PAR_INCLUDE_MODULES="$VIASH_PAR_INCLUDE_MODULES;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
@@ -832,7 +836,7 @@ while [[ $# -gt 0 ]]; do
            if [ -z "$VIASH_PAR_EXCLUDE_MODULES" ]; then
              VIASH_PAR_EXCLUDE_MODULES="$2"
            else
-              VIASH_PAR_EXCLUDE_MODULES="$VIASH_PAR_EXCLUDE_MODULES,""$2"
+              VIASH_PAR_EXCLUDE_MODULES="$VIASH_PAR_EXCLUDE_MODULES;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --exclude_modules. Use "--help" to get more information on the parameters. && exit 1
            shift 2
@@ -841,7 +845,7 @@ while [[ $# -gt 0 ]]; do
            if [ -z "$VIASH_PAR_EXCLUDE_MODULES" ]; then
              VIASH_PAR_EXCLUDE_MODULES=$(ViashRemoveFlags "$1")
            else
-              VIASH_PAR_EXCLUDE_MODULES="$VIASH_PAR_EXCLUDE_MODULES,"$(ViashRemoveFlags "$1")
+              VIASH_PAR_EXCLUDE_MODULES="$VIASH_PAR_EXCLUDE_MODULES;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
@@ -849,7 +853,7 @@ while [[ $# -gt 0 ]]; do
            if [ -z "$VIASH_PAR_IGNORE_ANALYSIS" ]; then
              VIASH_PAR_IGNORE_ANALYSIS="$2"
            else
-              VIASH_PAR_IGNORE_ANALYSIS="$VIASH_PAR_IGNORE_ANALYSIS,""$2"
+              VIASH_PAR_IGNORE_ANALYSIS="$VIASH_PAR_IGNORE_ANALYSIS;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --ignore_analysis. Use "--help" to get more information on the parameters. && exit 1
            shift 2
@@ -858,7 +862,7 @@ while [[ $# -gt 0 ]]; do
            if [ -z "$VIASH_PAR_IGNORE_ANALYSIS" ]; then
              VIASH_PAR_IGNORE_ANALYSIS=$(ViashRemoveFlags "$1")
            else
-              VIASH_PAR_IGNORE_ANALYSIS="$VIASH_PAR_IGNORE_ANALYSIS,"$(ViashRemoveFlags "$1")
+              VIASH_PAR_IGNORE_ANALYSIS="$VIASH_PAR_IGNORE_ANALYSIS;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
@@ -866,7 +870,7 @@ while [[ $# -gt 0 ]]; do
            if [ -z "$VIASH_PAR_IGNORE_SAMPLES" ]; then
              VIASH_PAR_IGNORE_SAMPLES="$2"
            else
-              VIASH_PAR_IGNORE_SAMPLES="$VIASH_PAR_IGNORE_SAMPLES,""$2"
+              VIASH_PAR_IGNORE_SAMPLES="$VIASH_PAR_IGNORE_SAMPLES;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --ignore_samples. Use "--help" to get more information on the parameters. && exit 1
            shift 2
@@ -875,7 +879,7 @@ while [[ $# -gt 0 ]]; do
            if [ -z "$VIASH_PAR_IGNORE_SAMPLES" ]; then
              VIASH_PAR_IGNORE_SAMPLES=$(ViashRemoveFlags "$1")
            else
-              VIASH_PAR_IGNORE_SAMPLES="$VIASH_PAR_IGNORE_SAMPLES,"$(ViashRemoveFlags "$1")
+              VIASH_PAR_IGNORE_SAMPLES="$VIASH_PAR_IGNORE_SAMPLES;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
@@ -1793,7 +1797,7 @@ IFS=";" read -ra inputs <<< \$par_input

 if [[ -n "\$par_include_modules" ]]; then
    include_modules=""
-    IFS="," read -ra incl_modules <<< \$par_include_modules
+    IFS=";" read -ra incl_modules <<< \$par_include_modules
    for i in "\${incl_modules[@]}"; do
        include_modules+="--include \$i "
    done
@@ -1802,7 +1806,7 @@ fi

 if [[ -n "\$par_exclude_modules" ]]; then
    exclude_modules=""
-    IFS="," read -ra excl_modules <<< \$par_exclude_modules
+    IFS=";" read -ra excl_modules <<< \$par_exclude_modules
    for i in "\${excl_modules[@]}"; do
        exclude_modules+="--exclude \$i"
    done
@@ -1811,7 +1815,7 @@ fi

 if [[ -n "\$par_ignore_analysis" ]]; then
    ignore=""
-    IFS="," read -ra ignore_analysis <<< \$par_ignore_analysis
+    IFS=";" read -ra ignore_analysis <<< \$par_ignore_analysis
    for i in "\${ignore_analysis[@]}"; do
        ignore+="--ignore \$i "
    done
@@ -1820,7 +1824,7 @@ fi

 if [[ -n "\$par_ignore_samples" ]]; then
    ignore_samples=""
-    IFS="," read -ra ign_samples <<< \$par_ignore_samples
+    IFS=";" read -ra ign_samples <<< \$par_ignore_samples
    for i in "\${ign_samples[@]}"; do
        ignore_samples+="--ignore-samples \$i"
    done