Build branch main with version main (f52978a)

Build pipeline: viash-hub.rnaseq.main-k4ttq

Source commit: f52978a0e2

Source message: Fix summarizedexperiment build (#42)

target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml

@@ -455,6 +455,9 @@ description: "A viash sub-workflow for genome alignment and quantification stage
   \ nf-core/rnaseq pipeline.\n"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -594,9 +597,9 @@ build_info:
   engine: "native"
   output: "target/executable/workflows/genome_alignment_and_quant"
   executable: "target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant"
-  viash_version: "0.9.0"
-  git_commit: "2b3d511b34246648b934fd1dc99b22e0a71c37f2"
-  git_remote: "https://x-access-token:ghs_mpjpezoXRPhvITbEzvFPaxzcp8yfML2ITu9P@github.com/viash-hub/rnaseq"
+  viash_version: "0.9.2"
+  git_commit: "f52978a0e25cae182b7874b4b8aa3afc183e880e"
+  git_remote: "https://github.com/viash-hub/rnaseq"
   dependencies:
   - "target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads"
   - "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort"
@@ -613,7 +616,7 @@ package_config:
   version: "main"
   info:
     test_resources:
-    - path: "gs://viash-hub-test-data/rnaseq/v1"
+    - path: "gs://viash-hub-resources/rnaseq/v1"
       dest: "testData"
   repositories:
   - type: "vsh"
@@ -624,7 +627,7 @@ package_config:
     name: "craftbox"
     repo: "craftbox"
     tag: "v0.1.0"
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:

target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant

@@ -2,7 +2,7 @@
 
 # genome_alignment_and_quant main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -169,6 +169,12 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
+
+# initialise variables
+VIASH_MODE='run'
+VIASH_ENGINE_ID='native'
+
+
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
   echo "genome_alignment_and_quant main"
@@ -363,12 +369,19 @@ function ViashHelp {
   echo "        type: file, output, file must exist"
   echo "        default: \$id.transcript.bam"
   echo "        Transcript BAM file (optional)"
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: native."
+  echo "        Default: native"
 }
 
-# initialise variables
-VIASH_MODE='run'
-VIASH_ENGINE_ID='native'
-
 # initialise array
 VIASH_POSITIONAL_ARGS=''