Build branch main with version main (05d48ac)

Build pipeline: viash-hub.rnaseq.main-c7sdt

Source commit: 05d48ac2f8

Source message: Multiple fixes (#26)

* unset argument if not paired

* fix argument name

* add count_read_pairs argument

* output star log

* move biotypes header file into multiqc_custom_biotype component

* move deseq2 header files into deseq2_qc component

* update output defaults

* use biobox main

* add parameters to example

* update component

* update component

* ribo database processing moved to workflow

* clean code, remove unused arguments

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

@@ -195,7 +195,7 @@ dependencies:
   repository:
     type: "vsh"
     repo: "vsh/biobox"
-    tag: "v0.2.0"
+    tag: "main"
 - name: "kallisto/kallisto_quant"
   repository:
     type: "local"
@@ -203,7 +203,7 @@ repositories:
 - type: "vsh"
   name: "biobox"
   repo: "vsh/biobox"
-  tag: "v0.2.0"
+  tag: "main"
 - type: "vsh"
   name: "craftbox"
   repo: "craftbox"
@@ -283,12 +283,13 @@ build_info:
   output: "target/executable/workflows/pseudo_alignment_and_quant"
   executable: "target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant"
   viash_version: "0.9.0"
-  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
+  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
   dependencies:
-  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant"
+  - "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant"
   - "target/nextflow/kallisto/kallisto_quant"
 package_config:
+  name: "rnaseq"
   version: "main"
   info:
     test_resources:
@@ -298,7 +299,7 @@ package_config:
   - type: "vsh"
     name: "biobox"
     repo: "vsh/biobox"
-    tag: "v0.2.0"
+    tag: "main"
   - type: "vsh"
     name: "craftbox"
     repo: "craftbox"

target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant

@@ -780,7 +780,7 @@ fi
 
 # set dependency paths
 VIASH_DEP_KALLISTO_KALLISTO_QUANT="$VIASH_META_RESOURCES_DIR/../../../nextflow/kallisto/kallisto_quant/main.nf"
-VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/main.nf"
+VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf"
 
 ViashDebug "Running command: $(echo $VIASH_CMD)"
 cat << VIASHEOF | eval $VIASH_CMD