Build branch main with version main (1d87dc7)

Build pipeline: viash-hub.rnaseq.main-g2rlq

Source commit: 1d87dc7c24

Source message: Multiple fixes (#23)

* multiple fixes

* update arguments and add test

* fix biobox module calls

* fix dependency

* add rsem merge counts

* exclude general stats in multiqc report

* output markduplicates metrics

* rename output reference files

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

@@ -139,8 +139,6 @@ argument_groups:
   - type: "file"
     name: "--pseudo_multiqc"
     info: null
-    default:
-    - "$id.quant.log"
     must_exist: true
     create_parent: true
     required: false
@@ -151,7 +149,7 @@ argument_groups:
     name: "--quant_out_dir"
     info: null
     default:
-    - "$id.salmon_quant"
+    - "$id.quant"
     must_exist: true
     create_parent: true
     required: false
@@ -285,8 +283,8 @@ 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: "64aad6a006818388eceffe024b1701b3eae06bee"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
   dependencies:
   - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant"
   - "target/nextflow/kallisto/kallisto_quant"

target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant

@@ -239,11 +239,10 @@ function ViashHelp {
   echo "Output:"
   echo "    --pseudo_multiqc"
   echo "        type: file, output, file must exist"
-  echo "        default: \$id.quant.log"
   echo ""
   echo "    --quant_out_dir"
   echo "        type: file, output, file must exist"
-  echo "        default: \$id.salmon_quant"
+  echo "        default: \$id.quant"
   echo ""
   echo "    --salmon_quant_results_file"
   echo "        type: file, output, file must exist"
@@ -608,11 +607,8 @@ fi
 if [ -z ${VIASH_PAR_LIB_TYPE+x} ]; then
   VIASH_PAR_LIB_TYPE=""
 fi
-if [ -z ${VIASH_PAR_PSEUDO_MULTIQC+x} ]; then
-  VIASH_PAR_PSEUDO_MULTIQC="\$id.quant.log"
-fi
 if [ -z ${VIASH_PAR_QUANT_OUT_DIR+x} ]; then
-  VIASH_PAR_QUANT_OUT_DIR="\$id.salmon_quant"
+  VIASH_PAR_QUANT_OUT_DIR="\$id.quant"
 fi
 if [ -z ${VIASH_PAR_SALMON_QUANT_RESULTS_FILE+x} ]; then
   VIASH_PAR_SALMON_QUANT_RESULTS_FILE="\$id.quant.sf"
@@ -852,11 +848,16 @@ workflow run_wf {
             lib_type: state.lib_type ]
         },
         toState: [ 
-          "quant_results_dir": "output",
+          "quant_out_dir": "output",
           "salmon_quant_results_file": "quant_results" 
         ]
     )
 
+    | map { id, state -> 
+      def mod_state = (state.pseudo_aligner == 'salmon') ? state + [pseudo_multiqc: state.quant_out_dir] : state
+      [ id, mod_state ]
+    }
+
     | kallisto_quant.run ( 
         runIf: { id, state -> state.pseudo_aligner == 'kallisto'},
         fromState: [