Build branch v0.3 with version v0.3.2 (7ad45f3)

Build pipeline: viash-hub.demultiplex.v0.3-92c55

Source commit: 7ad45f3597

Source message: Bump version to 0.3.2

CHANGELOG.md

@@ -1,3 +1,9 @@
+# demultiplex v0.3.2
+
+# Bug fixes
+
+* Ignore empty CSV entries when parsing sample information (PR #29).
+
 # demultiplex v0.3.1
 
 # Minor updates

_viash.yaml

@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.3.1
+version: v0.3.2
 description: |
   Demultiplexing pipeline
 license: MIT

src/dataflow/gather_fastqs_and_validate/main.nf

@@ -50,7 +50,10 @@ workflow run_wf {
               println "Found sample names column '${csv_items[sample_id_column_index]}'."
               return
             }
-            samples += csv_items[sample_id_column_index]
+            def candidate_sample_id = csv_items[sample_id_column_index]
+            if (candidate_sample_id?.trim()) { // Don't add empty csv entries.
+              samples += csv_items[sample_id_column_index]
+            }
           }
           // This return is important! (If 'true' is returned, the parsing stops.)
           return 

target/executable/io/interop_summary_to_csv/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "interop_summary_to_csv"
 namespace: "io"
-version: "v0.3.1"
+version: "v0.3.2"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -116,7 +116,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.1"
+  target_tag: "v0.3.2"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -141,12 +141,12 @@ build_info:
   output: "target/executable/io/interop_summary_to_csv"
   executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
   viash_version: "0.9.0"
-  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+  git_commit: "7ad45f359753205547f96df54ee07733ece655e1"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
+  git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.0-4-g35e1ab8"
+  git_tag: "v0.3.1-3-g7ad45f3"
 package_config:
   name: "demultiplex"
-  version: "v0.3.1"
+  version: "v0.3.2"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -160,7 +160,7 @@ package_config:
     \ := '$id'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/executable/io/interop_summary_to_csv/interop_summary_to_csv

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# interop_summary_to_csv v0.3.1
+# interop_summary_to_csv v0.3.2
 # 
 # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "interop_summary_to_csv v0.3.1"
+  echo "interop_summary_to_csv v0.3.2"
   echo ""
   echo "Input arguments:"
   echo "    --input"
@@ -470,10 +470,10 @@ tar -C /tmp/ --no-same-owner --no-same-permissions -xvf /tmp/interop.tar.gz && \
 mv /tmp/interop-1.3.1-Linux-GNU/bin/index-summary /tmp/interop-1.3.1-Linux-GNU/bin/summary /usr/local/bin/
 
 LABEL org.opencontainers.image.description="Companion container for running component io interop_summary_to_csv"
-LABEL org.opencontainers.image.created="2024-12-11T15:30:29Z"
+LABEL org.opencontainers.image.created="2024-12-11T17:51:30Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+LABEL org.opencontainers.image.revision="7ad45f359753205547f96df54ee07733ece655e1"
-LABEL org.opencontainers.image.version="v0.3.1"
+LABEL org.opencontainers.image.version="v0.3.2"
 
 VIASHDOCKER
   fi
@@ -609,7 +609,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "interop_summary_to_csv v0.3.1"
+            echo "interop_summary_to_csv v0.3.2"
             exit
             ;;
         --input)
@@ -733,7 +733,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.3.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.3.2'
   fi
 
   # print dockerfile

target/executable/io/publish/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "publish"
 namespace: "io"
-version: "v0.3.1"
+version: "v0.3.2"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -152,7 +152,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.1"
+  target_tag: "v0.3.2"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -170,12 +170,12 @@ build_info:
   output: "target/executable/io/publish"
   executable: "target/executable/io/publish/publish"
   viash_version: "0.9.0"
-  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+  git_commit: "7ad45f359753205547f96df54ee07733ece655e1"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
+  git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.0-4-g35e1ab8"
+  git_tag: "v0.3.1-3-g7ad45f3"
 package_config:
   name: "demultiplex"
-  version: "v0.3.1"
+  version: "v0.3.2"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -189,7 +189,7 @@ package_config:
     \ := '$id'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/executable/io/publish/publish

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# publish v0.3.1
+# publish v0.3.2
 # 
 # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "publish v0.3.1"
+  echo "publish v0.3.2"
   echo ""
   echo "Publish the processed results of the run"
   echo ""
@@ -482,10 +482,10 @@ RUN apt-get update && \
   rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.description="Companion container for running component io publish"
-LABEL org.opencontainers.image.created="2024-12-11T15:30:29Z"
+LABEL org.opencontainers.image.created="2024-12-11T17:51:30Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+LABEL org.opencontainers.image.revision="7ad45f359753205547f96df54ee07733ece655e1"
-LABEL org.opencontainers.image.version="v0.3.1"
+LABEL org.opencontainers.image.version="v0.3.2"
 
 VIASHDOCKER
   fi
@@ -621,7 +621,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "publish v0.3.1"
+            echo "publish v0.3.2"
             exit
             ;;
         --input)
@@ -778,7 +778,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.3.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.3.2'
   fi
 
   # print dockerfile

target/executable/io/untar/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "untar"
 namespace: "io"
-version: "v0.3.1"
+version: "v0.3.2"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -130,7 +130,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.1"
+  target_tag: "v0.3.2"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -148,12 +148,12 @@ build_info:
   output: "target/executable/io/untar"
   executable: "target/executable/io/untar/untar"
   viash_version: "0.9.0"
-  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+  git_commit: "7ad45f359753205547f96df54ee07733ece655e1"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
+  git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.0-4-g35e1ab8"
+  git_tag: "v0.3.1-3-g7ad45f3"
 package_config:
   name: "demultiplex"
-  version: "v0.3.1"
+  version: "v0.3.2"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -167,7 +167,7 @@ package_config:
     \ := '$id'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/executable/io/untar/untar

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# untar v0.3.1
+# untar v0.3.2
 # 
 # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "untar v0.3.1"
+  echo "untar v0.3.2"
   echo ""
   echo "Unpack a .tar file. When the contents of the .tar file is just a single"
   echo "directory,"
@@ -476,10 +476,10 @@ RUN apt-get update && \
   rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.description="Companion container for running component io untar"
-LABEL org.opencontainers.image.created="2024-12-11T15:30:29Z"
+LABEL org.opencontainers.image.created="2024-12-11T17:51:30Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+LABEL org.opencontainers.image.revision="7ad45f359753205547f96df54ee07733ece655e1"
-LABEL org.opencontainers.image.version="v0.3.1"
+LABEL org.opencontainers.image.version="v0.3.2"
 
 VIASHDOCKER
   fi
@@ -615,7 +615,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "untar v0.3.1"
+            echo "untar v0.3.2"
             exit
             ;;
         --input)
@@ -745,7 +745,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.3.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.3.2'
   fi
 
   # print dockerfile

target/nextflow/dataflow/combine_samples/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "combine_samples"
 namespace: "dataflow"
-version: "v0.3.1"
+version: "v0.3.2"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -139,12 +139,12 @@ build_info:
   output: "target/nextflow/dataflow/combine_samples"
   executable: "target/nextflow/dataflow/combine_samples/main.nf"
   viash_version: "0.9.0"
-  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+  git_commit: "7ad45f359753205547f96df54ee07733ece655e1"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
+  git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.0-4-g35e1ab8"
+  git_tag: "v0.3.1-3-g7ad45f3"
 package_config:
   name: "demultiplex"
-  version: "v0.3.1"
+  version: "v0.3.2"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -158,7 +158,7 @@ package_config:
     \ := '$id'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/dataflow/combine_samples/main.nf

@@ -1,4 +1,4 @@
-// combine_samples v0.3.1
+// combine_samples v0.3.2
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "combine_samples",
   "namespace" : "dataflow",
-  "version" : "v0.3.1",
+  "version" : "v0.3.2",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -2972,13 +2972,13 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/dataflow/combine_samples",
     "viash_version" : "0.9.0",
-    "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9",
+    "git_commit" : "7ad45f359753205547f96df54ee07733ece655e1",
-    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
+    "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.0-4-g35e1ab8"
+    "git_tag" : "v0.3.1-3-g7ad45f3"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.3.1",
+    "version" : "v0.3.2",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -2995,7 +2995,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
     ],
     "keywords" : [
       "bioinformatics",

target/nextflow/dataflow/combine_samples/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'dataflow/combine_samples'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.1'
+  version = 'v0.3.2'
   description = 'Combine fastq files from across samples into one event with a list of fastq files per orientation.'
 }
 

target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "gather_fastqs_and_validate"
 namespace: "dataflow"
-version: "v0.3.1"
+version: "v0.3.2"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -133,12 +133,12 @@ build_info:
   output: "target/nextflow/dataflow/gather_fastqs_and_validate"
   executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
   viash_version: "0.9.0"
-  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+  git_commit: "7ad45f359753205547f96df54ee07733ece655e1"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
+  git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.0-4-g35e1ab8"
+  git_tag: "v0.3.1-3-g7ad45f3"
 package_config:
   name: "demultiplex"
-  version: "v0.3.1"
+  version: "v0.3.2"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -152,7 +152,7 @@ package_config:
     \ := '$id'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/dataflow/gather_fastqs_and_validate/main.nf

@@ -1,4 +1,4 @@
-// gather_fastqs_and_validate v0.3.1
+// gather_fastqs_and_validate v0.3.2
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "gather_fastqs_and_validate",
   "namespace" : "dataflow",
-  "version" : "v0.3.1",
+  "version" : "v0.3.2",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -2965,13 +2965,13 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
     "viash_version" : "0.9.0",
-    "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9",
+    "git_commit" : "7ad45f359753205547f96df54ee07733ece655e1",
-    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
+    "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.0-4-g35e1ab8"
+    "git_tag" : "v0.3.1-3-g7ad45f3"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.3.1",
+    "version" : "v0.3.2",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -2988,7 +2988,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3063,7 +3063,10 @@ workflow run_wf {
               println "Found sample names column '${csv_items[sample_id_column_index]}'."
               return
             }
-            samples += csv_items[sample_id_column_index]
+            def candidate_sample_id = csv_items[sample_id_column_index]
+            if (candidate_sample_id?.trim()) { // Don't add empty csv entries.
+              samples += csv_items[sample_id_column_index]
+            }
           }
           // This return is important! (If 'true' is returned, the parsing stops.)
           return 

target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'dataflow/gather_fastqs_and_validate'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.1'
+  version = 'v0.3.2'
   description = 'From a directory containing fastq files, gather the files per sample \nand validate according to the contents of the sample sheet.\n'
 }
 

target/nextflow/demultiplex/.config.vsh.yaml

@@ -1,5 +1,5 @@
 name: "demultiplex"
-version: "v0.3.1"
+version: "v0.3.2"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -220,9 +220,9 @@ build_info:
   output: "target/nextflow/demultiplex"
   executable: "target/nextflow/demultiplex/main.nf"
   viash_version: "0.9.0"
-  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+  git_commit: "7ad45f359753205547f96df54ee07733ece655e1"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
+  git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.0-4-g35e1ab8"
+  git_tag: "v0.3.1-3-g7ad45f3"
   dependencies:
   - "target/nextflow/io/untar"
   - "target/nextflow/dataflow/gather_fastqs_and_validate"
@@ -234,7 +234,7 @@ build_info:
   - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/multiqc"
 package_config:
   name: "demultiplex"
-  version: "v0.3.1"
+  version: "v0.3.2"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -248,7 +248,7 @@ package_config:
     \ := '$id'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/demultiplex/main.nf

@@ -1,4 +1,4 @@
-// demultiplex v0.3.1
+// demultiplex v0.3.2
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2805,7 +2805,7 @@ meta = [
   "resources_dir": moduleDir.toRealPath().normalize(),
   "config": processConfig(readJsonBlob('''{
   "name" : "demultiplex",
-  "version" : "v0.3.1",
+  "version" : "v0.3.2",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3088,13 +3088,13 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/demultiplex",
     "viash_version" : "0.9.0",
-    "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9",
+    "git_commit" : "7ad45f359753205547f96df54ee07733ece655e1",
-    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
+    "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.0-4-g35e1ab8"
+    "git_tag" : "v0.3.1-3-g7ad45f3"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.3.1",
+    "version" : "v0.3.2",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3111,7 +3111,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
     ],
     "keywords" : [
       "bioinformatics",

target/nextflow/demultiplex/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'demultiplex'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.1'
+  version = 'v0.3.2'
   description = 'Demultiplexing of raw sequencing data'
 }
 

target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "interop_summary_to_csv"
 namespace: "io"
-version: "v0.3.1"
+version: "v0.3.2"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -116,7 +116,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.1"
+  target_tag: "v0.3.2"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -141,12 +141,12 @@ build_info:
   output: "target/nextflow/io/interop_summary_to_csv"
   executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
   viash_version: "0.9.0"
-  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+  git_commit: "7ad45f359753205547f96df54ee07733ece655e1"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
+  git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.0-4-g35e1ab8"
+  git_tag: "v0.3.1-3-g7ad45f3"
 package_config:
   name: "demultiplex"
-  version: "v0.3.1"
+  version: "v0.3.2"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -160,7 +160,7 @@ package_config:
     \ := '$id'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/io/interop_summary_to_csv/main.nf

@@ -1,4 +1,4 @@
-// interop_summary_to_csv v0.3.1
+// interop_summary_to_csv v0.3.2
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "interop_summary_to_csv",
   "namespace" : "io",
-  "version" : "v0.3.1",
+  "version" : "v0.3.2",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -2947,7 +2947,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.1",
+      "target_tag" : "v0.3.2",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -2977,13 +2977,13 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/interop_summary_to_csv",
     "viash_version" : "0.9.0",
-    "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9",
+    "git_commit" : "7ad45f359753205547f96df54ee07733ece655e1",
-    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
+    "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.0-4-g35e1ab8"
+    "git_tag" : "v0.3.1-3-g7ad45f3"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.3.1",
+    "version" : "v0.3.2",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3000,7 +3000,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3423,7 +3423,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/demultiplex/io/interop_summary_to_csv",
-    "tag" : "v0.3.1"
+    "tag" : "v0.3.2"
   },
   "tag" : "$id"
 }'''),

target/nextflow/io/interop_summary_to_csv/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'io/interop_summary_to_csv'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.1'
+  version = 'v0.3.2'
 }
 
 process.container = 'nextflow/bash:latest'

target/nextflow/io/publish/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "publish"
 namespace: "io"
-version: "v0.3.1"
+version: "v0.3.2"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -152,7 +152,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.1"
+  target_tag: "v0.3.2"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -170,12 +170,12 @@ build_info:
   output: "target/nextflow/io/publish"
   executable: "target/nextflow/io/publish/main.nf"
   viash_version: "0.9.0"
-  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+  git_commit: "7ad45f359753205547f96df54ee07733ece655e1"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
+  git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.0-4-g35e1ab8"
+  git_tag: "v0.3.1-3-g7ad45f3"
 package_config:
   name: "demultiplex"
-  version: "v0.3.1"
+  version: "v0.3.2"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -189,7 +189,7 @@ package_config:
     \ := '$id'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/io/publish/main.nf

@@ -1,4 +1,4 @@
-// publish v0.3.1
+// publish v0.3.2
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "publish",
   "namespace" : "io",
-  "version" : "v0.3.1",
+  "version" : "v0.3.2",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -2989,7 +2989,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.1",
+      "target_tag" : "v0.3.2",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3012,13 +3012,13 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish",
     "viash_version" : "0.9.0",
-    "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9",
+    "git_commit" : "7ad45f359753205547f96df54ee07733ece655e1",
-    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
+    "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.0-4-g35e1ab8"
+    "git_tag" : "v0.3.1-3-g7ad45f3"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.3.1",
+    "version" : "v0.3.2",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3035,7 +3035,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3481,7 +3481,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/demultiplex/io/publish",
-    "tag" : "v0.3.1"
+    "tag" : "v0.3.2"
   },
   "tag" : "$id"
 }'''),

target/nextflow/io/publish/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'io/publish'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.1'
+  version = 'v0.3.2'
   description = 'Publish the processed results of the run'
 }
 

target/nextflow/io/untar/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "untar"
 namespace: "io"
-version: "v0.3.1"
+version: "v0.3.2"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -130,7 +130,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.1"
+  target_tag: "v0.3.2"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -148,12 +148,12 @@ build_info:
   output: "target/nextflow/io/untar"
   executable: "target/nextflow/io/untar/main.nf"
   viash_version: "0.9.0"
-  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+  git_commit: "7ad45f359753205547f96df54ee07733ece655e1"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
+  git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.0-4-g35e1ab8"
+  git_tag: "v0.3.1-3-g7ad45f3"
 package_config:
   name: "demultiplex"
-  version: "v0.3.1"
+  version: "v0.3.2"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -167,7 +167,7 @@ package_config:
     \ := '$id'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/io/untar/main.nf

@@ -1,4 +1,4 @@
-// untar v0.3.1
+// untar v0.3.2
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "untar",
   "namespace" : "io",
-  "version" : "v0.3.1",
+  "version" : "v0.3.2",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -2966,7 +2966,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.1",
+      "target_tag" : "v0.3.2",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -2989,13 +2989,13 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/untar",
     "viash_version" : "0.9.0",
-    "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9",
+    "git_commit" : "7ad45f359753205547f96df54ee07733ece655e1",
-    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
+    "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.0-4-g35e1ab8"
+    "git_tag" : "v0.3.1-3-g7ad45f3"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.3.1",
+    "version" : "v0.3.2",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3012,7 +3012,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3465,7 +3465,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/demultiplex/io/untar",
-    "tag" : "v0.3.1"
+    "tag" : "v0.3.2"
   },
   "tag" : "$id"
 }'''),

target/nextflow/io/untar/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'io/untar'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.1'
+  version = 'v0.3.2'
   description = 'Unpack a .tar file. When the contents of the .tar file is just a single directory,\nput the contents of the directory into the output folder instead of that directory.\n'
 }
 

target/nextflow/runner/.config.vsh.yaml

@@ -1,5 +1,5 @@
 name: "runner"
-version: "v0.3.1"
+version: "v0.3.2"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -182,15 +182,15 @@ build_info:
   output: "target/nextflow/runner"
   executable: "target/nextflow/runner/main.nf"
   viash_version: "0.9.0"
-  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+  git_commit: "7ad45f359753205547f96df54ee07733ece655e1"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
+  git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.0-4-g35e1ab8"
+  git_tag: "v0.3.1-3-g7ad45f3"
   dependencies:
   - "target/nextflow/demultiplex"
   - "target/nextflow/io/publish"
 package_config:
   name: "demultiplex"
-  version: "v0.3.1"
+  version: "v0.3.2"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -204,7 +204,7 @@ package_config:
     \ := '$id'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/runner/main.nf

@@ -1,4 +1,4 @@
-// runner v0.3.1
+// runner v0.3.2
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2805,7 +2805,7 @@ meta = [
   "resources_dir": moduleDir.toRealPath().normalize(),
   "config": processConfig(readJsonBlob('''{
   "name" : "runner",
-  "version" : "v0.3.1",
+  "version" : "v0.3.2",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3027,13 +3027,13 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/runner",
     "viash_version" : "0.9.0",
-    "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9",
+    "git_commit" : "7ad45f359753205547f96df54ee07733ece655e1",
-    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
+    "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.0-4-g35e1ab8"
+    "git_tag" : "v0.3.1-3-g7ad45f3"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.3.1",
+    "version" : "v0.3.2",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3050,7 +3050,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
     ],
     "keywords" : [
       "bioinformatics",

target/nextflow/runner/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'runner'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.1'
+  version = 'v0.3.2'
   description = 'Runner for demultiplexing of raw sequencing data'
 }