Build branch demultiplex/v0.5 with version v0.5.1 to demultiplex on branch v0.5 (85af189)

Build pipeline: viash-hub.demultiplex.v0.5-g6gfq

Source commit: 85af1895d7

Source message: Bump version to v0.5.1

CHANGELOG.md

@@ -1,3 +1,11 @@
+# demultiplex v0.5.1
+
+## Bug fixes
+
+* Fix disabling `publishFilesProc` and `publishStateProc` for `runner` workflow (PR #63).
+
+* Avoid double slashes in the publish directory path in order to not create empty objects on S3 (PR #64).
+
 # demultiplex v0.5.0
 
 ## Breaking changes

_viash.yaml

@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.5.0
+version: v0.5.1
 description: |
   Demultiplexing pipeline
 license: MIT
@@ -16,6 +16,6 @@ config_mods: |
   .requirements.commands += ['ps']
   .runners[.type == 'nextflow'].directives.tag := '$id'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 organization: vsh

src/runner/config.vsh.yaml

@@ -64,7 +64,7 @@ resources:
   - type: nextflow_script
     path: main.nf
     entrypoint: run_wf
-  - path: disable_publishfiles_process.config
+  - path: disable_publish_processes.config
 test_resources:
   - type: nextflow_script
     path: test.nf
@@ -80,7 +80,7 @@ runners:
   - type: nextflow
     config: 
       script: 
-        - includeConfig("disable_publishfiles_process.config")
+        - includeConfig("disable_publish_processes.config")
 
 engines:
   - type: native

src/runner/disable_publish_processes.config

@@ -2,4 +2,8 @@ process {
   withName: publishFilesProc {
     publishDir = [ enabled: false ]
   }
+
+  withName: publishStatesProc {
+    publishDir = [ enabled: false ]
+  }
 }

src/runner/main.nf

@@ -9,6 +9,10 @@ session = nextflow.Nextflow.getSession()
 final service = session.publishDirExecutorService()
 
 
+// S3 paths containing double slashes might cause issues with empty objects being created
+// Remove trailing slashes from the publish dir. The params map is immutable, so create a copy
+def publish_dir = params.publish_dir - ~/\/+$/
+
 workflow run_wf {
   take:
     input_ch
@@ -67,7 +71,7 @@ workflow run_wf {
           // The name of the output file for the run information is determined by the input file name.
           def run_information_output_1 = "${prefix}${state.output_run_information.getName()}"
 
-          println("Publising to ${params.publish_dir}/${prefix}")
+          println("Publishing to ${publish_dir}/${prefix}")
           [
             input: state.output,
             input_sample_qc: state.output_sample_qc,
@@ -91,7 +95,7 @@ workflow run_wf {
         },
         directives: [
           publishDir: [
-            path: "${params.publish_dir}", 
+            path: publish_dir,
             overwrite: false,
             mode: "copy"
           ]

src/runner/nextflow.config

@@ -6,6 +6,10 @@ process {
   withName: publishStatesProc {
     publishDir = [ enabled: false ]
   }
+
+  withName: publishFilesProc {
+    publishDir = [ enabled: false ]
+  }
 }
 
 params {

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

@@ -1,6 +1,6 @@
 name: "interop_summary_to_csv"
 namespace: "io"
-version: "v0.5.0"
+version: "v0.5.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -135,7 +135,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.0"
+  target_tag: "v0.5.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -160,11 +160,11 @@ build_info:
   output: "target/executable/io/interop_summary_to_csv"
   executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
   viash_version: "0.9.4"
-  git_commit: "c516993b851efad3beee4db280ab24ef4c4bfb98"
+  git_commit: "85af1895d7dccec3ce70ec2a180a85ccd4e7c47c"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"
-  version: "v0.5.0"
+  version: "v0.5.1"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -176,11 +176,11 @@ package_config:
   config_mods:
   - ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag\
     \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
-    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    .runners[.type == 'nextflow'].config.script += 'includeConfig(\"nextflow_labels.config\"\
     )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/executable/io/interop_summary_to_csv/_viash.yaml

@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.5.0
+version: v0.5.1
 description: |
   Demultiplexing pipeline
 license: MIT
@@ -16,6 +16,6 @@ config_mods: |
   .requirements.commands += ['ps']
   .runners[.type == 'nextflow'].directives.tag := '$id'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 organization: vsh

target/executable/io/interop_summary_to_csv/interop_summary_to_csv

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# interop_summary_to_csv v0.5.0
+# interop_summary_to_csv v0.5.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -454,10 +454,10 @@ 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="2025-09-03T12:57:50Z"
+LABEL org.opencontainers.image.created="2025-09-11T09:44:31Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="c516993b851efad3beee4db280ab24ef4c4bfb98"
-LABEL org.opencontainers.image.version="v0.5.0"
+LABEL org.opencontainers.image.revision="85af1895d7dccec3ce70ec2a180a85ccd4e7c47c"
+LABEL org.opencontainers.image.version="v0.5.1"
 
 VIASHDOCKER
   fi
@@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "interop_summary_to_csv v0.5.0"
+  echo "interop_summary_to_csv v0.5.1"
   echo ""
   echo "Input arguments:"
   echo "    --input"
@@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "interop_summary_to_csv v0.5.0"
+            echo "interop_summary_to_csv v0.5.1"
             exit
             ;;
         --input)
@@ -759,7 +759,7 @@ if [[ "$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:v0.5.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.5.1'
   fi
 
   # print dockerfile

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

@@ -1,6 +1,6 @@
 name: "publish"
 namespace: "io"
-version: "v0.5.0"
+version: "v0.5.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -204,7 +204,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.0"
+  target_tag: "v0.5.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -222,11 +222,11 @@ build_info:
   output: "target/executable/io/publish"
   executable: "target/executable/io/publish/publish"
   viash_version: "0.9.4"
-  git_commit: "c516993b851efad3beee4db280ab24ef4c4bfb98"
+  git_commit: "85af1895d7dccec3ce70ec2a180a85ccd4e7c47c"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"
-  version: "v0.5.0"
+  version: "v0.5.1"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -238,11 +238,11 @@ package_config:
   config_mods:
   - ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag\
     \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
-    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    .runners[.type == 'nextflow'].config.script += 'includeConfig(\"nextflow_labels.config\"\
     )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/executable/io/publish/_viash.yaml

@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.5.0
+version: v0.5.1
 description: |
   Demultiplexing pipeline
 license: MIT
@@ -16,6 +16,6 @@ config_mods: |
   .requirements.commands += ['ps']
   .runners[.type == 'nextflow'].directives.tag := '$id'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 organization: vsh

target/executable/io/publish/publish

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# publish v0.5.0
+# publish v0.5.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -450,10 +450,10 @@ 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="2025-09-03T12:57:51Z"
+LABEL org.opencontainers.image.created="2025-09-11T09:44:31Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="c516993b851efad3beee4db280ab24ef4c4bfb98"
-LABEL org.opencontainers.image.version="v0.5.0"
+LABEL org.opencontainers.image.revision="85af1895d7dccec3ce70ec2a180a85ccd4e7c47c"
+LABEL org.opencontainers.image.version="v0.5.1"
 
 VIASHDOCKER
   fi
@@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "publish v0.5.0"
+  echo "publish v0.5.1"
   echo ""
   echo "Publish the processed results of the run"
   echo ""
@@ -662,7 +662,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "publish v0.5.0"
+            echo "publish v0.5.1"
             exit
             ;;
         --input)
@@ -869,7 +869,7 @@ if [[ "$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:v0.5.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.5.1'
   fi
 
   # print dockerfile

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

@@ -1,6 +1,6 @@
 name: "untar"
 namespace: "io"
-version: "v0.5.0"
+version: "v0.5.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -141,7 +141,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.0"
+  target_tag: "v0.5.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -159,11 +159,11 @@ build_info:
   output: "target/executable/io/untar"
   executable: "target/executable/io/untar/untar"
   viash_version: "0.9.4"
-  git_commit: "c516993b851efad3beee4db280ab24ef4c4bfb98"
+  git_commit: "85af1895d7dccec3ce70ec2a180a85ccd4e7c47c"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"
-  version: "v0.5.0"
+  version: "v0.5.1"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -175,11 +175,11 @@ package_config:
   config_mods:
   - ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag\
     \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
-    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    .runners[.type == 'nextflow'].config.script += 'includeConfig(\"nextflow_labels.config\"\
     )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/executable/io/untar/_viash.yaml

@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.5.0
+version: v0.5.1
 description: |
   Demultiplexing pipeline
 license: MIT
@@ -16,6 +16,6 @@ config_mods: |
   .requirements.commands += ['ps']
   .runners[.type == 'nextflow'].directives.tag := '$id'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 organization: vsh

target/executable/io/untar/untar

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# untar v0.5.0
+# untar v0.5.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -450,10 +450,10 @@ 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="2025-09-03T12:57:50Z"
+LABEL org.opencontainers.image.created="2025-09-11T09:44:30Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="c516993b851efad3beee4db280ab24ef4c4bfb98"
-LABEL org.opencontainers.image.version="v0.5.0"
+LABEL org.opencontainers.image.revision="85af1895d7dccec3ce70ec2a180a85ccd4e7c47c"
+LABEL org.opencontainers.image.version="v0.5.1"
 
 VIASHDOCKER
   fi
@@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "untar v0.5.0"
+  echo "untar v0.5.1"
   echo ""
   echo "Unpack a .tar file. When the contents of the .tar file is just a single"
   echo "directory,"
@@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "untar v0.5.0"
+            echo "untar v0.5.1"
             exit
             ;;
         --input)
@@ -771,7 +771,7 @@ if [[ "$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:v0.5.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.5.1'
   fi
 
   # print dockerfile

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

@@ -1,6 +1,6 @@
 name: "combine_samples"
 namespace: "dataflow"
-version: "v0.5.0"
+version: "v0.5.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -168,11 +168,11 @@ build_info:
   output: "target/nextflow/dataflow/combine_samples"
   executable: "target/nextflow/dataflow/combine_samples/main.nf"
   viash_version: "0.9.4"
-  git_commit: "c516993b851efad3beee4db280ab24ef4c4bfb98"
+  git_commit: "85af1895d7dccec3ce70ec2a180a85ccd4e7c47c"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"
-  version: "v0.5.0"
+  version: "v0.5.1"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -184,11 +184,11 @@ package_config:
   config_mods:
   - ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag\
     \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
-    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    .runners[.type == 'nextflow'].config.script += 'includeConfig(\"nextflow_labels.config\"\
     )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/dataflow/combine_samples/_viash.yaml

@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.5.0
+version: v0.5.1
 description: |
   Demultiplexing pipeline
 license: MIT
@@ -16,6 +16,6 @@ config_mods: |
   .requirements.commands += ['ps']
   .runners[.type == 'nextflow'].directives.tag := '$id'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 organization: vsh

target/nextflow/dataflow/combine_samples/main.nf

@@ -1,4 +1,4 @@
-// combine_samples v0.5.0
+// combine_samples v0.5.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "combine_samples",
   "namespace" : "dataflow",
-  "version" : "v0.5.0",
+  "version" : "v0.5.1",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3235,12 +3235,12 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/dataflow/combine_samples",
     "viash_version" : "0.9.4",
-    "git_commit" : "c516993b851efad3beee4db280ab24ef4c4bfb98",
+    "git_commit" : "85af1895d7dccec3ce70ec2a180a85ccd4e7c47c",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.5.0",
+    "version" : "v0.5.1",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3254,10 +3254,10 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
+      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.5.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
     ],
     "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 = 'v0.5.0'
+  version = 'v0.5.1'
   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: "v0.5.0"
+version: "v0.5.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -159,11 +159,11 @@ build_info:
   output: "target/nextflow/dataflow/gather_fastqs_and_validate"
   executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
   viash_version: "0.9.4"
-  git_commit: "c516993b851efad3beee4db280ab24ef4c4bfb98"
+  git_commit: "85af1895d7dccec3ce70ec2a180a85ccd4e7c47c"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"
-  version: "v0.5.0"
+  version: "v0.5.1"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -175,11 +175,11 @@ package_config:
   config_mods:
   - ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag\
     \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
-    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    .runners[.type == 'nextflow'].config.script += 'includeConfig(\"nextflow_labels.config\"\
     )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/dataflow/gather_fastqs_and_validate/_viash.yaml

@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.5.0
+version: v0.5.1
 description: |
   Demultiplexing pipeline
 license: MIT
@@ -16,6 +16,6 @@ config_mods: |
   .requirements.commands += ['ps']
   .runners[.type == 'nextflow'].directives.tag := '$id'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 organization: vsh

target/nextflow/dataflow/gather_fastqs_and_validate/main.nf

@@ -1,4 +1,4 @@
-// gather_fastqs_and_validate v0.5.0
+// gather_fastqs_and_validate v0.5.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "gather_fastqs_and_validate",
   "namespace" : "dataflow",
-  "version" : "v0.5.0",
+  "version" : "v0.5.1",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3232,12 +3232,12 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
     "viash_version" : "0.9.4",
-    "git_commit" : "c516993b851efad3beee4db280ab24ef4c4bfb98",
+    "git_commit" : "85af1895d7dccec3ce70ec2a180a85ccd4e7c47c",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.5.0",
+    "version" : "v0.5.1",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3251,10 +3251,10 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
+      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.5.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
     ],
     "keywords" : [
       "bioinformatics",

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 = 'v0.5.0'
+  version = 'v0.5.1'
   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: "v0.5.0"
+version: "v0.5.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -268,7 +268,7 @@ build_info:
   output: "target/nextflow/demultiplex"
   executable: "target/nextflow/demultiplex/main.nf"
   viash_version: "0.9.4"
-  git_commit: "c516993b851efad3beee4db280ab24ef4c4bfb98"
+  git_commit: "85af1895d7dccec3ce70ec2a180a85ccd4e7c47c"
   git_remote: "https://github.com/viash-hub/demultiplex"
   dependencies:
   - "target/nextflow/io/untar"
@@ -282,7 +282,7 @@ build_info:
   - "target/nextflow/detect_demultiplexer"
 package_config:
   name: "demultiplex"
-  version: "v0.5.0"
+  version: "v0.5.1"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -294,11 +294,11 @@ package_config:
   config_mods:
   - ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag\
     \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
-    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    .runners[.type == 'nextflow'].config.script += 'includeConfig(\"nextflow_labels.config\"\
     )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/demultiplex/_viash.yaml

@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.5.0
+version: v0.5.1
 description: |
   Demultiplexing pipeline
 license: MIT
@@ -16,6 +16,6 @@ config_mods: |
   .requirements.commands += ['ps']
   .runners[.type == 'nextflow'].directives.tag := '$id'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 organization: vsh

target/nextflow/demultiplex/main.nf

@@ -1,4 +1,4 @@
-// demultiplex v0.5.0
+// demultiplex v0.5.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3031,7 +3031,7 @@ meta = [
   "resources_dir": moduleDir.toRealPath().normalize(),
   "config": processConfig(readJsonBlob('''{
   "name" : "demultiplex",
-  "version" : "v0.5.0",
+  "version" : "v0.5.1",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3380,12 +3380,12 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/demultiplex",
     "viash_version" : "0.9.4",
-    "git_commit" : "c516993b851efad3beee4db280ab24ef4c4bfb98",
+    "git_commit" : "85af1895d7dccec3ce70ec2a180a85ccd4e7c47c",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.5.0",
+    "version" : "v0.5.1",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3399,10 +3399,10 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
+      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.5.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
     ],
     "keywords" : [
       "bioinformatics",

target/nextflow/demultiplex/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'demultiplex'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.5.0'
+  version = 'v0.5.1'
   description = 'Demultiplexing of raw sequencing data'
 }
 

target/nextflow/detect_demultiplexer/.config.vsh.yaml

@@ -1,5 +1,5 @@
 name: "detect_demultiplexer"
-version: "v0.5.0"
+version: "v0.5.1"
 argument_groups:
 - name: "Arguments"
   arguments:
@@ -168,11 +168,11 @@ build_info:
   output: "target/nextflow/detect_demultiplexer"
   executable: "target/nextflow/detect_demultiplexer/main.nf"
   viash_version: "0.9.4"
-  git_commit: "c516993b851efad3beee4db280ab24ef4c4bfb98"
+  git_commit: "85af1895d7dccec3ce70ec2a180a85ccd4e7c47c"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"
-  version: "v0.5.0"
+  version: "v0.5.1"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -184,11 +184,11 @@ package_config:
   config_mods:
   - ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag\
     \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
-    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    .runners[.type == 'nextflow'].config.script += 'includeConfig(\"nextflow_labels.config\"\
     )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/detect_demultiplexer/_viash.yaml

@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.5.0
+version: v0.5.1
 description: |
   Demultiplexing pipeline
 license: MIT
@@ -16,6 +16,6 @@ config_mods: |
   .requirements.commands += ['ps']
   .runners[.type == 'nextflow'].directives.tag := '$id'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 organization: vsh

target/nextflow/detect_demultiplexer/main.nf

@@ -1,4 +1,4 @@
-// detect_demultiplexer v0.5.0
+// detect_demultiplexer v0.5.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3031,7 +3031,7 @@ meta = [
   "resources_dir": moduleDir.toRealPath().normalize(),
   "config": processConfig(readJsonBlob('''{
   "name" : "detect_demultiplexer",
-  "version" : "v0.5.0",
+  "version" : "v0.5.1",
   "argument_groups" : [
     {
       "name" : "Arguments",
@@ -3224,12 +3224,12 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/detect_demultiplexer",
     "viash_version" : "0.9.4",
-    "git_commit" : "c516993b851efad3beee4db280ab24ef4c4bfb98",
+    "git_commit" : "85af1895d7dccec3ce70ec2a180a85ccd4e7c47c",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.5.0",
+    "version" : "v0.5.1",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3243,10 +3243,10 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
+      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.5.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
     ],
     "keywords" : [
       "bioinformatics",

target/nextflow/detect_demultiplexer/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'detect_demultiplexer'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.5.0'
+  version = 'v0.5.1'
   description = 'Detects the demultiplexer and accompanying sample information file which can be \nused to generate the fastq files.\n'
 }
 

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

@@ -1,6 +1,6 @@
 name: "interop_summary_to_csv"
 namespace: "io"
-version: "v0.5.0"
+version: "v0.5.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -135,7 +135,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.0"
+  target_tag: "v0.5.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -160,11 +160,11 @@ build_info:
   output: "target/nextflow/io/interop_summary_to_csv"
   executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
   viash_version: "0.9.4"
-  git_commit: "c516993b851efad3beee4db280ab24ef4c4bfb98"
+  git_commit: "85af1895d7dccec3ce70ec2a180a85ccd4e7c47c"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"
-  version: "v0.5.0"
+  version: "v0.5.1"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -176,11 +176,11 @@ package_config:
   config_mods:
   - ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag\
     \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
-    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    .runners[.type == 'nextflow'].config.script += 'includeConfig(\"nextflow_labels.config\"\
     )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/io/interop_summary_to_csv/_viash.yaml

@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.5.0
+version: v0.5.1
 description: |
   Demultiplexing pipeline
 license: MIT
@@ -16,6 +16,6 @@ config_mods: |
   .requirements.commands += ['ps']
   .runners[.type == 'nextflow'].directives.tag := '$id'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 organization: vsh

target/nextflow/io/interop_summary_to_csv/main.nf

@@ -1,4 +1,4 @@
-// interop_summary_to_csv v0.5.0
+// interop_summary_to_csv v0.5.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "interop_summary_to_csv",
   "namespace" : "io",
-  "version" : "v0.5.0",
+  "version" : "v0.5.1",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3203,7 +3203,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.5.0",
+      "target_tag" : "v0.5.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3233,12 +3233,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/interop_summary_to_csv",
     "viash_version" : "0.9.4",
-    "git_commit" : "c516993b851efad3beee4db280ab24ef4c4bfb98",
+    "git_commit" : "85af1895d7dccec3ce70ec2a180a85ccd4e7c47c",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.5.0",
+    "version" : "v0.5.1",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3252,10 +3252,10 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
+      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.5.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3699,7 +3699,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/demultiplex/io/interop_summary_to_csv",
-    "tag" : "v0.5.0"
+    "tag" : "v0.5.1"
   },
   "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 = 'v0.5.0'
+  version = 'v0.5.1'
 }
 
 process.container = 'nextflow/bash:latest'

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

@@ -1,6 +1,6 @@
 name: "publish"
 namespace: "io"
-version: "v0.5.0"
+version: "v0.5.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -204,7 +204,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.0"
+  target_tag: "v0.5.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -222,11 +222,11 @@ build_info:
   output: "target/nextflow/io/publish"
   executable: "target/nextflow/io/publish/main.nf"
   viash_version: "0.9.4"
-  git_commit: "c516993b851efad3beee4db280ab24ef4c4bfb98"
+  git_commit: "85af1895d7dccec3ce70ec2a180a85ccd4e7c47c"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"
-  version: "v0.5.0"
+  version: "v0.5.1"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -238,11 +238,11 @@ package_config:
   config_mods:
   - ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag\
     \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
-    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    .runners[.type == 'nextflow'].config.script += 'includeConfig(\"nextflow_labels.config\"\
     )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/io/publish/_viash.yaml

@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.5.0
+version: v0.5.1
 description: |
   Demultiplexing pipeline
 license: MIT
@@ -16,6 +16,6 @@ config_mods: |
   .requirements.commands += ['ps']
   .runners[.type == 'nextflow'].directives.tag := '$id'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 organization: vsh

target/nextflow/io/publish/main.nf

@@ -1,4 +1,4 @@
-// publish v0.5.0
+// publish v0.5.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "publish",
   "namespace" : "io",
-  "version" : "v0.5.0",
+  "version" : "v0.5.1",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3279,7 +3279,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.5.0",
+      "target_tag" : "v0.5.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3302,12 +3302,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish",
     "viash_version" : "0.9.4",
-    "git_commit" : "c516993b851efad3beee4db280ab24ef4c4bfb98",
+    "git_commit" : "85af1895d7dccec3ce70ec2a180a85ccd4e7c47c",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.5.0",
+    "version" : "v0.5.1",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3321,10 +3321,10 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
+      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.5.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3799,7 +3799,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/demultiplex/io/publish",
-    "tag" : "v0.5.0"
+    "tag" : "v0.5.1"
   },
   "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 = 'v0.5.0'
+  version = 'v0.5.1'
   description = 'Publish the processed results of the run'
 }
 

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

@@ -1,6 +1,6 @@
 name: "untar"
 namespace: "io"
-version: "v0.5.0"
+version: "v0.5.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -141,7 +141,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.0"
+  target_tag: "v0.5.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -159,11 +159,11 @@ build_info:
   output: "target/nextflow/io/untar"
   executable: "target/nextflow/io/untar/main.nf"
   viash_version: "0.9.4"
-  git_commit: "c516993b851efad3beee4db280ab24ef4c4bfb98"
+  git_commit: "85af1895d7dccec3ce70ec2a180a85ccd4e7c47c"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"
-  version: "v0.5.0"
+  version: "v0.5.1"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -175,11 +175,11 @@ package_config:
   config_mods:
   - ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag\
     \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
-    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    .runners[.type == 'nextflow'].config.script += 'includeConfig(\"nextflow_labels.config\"\
     )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/io/untar/_viash.yaml

@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.5.0
+version: v0.5.1
 description: |
   Demultiplexing pipeline
 license: MIT
@@ -16,6 +16,6 @@ config_mods: |
   .requirements.commands += ['ps']
   .runners[.type == 'nextflow'].directives.tag := '$id'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 organization: vsh

target/nextflow/io/untar/main.nf

@@ -1,4 +1,4 @@
-// untar v0.5.0
+// untar v0.5.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "untar",
   "namespace" : "io",
-  "version" : "v0.5.0",
+  "version" : "v0.5.1",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3209,7 +3209,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.5.0",
+      "target_tag" : "v0.5.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3232,12 +3232,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/untar",
     "viash_version" : "0.9.4",
-    "git_commit" : "c516993b851efad3beee4db280ab24ef4c4bfb98",
+    "git_commit" : "85af1895d7dccec3ce70ec2a180a85ccd4e7c47c",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.5.0",
+    "version" : "v0.5.1",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3251,10 +3251,10 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
+      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.5.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3728,7 +3728,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/demultiplex/io/untar",
-    "tag" : "v0.5.0"
+    "tag" : "v0.5.1"
   },
   "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 = 'v0.5.0'
+  version = 'v0.5.1'
   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: "v0.5.0"
+version: "v0.5.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -109,7 +109,7 @@ resources:
   is_executable: true
   entrypoint: "run_wf"
 - type: "file"
-  path: "disable_publishfiles_process.config"
+  path: "disable_publish_processes.config"
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
@@ -201,6 +201,7 @@ runners:
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
     script:
+    - "includeConfig(\"disable_publish_processes.config\")"
     - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
@@ -216,14 +217,14 @@ build_info:
   output: "target/nextflow/runner"
   executable: "target/nextflow/runner/main.nf"
   viash_version: "0.9.4"
-  git_commit: "c516993b851efad3beee4db280ab24ef4c4bfb98"
+  git_commit: "85af1895d7dccec3ce70ec2a180a85ccd4e7c47c"
   git_remote: "https://github.com/viash-hub/demultiplex"
   dependencies:
   - "target/nextflow/demultiplex"
   - "target/nextflow/io/publish"
 package_config:
   name: "demultiplex"
-  version: "v0.5.0"
+  version: "v0.5.1"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -235,11 +236,11 @@ package_config:
   config_mods:
   - ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag\
     \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
-    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    .runners[.type == 'nextflow'].config.script += 'includeConfig(\"nextflow_labels.config\"\
     )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/runner/_viash.yaml

@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.5.0
+version: v0.5.1
 description: |
   Demultiplexing pipeline
 license: MIT
@@ -16,6 +16,6 @@ config_mods: |
   .requirements.commands += ['ps']
   .runners[.type == 'nextflow'].directives.tag := '$id'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 organization: vsh

target/nextflow/runner/disable_publish_processes.config

@@ -2,4 +2,8 @@ process {
   withName: publishFilesProc {
     publishDir = [ enabled: false ]
   }
+
+  withName: publishStatesProc {
+    publishDir = [ enabled: false ]
+  }
 }

target/nextflow/runner/main.nf

@@ -1,4 +1,4 @@
-// runner v0.5.0
+// runner v0.5.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3031,7 +3031,7 @@ meta = [
   "resources_dir": moduleDir.toRealPath().normalize(),
   "config": processConfig(readJsonBlob('''{
   "name" : "runner",
-  "version" : "v0.5.0",
+  "version" : "v0.5.1",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3162,7 +3162,7 @@ meta = [
     },
     {
       "type" : "file",
-      "path" : "disable_publishfiles_process.config"
+      "path" : "disable_publish_processes.config"
     },
     {
       "type" : "file",
@@ -3277,6 +3277,7 @@ meta = [
           "cpu1000" : "cpus = 1000"
         },
         "script" : [
+          "includeConfig(\\"disable_publish_processes.config\\")",
           "includeConfig(\\"nextflow_labels.config\\")"
         ]
       },
@@ -3300,12 +3301,12 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/runner",
     "viash_version" : "0.9.4",
-    "git_commit" : "c516993b851efad3beee4db280ab24ef4c4bfb98",
+    "git_commit" : "85af1895d7dccec3ce70ec2a180a85ccd4e7c47c",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.5.0",
+    "version" : "v0.5.1",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3319,10 +3320,10 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
+      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.5.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3358,6 +3359,10 @@ session = nextflow.Nextflow.getSession()
 final service = session.publishDirExecutorService()
 
 
+// S3 paths containing double slashes might cause issues with empty objects being created
+// Remove trailing slashes from the publish dir. The params map is immutable, so create a copy
+def publish_dir = params.publish_dir - ~/\/+$/
+
 workflow run_wf {
   take:
     input_ch
@@ -3416,7 +3421,7 @@ workflow run_wf {
           // The name of the output file for the run information is determined by the input file name.
           def run_information_output_1 = "${prefix}${state.output_run_information.getName()}"
 
-          println("Publising to ${params.publish_dir}/${prefix}")
+          println("Publishing to ${publish_dir}/${prefix}")
           [
             input: state.output,
             input_sample_qc: state.output_sample_qc,
@@ -3440,7 +3445,7 @@ workflow run_wf {
         },
         directives: [
           publishDir: [
-            path: "${params.publish_dir}", 
+            path: publish_dir,
             overwrite: false,
             mode: "copy"
           ]

target/nextflow/runner/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'runner'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.5.0'
+  version = 'v0.5.1'
   description = 'Runner for demultiplexing of raw sequencing data'
 }
 
@@ -122,4 +122,5 @@ process{
   withLabel: cpu1000 { cpus = 1000 }
 }
 
+includeConfig("disable_publish_processes.config")
 includeConfig("nextflow_labels.config")