Build branch v0.3 with version v0.3.8 (dafe2d8)

Build pipeline: viash-hub.demultiplex.v0.3-brf8v

Source commit: dafe2d8290

Source message: Bump version to v0.3.8

CHANGELOG.md

@@ -1,3 +1,15 @@
+# demultiplex v0.3.8
+
+## Bug fixes
+
+* Provide a proper error when a FASTQ file is empty after demultiplexing (PR #40).
+
+# demultiplex v0.3.7
+
+## Minor updates
+
+* Ignore lines starting with '#' when parsing run information CSV (PR #39).
+
 # demultiplex v0.3.6
 
 ## Minor updates

_viash.yaml

@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.3.6
+version: v0.3.8
 description: |
   Demultiplexing pipeline
 license: MIT

src/dataflow/gather_fastqs_and_validate/main.nf

@@ -1,3 +1,26 @@
+import java.util.zip.GZIPInputStream
+import java.nio.file.Files
+import java.io.BufferedInputStream
+
+def is_empty(file_to_check){
+  /* 
+  Checks if a file has content
+  */
+  if (file_to_check.size() == 0) {
+    return true
+  }
+  def input_stream = Files.newInputStream(file_to_check)
+  def gzInputStream
+  try {
+    gzInputStream = new GZIPInputStream(new BufferedInputStream(input_stream))
+  } catch (java.io.EOFException ex) {
+    // This is not a gzipfile...
+    return false
+  }
+  def read_one_byte = gzInputStream.read()
+  return read_one_byte == -1
+}
+
 workflow run_wf {
   take:
     input_ch
@@ -17,8 +40,8 @@ workflow run_wf {
         println "Processing run information file ${sample_sheet}"
         csv_lines = sample_sheet.splitCsv(header: false, sep: ',')
         csv_lines.any { csv_items ->
-          if (csv_items.isEmpty()) {
+          if (csv_items.isEmpty() || csv_items[0].startsWith("#")) {
-            // skip empty line
+            // skip empty or commented line 
             return
           }
           def possible_header = csv_items[0]
@@ -78,6 +101,9 @@ workflow run_wf {
             "Found forward: ${forward_fastq} and reverse: ${reverse_fastq}."
           println "Found ${forward_fastq.size()} forward and ${reverse_fastq.size()} reverse " +
             "fastq files for sample ${sample_id}"
+
+          assert forward_fastq.every{!is_empty(it)} && reverse_fastq.every{!is_empty(it)}:
+            "A fastq file for sample '${sample_id}' appears to be empty!"
           def fastqs_state = [
             "fastq_forward": forward_fastq,
             "fastq_reverse": reverse_fastq,

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

@@ -1,6 +1,6 @@
 name: "interop_summary_to_csv"
 namespace: "io"
-version: "v0.3.6"
+version: "v0.3.8"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -121,7 +121,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.6"
+  target_tag: "v0.3.8"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -146,12 +146,12 @@ 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: "3a985c83869bcd78ba6d325f1a817514b52a132a"
+  git_commit: "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.5-3-g3a985c8"
+  git_tag: "v0.3.5-9-gdafe2d8"
 package_config:
   name: "demultiplex"
-  version: "v0.3.6"
+  version: "v0.3.8"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -167,7 +167,7 @@ package_config:
     )'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
   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 v0.3.6
+# interop_summary_to_csv v0.3.8
 # 
 # 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 v0.3.6"
+  echo "interop_summary_to_csv v0.3.8"
   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="2025-03-20T19:41:31Z"
+LABEL org.opencontainers.image.created="2025-03-27T16:00:55Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="3a985c83869bcd78ba6d325f1a817514b52a132a"
+LABEL org.opencontainers.image.revision="dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
-LABEL org.opencontainers.image.version="v0.3.6"
+LABEL org.opencontainers.image.version="v0.3.8"
 
 VIASHDOCKER
   fi
@@ -609,7 +609,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "interop_summary_to_csv v0.3.6"
+            echo "interop_summary_to_csv v0.3.8"
             exit
             ;;
         --input)
@@ -733,7 +733,7 @@ if [[ "$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:v0.3.6'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.3.8'
   fi
 
   # print dockerfile

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

@@ -1,6 +1,6 @@
 name: "publish"
 namespace: "io"
-version: "v0.3.6"
+version: "v0.3.8"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -178,7 +178,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.6"
+  target_tag: "v0.3.8"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -196,12 +196,12 @@ build_info:
   output: "target/executable/io/publish"
   executable: "target/executable/io/publish/publish"
   viash_version: "0.9.0"
-  git_commit: "3a985c83869bcd78ba6d325f1a817514b52a132a"
+  git_commit: "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.5-3-g3a985c8"
+  git_tag: "v0.3.5-9-gdafe2d8"
 package_config:
   name: "demultiplex"
-  version: "v0.3.6"
+  version: "v0.3.8"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -217,7 +217,7 @@ package_config:
     )'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/executable/io/publish/publish

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# publish v0.3.6
+# publish v0.3.8
 # 
 # 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 v0.3.6"
+  echo "publish v0.3.8"
   echo ""
   echo "Publish the processed results of the run"
   echo ""
@@ -490,10 +490,10 @@ 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="2025-03-20T19:41:30Z"
+LABEL org.opencontainers.image.created="2025-03-27T16:00:54Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="3a985c83869bcd78ba6d325f1a817514b52a132a"
+LABEL org.opencontainers.image.revision="dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
-LABEL org.opencontainers.image.version="v0.3.6"
+LABEL org.opencontainers.image.version="v0.3.8"
 
 VIASHDOCKER
   fi
@@ -629,7 +629,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "publish v0.3.6"
+            echo "publish v0.3.8"
             exit
             ;;
         --input)
@@ -814,7 +814,7 @@ if [[ "$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:v0.3.6'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.3.8'
   fi
 
   # print dockerfile

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

@@ -1,6 +1,6 @@
 name: "untar"
 namespace: "io"
-version: "v0.3.6"
+version: "v0.3.8"
 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: "v0.3.6"
+  target_tag: "v0.3.8"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -153,12 +153,12 @@ build_info:
   output: "target/executable/io/untar"
   executable: "target/executable/io/untar/untar"
   viash_version: "0.9.0"
-  git_commit: "3a985c83869bcd78ba6d325f1a817514b52a132a"
+  git_commit: "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.5-3-g3a985c8"
+  git_tag: "v0.3.5-9-gdafe2d8"
 package_config:
   name: "demultiplex"
-  version: "v0.3.6"
+  version: "v0.3.8"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -174,7 +174,7 @@ package_config:
     )'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/executable/io/untar/untar

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# untar v0.3.6
+# untar v0.3.8
 # 
 # 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 v0.3.6"
+  echo "untar v0.3.8"
   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="2025-03-20T19:41:30Z"
+LABEL org.opencontainers.image.created="2025-03-27T16:00:54Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="3a985c83869bcd78ba6d325f1a817514b52a132a"
+LABEL org.opencontainers.image.revision="dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
-LABEL org.opencontainers.image.version="v0.3.6"
+LABEL org.opencontainers.image.version="v0.3.8"
 
 VIASHDOCKER
   fi
@@ -615,7 +615,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "untar v0.3.6"
+            echo "untar v0.3.8"
             exit
             ;;
         --input)
@@ -745,7 +745,7 @@ if [[ "$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:v0.3.6'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.3.8'
   fi
 
   # print dockerfile

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

@@ -1,6 +1,6 @@
 name: "combine_samples"
 namespace: "dataflow"
-version: "v0.3.6"
+version: "v0.3.8"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -162,12 +162,12 @@ build_info:
   output: "target/nextflow/dataflow/combine_samples"
   executable: "target/nextflow/dataflow/combine_samples/main.nf"
   viash_version: "0.9.0"
-  git_commit: "3a985c83869bcd78ba6d325f1a817514b52a132a"
+  git_commit: "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.5-3-g3a985c8"
+  git_tag: "v0.3.5-9-gdafe2d8"
 package_config:
   name: "demultiplex"
-  version: "v0.3.6"
+  version: "v0.3.8"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -183,7 +183,7 @@ package_config:
     )'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/dataflow/combine_samples/main.nf

@@ -1,4 +1,4 @@
-// combine_samples v0.3.6
+// combine_samples v0.3.8
 // 
 // 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" : "v0.3.6",
+  "version" : "v0.3.8",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3000,13 +3000,13 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/dataflow/combine_samples",
     "viash_version" : "0.9.0",
-    "git_commit" : "3a985c83869bcd78ba6d325f1a817514b52a132a",
+    "git_commit" : "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.5-3-g3a985c8"
+    "git_tag" : "v0.3.5-9-gdafe2d8"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.3.6",
+    "version" : "v0.3.8",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3023,7 +3023,7 @@ meta = [
       ".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",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.6'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
     ],
     "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 = 'v0.3.6'
+  version = 'v0.3.8'
   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: "v0.3.6"
+version: "v0.3.8"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -138,12 +138,12 @@ 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: "3a985c83869bcd78ba6d325f1a817514b52a132a"
+  git_commit: "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.5-3-g3a985c8"
+  git_tag: "v0.3.5-9-gdafe2d8"
 package_config:
   name: "demultiplex"
-  version: "v0.3.6"
+  version: "v0.3.8"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -159,7 +159,7 @@ package_config:
     )'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/dataflow/gather_fastqs_and_validate/main.nf

@@ -1,4 +1,4 @@
-// gather_fastqs_and_validate v0.3.6
+// gather_fastqs_and_validate v0.3.8
 // 
 // 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" : "v0.3.6",
+  "version" : "v0.3.8",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -2973,13 +2973,13 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
     "viash_version" : "0.9.0",
-    "git_commit" : "3a985c83869bcd78ba6d325f1a817514b52a132a",
+    "git_commit" : "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.5-3-g3a985c8"
+    "git_tag" : "v0.3.5-9-gdafe2d8"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.3.6",
+    "version" : "v0.3.8",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -2996,7 +2996,7 @@ meta = [
       ".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",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.6'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3019,6 +3019,29 @@ meta = [
 
 // inner workflow
 // user-provided Nextflow code
+import java.util.zip.GZIPInputStream
+import java.nio.file.Files
+import java.io.BufferedInputStream
+
+def is_empty(file_to_check){
+  /* 
+  Checks if a file has content
+  */
+  if (file_to_check.size() == 0) {
+    return true
+  }
+  def input_stream = Files.newInputStream(file_to_check)
+  def gzInputStream
+  try {
+    gzInputStream = new GZIPInputStream(new BufferedInputStream(input_stream))
+  } catch (java.io.EOFException ex) {
+    // This is not a gzipfile...
+    return false
+  }
+  def read_one_byte = gzInputStream.read()
+  return read_one_byte == -1
+}
+
 workflow run_wf {
   take:
     input_ch
@@ -3038,8 +3061,8 @@ workflow run_wf {
         println "Processing run information file ${sample_sheet}"
         csv_lines = sample_sheet.splitCsv(header: false, sep: ',')
         csv_lines.any { csv_items ->
-          if (csv_items.isEmpty()) {
+          if (csv_items.isEmpty() || csv_items[0].startsWith("#")) {
-            // skip empty line
+            // skip empty or commented line 
             return
           }
           def possible_header = csv_items[0]
@@ -3099,6 +3122,9 @@ workflow run_wf {
             "Found forward: ${forward_fastq} and reverse: ${reverse_fastq}."
           println "Found ${forward_fastq.size()} forward and ${reverse_fastq.size()} reverse " +
             "fastq files for sample ${sample_id}"
+
+          assert forward_fastq.every{!is_empty(it)} && reverse_fastq.every{!is_empty(it)}:
+            "A fastq file for sample '${sample_id}' appears to be empty!"
           def fastqs_state = [
             "fastq_forward": forward_fastq,
             "fastq_reverse": reverse_fastq,

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 = 'v0.3.6'
+  version = 'v0.3.8'
   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: "v0.3.6"
+version: "v0.3.8"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -244,9 +244,9 @@ build_info:
   output: "target/nextflow/demultiplex"
   executable: "target/nextflow/demultiplex/main.nf"
   viash_version: "0.9.0"
-  git_commit: "3a985c83869bcd78ba6d325f1a817514b52a132a"
+  git_commit: "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.5-3-g3a985c8"
+  git_tag: "v0.3.5-9-gdafe2d8"
   dependencies:
   - "target/nextflow/io/untar"
   - "target/nextflow/dataflow/gather_fastqs_and_validate"
@@ -258,7 +258,7 @@ build_info:
   - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/multiqc"
 package_config:
   name: "demultiplex"
-  version: "v0.3.6"
+  version: "v0.3.8"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -274,7 +274,7 @@ package_config:
     )'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/demultiplex/main.nf

@@ -1,4 +1,4 @@
-// demultiplex v0.3.6
+// demultiplex v0.3.8
 // 
 // 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" : "v0.3.6",
+  "version" : "v0.3.8",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3120,13 +3120,13 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/demultiplex",
     "viash_version" : "0.9.0",
-    "git_commit" : "3a985c83869bcd78ba6d325f1a817514b52a132a",
+    "git_commit" : "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.5-3-g3a985c8"
+    "git_tag" : "v0.3.5-9-gdafe2d8"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.3.6",
+    "version" : "v0.3.8",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3143,7 +3143,7 @@ meta = [
       ".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",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.6'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
     ],
     "keywords" : [
       "bioinformatics",

target/nextflow/demultiplex/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'demultiplex'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.6'
+  version = 'v0.3.8'
   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: "v0.3.6"
+version: "v0.3.8"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -121,7 +121,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.6"
+  target_tag: "v0.3.8"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -146,12 +146,12 @@ 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: "3a985c83869bcd78ba6d325f1a817514b52a132a"
+  git_commit: "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.5-3-g3a985c8"
+  git_tag: "v0.3.5-9-gdafe2d8"
 package_config:
   name: "demultiplex"
-  version: "v0.3.6"
+  version: "v0.3.8"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -167,7 +167,7 @@ package_config:
     )'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/io/interop_summary_to_csv/main.nf

@@ -1,4 +1,4 @@
-// interop_summary_to_csv v0.3.6
+// interop_summary_to_csv v0.3.8
 // 
 // 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" : "v0.3.6",
+  "version" : "v0.3.8",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -2955,7 +2955,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.6",
+      "target_tag" : "v0.3.8",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -2985,13 +2985,13 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/interop_summary_to_csv",
     "viash_version" : "0.9.0",
-    "git_commit" : "3a985c83869bcd78ba6d325f1a817514b52a132a",
+    "git_commit" : "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.5-3-g3a985c8"
+    "git_tag" : "v0.3.5-9-gdafe2d8"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.3.6",
+    "version" : "v0.3.8",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3008,7 +3008,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.6'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3431,7 +3431,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/demultiplex/io/interop_summary_to_csv",
-    "tag" : "v0.3.6"
+    "tag" : "v0.3.8"
   },
   "tag" : "$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 = 'v0.3.6'
+  version = 'v0.3.8'
 }
 
 process.container = 'nextflow/bash:latest'

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

@@ -1,6 +1,6 @@
 name: "publish"
 namespace: "io"
-version: "v0.3.6"
+version: "v0.3.8"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -178,7 +178,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.6"
+  target_tag: "v0.3.8"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -196,12 +196,12 @@ build_info:
   output: "target/nextflow/io/publish"
   executable: "target/nextflow/io/publish/main.nf"
   viash_version: "0.9.0"
-  git_commit: "3a985c83869bcd78ba6d325f1a817514b52a132a"
+  git_commit: "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.5-3-g3a985c8"
+  git_tag: "v0.3.5-9-gdafe2d8"
 package_config:
   name: "demultiplex"
-  version: "v0.3.6"
+  version: "v0.3.8"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -217,7 +217,7 @@ package_config:
     )'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/io/publish/main.nf

@@ -1,4 +1,4 @@
-// publish v0.3.6
+// publish v0.3.8
 // 
 // 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" : "v0.3.6",
+  "version" : "v0.3.8",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3021,7 +3021,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.6",
+      "target_tag" : "v0.3.8",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3044,13 +3044,13 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish",
     "viash_version" : "0.9.0",
-    "git_commit" : "3a985c83869bcd78ba6d325f1a817514b52a132a",
+    "git_commit" : "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.5-3-g3a985c8"
+    "git_tag" : "v0.3.5-9-gdafe2d8"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.3.6",
+    "version" : "v0.3.8",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3067,7 +3067,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.6'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3518,7 +3518,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/demultiplex/io/publish",
-    "tag" : "v0.3.6"
+    "tag" : "v0.3.8"
   },
   "tag" : "$id"
 }'''),

target/nextflow/io/publish/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'io/publish'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.6'
+  version = 'v0.3.8'
   description = 'Publish the processed results of the run'
 }
 

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

@@ -1,6 +1,6 @@
 name: "untar"
 namespace: "io"
-version: "v0.3.6"
+version: "v0.3.8"
 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: "v0.3.6"
+  target_tag: "v0.3.8"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -153,12 +153,12 @@ build_info:
   output: "target/nextflow/io/untar"
   executable: "target/nextflow/io/untar/main.nf"
   viash_version: "0.9.0"
-  git_commit: "3a985c83869bcd78ba6d325f1a817514b52a132a"
+  git_commit: "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.5-3-g3a985c8"
+  git_tag: "v0.3.5-9-gdafe2d8"
 package_config:
   name: "demultiplex"
-  version: "v0.3.6"
+  version: "v0.3.8"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -174,7 +174,7 @@ package_config:
     )'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/io/untar/main.nf

@@ -1,4 +1,4 @@
-// untar v0.3.6
+// untar v0.3.8
 // 
 // 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" : "v0.3.6",
+  "version" : "v0.3.8",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -2974,7 +2974,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.6",
+      "target_tag" : "v0.3.8",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -2997,13 +2997,13 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/untar",
     "viash_version" : "0.9.0",
-    "git_commit" : "3a985c83869bcd78ba6d325f1a817514b52a132a",
+    "git_commit" : "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.5-3-g3a985c8"
+    "git_tag" : "v0.3.5-9-gdafe2d8"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.3.6",
+    "version" : "v0.3.8",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3020,7 +3020,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.6'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3473,7 +3473,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/demultiplex/io/untar",
-    "tag" : "v0.3.6"
+    "tag" : "v0.3.8"
   },
   "tag" : "$id"
 }'''),

target/nextflow/io/untar/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'io/untar'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.6'
+  version = 'v0.3.8'
   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: "v0.3.6"
+version: "v0.3.8"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -192,15 +192,15 @@ build_info:
   output: "target/nextflow/runner"
   executable: "target/nextflow/runner/main.nf"
   viash_version: "0.9.0"
-  git_commit: "3a985c83869bcd78ba6d325f1a817514b52a132a"
+  git_commit: "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.5-3-g3a985c8"
+  git_tag: "v0.3.5-9-gdafe2d8"
   dependencies:
   - "target/nextflow/demultiplex"
   - "target/nextflow/io/publish"
 package_config:
   name: "demultiplex"
-  version: "v0.3.6"
+  version: "v0.3.8"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -216,7 +216,7 @@ package_config:
     )'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/runner/main.nf

@@ -1,4 +1,4 @@
-// runner v0.3.6
+// runner v0.3.8
 // 
 // 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" : "v0.3.6",
+  "version" : "v0.3.8",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3040,13 +3040,13 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/runner",
     "viash_version" : "0.9.0",
-    "git_commit" : "3a985c83869bcd78ba6d325f1a817514b52a132a",
+    "git_commit" : "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.5-3-g3a985c8"
+    "git_tag" : "v0.3.5-9-gdafe2d8"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.3.6",
+    "version" : "v0.3.8",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3063,7 +3063,7 @@ meta = [
       ".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",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.6'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
     ],
     "keywords" : [
       "bioinformatics",

target/nextflow/runner/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'runner'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.6'
+  version = 'v0.3.8'
   description = 'Runner for demultiplexing of raw sequencing data'
 }