Build branch main with version main (ef44f4d)

Build pipeline: viash-hub.demultiplex.main-xsnpt Source commit: ef44f4d20e Source message: Return output from runner (#56)
2025-07-28 13:06:10 +00:00
parent abe9c15aef
commit 94f9d77fb2
24 changed files with 66 additions and 50 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,17 @@
+# demultiplex v0.4.2
+
+## Minor changes
+
+* Provide output from `runner` workflow so it can be used as part of a larger workflow (PR #56).
+* Add workflow identifier to version information during pipeline run (PR #56).
+
+# demultiplex v0.4.1
+
+## Minor changes
+
+* Split off part of the workflow logic (`detect_demultiplexer`) from the main workflow to a dedicated subworkflow (PR #52).
+* Add the package config (`_viash.yaml`) to every component's target dir. This makes introspection from, e.g. a `runner` workflow much more robust (PR #53).
+
 # demultiplex v0.4.0

 ## Breaking changes
--- a/src/runner/main.nf
+++ b/src/runner/main.nf
@@ -47,7 +47,8 @@ workflow run_wf {
          state_to_pass
        },
        toState: { id, result, state ->
-          state + result
+          // Duplicate the results under its own key, makes it easier to access later.
+          state + result + [ to_return: result ]
        },
      )
      | publish.run(
@@ -80,7 +81,7 @@ workflow run_wf {
            output_demultiplexer_logs: demultiplexer_logs_output,
          ]
        },
-        toState: { id, result, state -> [:] },
+        toState: { id, result, state -> [ fastq_output: state.to_return.output ] },
        directives: [
          publishDir: [
            path: "${params.publish_dir}", 
@@ -103,6 +104,6 @@ def get_version(input) {
  def yamlSlurper = new groovy.yaml.YamlSlurper()
  def loaded_viash_config = yamlSlurper.parse(inputFile)
  def version = (loaded_viash_config.version) ? loaded_viash_config.version : "unknown_version"
-  println("Version to be used: ${version}")
+  println("Version of demultiplex to be used: ${version}")
  return version
 }
--- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
@@ -160,9 +160,9 @@ 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: "88d11c39262ea9952e2f2f119194b1e499e5efc3"
+  git_commit: "ef44f4d20ee76b6720fdb475ed633469add1869d"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-33-g88d11c3"
+  git_tag: "v0.1.1-35-gef44f4d"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
+++ b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
@@ -454,9 +454,9 @@ 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="2025-07-25T08:27:30Z"
+LABEL org.opencontainers.image.created="2025-07-28T12:40:14Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="88d11c39262ea9952e2f2f119194b1e499e5efc3"
+LABEL org.opencontainers.image.revision="ef44f4d20ee76b6720fdb475ed633469add1869d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/io/publish/.config.vsh.yaml
+++ b/target/executable/io/publish/.config.vsh.yaml
@@ -222,9 +222,9 @@ build_info:
  output: "target/executable/io/publish"
  executable: "target/executable/io/publish/publish"
  viash_version: "0.9.4"
-  git_commit: "88d11c39262ea9952e2f2f119194b1e499e5efc3"
+  git_commit: "ef44f4d20ee76b6720fdb475ed633469add1869d"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-33-g88d11c3"
+  git_tag: "v0.1.1-35-gef44f4d"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/executable/io/publish/publish
+++ b/target/executable/io/publish/publish
@@ -450,9 +450,9 @@ 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="2025-07-25T08:27:29Z"
+LABEL org.opencontainers.image.created="2025-07-28T12:40:14Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="88d11c39262ea9952e2f2f119194b1e499e5efc3"
+LABEL org.opencontainers.image.revision="ef44f4d20ee76b6720fdb475ed633469add1869d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/io/untar/.config.vsh.yaml
+++ b/target/executable/io/untar/.config.vsh.yaml
@@ -159,9 +159,9 @@ build_info:
  output: "target/executable/io/untar"
  executable: "target/executable/io/untar/untar"
  viash_version: "0.9.4"
-  git_commit: "88d11c39262ea9952e2f2f119194b1e499e5efc3"
+  git_commit: "ef44f4d20ee76b6720fdb475ed633469add1869d"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-33-g88d11c3"
+  git_tag: "v0.1.1-35-gef44f4d"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/executable/io/untar/untar
+++ b/target/executable/io/untar/untar
@@ -450,9 +450,9 @@ 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="2025-07-25T08:27:29Z"
+LABEL org.opencontainers.image.created="2025-07-28T12:40:14Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="88d11c39262ea9952e2f2f119194b1e499e5efc3"
+LABEL org.opencontainers.image.revision="ef44f4d20ee76b6720fdb475ed633469add1869d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
+++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
@@ -168,9 +168,9 @@ build_info:
  output: "target/nextflow/dataflow/combine_samples"
  executable: "target/nextflow/dataflow/combine_samples/main.nf"
  viash_version: "0.9.4"
-  git_commit: "88d11c39262ea9952e2f2f119194b1e499e5efc3"
+  git_commit: "ef44f4d20ee76b6720fdb475ed633469add1869d"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-33-g88d11c3"
+  git_tag: "v0.1.1-35-gef44f4d"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/nextflow/dataflow/combine_samples/main.nf
+++ b/target/nextflow/dataflow/combine_samples/main.nf
@@ -3235,9 +3235,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/combine_samples",
    "viash_version" : "0.9.4",
-    "git_commit" : "88d11c39262ea9952e2f2f119194b1e499e5efc3",
+    "git_commit" : "ef44f4d20ee76b6720fdb475ed633469add1869d",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-33-g88d11c3"
+    "git_tag" : "v0.1.1-35-gef44f4d"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
@@ -159,9 +159,9 @@ 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: "88d11c39262ea9952e2f2f119194b1e499e5efc3"
+  git_commit: "ef44f4d20ee76b6720fdb475ed633469add1869d"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-33-g88d11c3"
+  git_tag: "v0.1.1-35-gef44f4d"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
@@ -3232,9 +3232,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
    "viash_version" : "0.9.4",
-    "git_commit" : "88d11c39262ea9952e2f2f119194b1e499e5efc3",
+    "git_commit" : "ef44f4d20ee76b6720fdb475ed633469add1869d",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-33-g88d11c3"
+    "git_tag" : "v0.1.1-35-gef44f4d"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/demultiplex/.config.vsh.yaml
+++ b/target/nextflow/demultiplex/.config.vsh.yaml
@@ -268,9 +268,9 @@ build_info:
  output: "target/nextflow/demultiplex"
  executable: "target/nextflow/demultiplex/main.nf"
  viash_version: "0.9.4"
-  git_commit: "88d11c39262ea9952e2f2f119194b1e499e5efc3"
+  git_commit: "ef44f4d20ee76b6720fdb475ed633469add1869d"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-33-g88d11c3"
+  git_tag: "v0.1.1-35-gef44f4d"
  dependencies:
  - "target/nextflow/io/untar"
  - "target/nextflow/dataflow/gather_fastqs_and_validate"
--- a/target/nextflow/demultiplex/main.nf
+++ b/target/nextflow/demultiplex/main.nf
@@ -3380,9 +3380,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/demultiplex",
    "viash_version" : "0.9.4",
-    "git_commit" : "88d11c39262ea9952e2f2f119194b1e499e5efc3",
+    "git_commit" : "ef44f4d20ee76b6720fdb475ed633469add1869d",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-33-g88d11c3"
+    "git_tag" : "v0.1.1-35-gef44f4d"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/detect_demultiplexer/.config.vsh.yaml
+++ b/target/nextflow/detect_demultiplexer/.config.vsh.yaml
@@ -168,9 +168,9 @@ build_info:
  output: "target/nextflow/detect_demultiplexer"
  executable: "target/nextflow/detect_demultiplexer/main.nf"
  viash_version: "0.9.4"
-  git_commit: "88d11c39262ea9952e2f2f119194b1e499e5efc3"
+  git_commit: "ef44f4d20ee76b6720fdb475ed633469add1869d"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-33-g88d11c3"
+  git_tag: "v0.1.1-35-gef44f4d"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/nextflow/detect_demultiplexer/main.nf
+++ b/target/nextflow/detect_demultiplexer/main.nf
@@ -3224,9 +3224,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/detect_demultiplexer",
    "viash_version" : "0.9.4",
-    "git_commit" : "88d11c39262ea9952e2f2f119194b1e499e5efc3",
+    "git_commit" : "ef44f4d20ee76b6720fdb475ed633469add1869d",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-33-g88d11c3"
+    "git_tag" : "v0.1.1-35-gef44f4d"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
@@ -160,9 +160,9 @@ 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: "88d11c39262ea9952e2f2f119194b1e499e5efc3"
+  git_commit: "ef44f4d20ee76b6720fdb475ed633469add1869d"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-33-g88d11c3"
+  git_tag: "v0.1.1-35-gef44f4d"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/nextflow/io/interop_summary_to_csv/main.nf
+++ b/target/nextflow/io/interop_summary_to_csv/main.nf
@@ -3233,9 +3233,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/interop_summary_to_csv",
    "viash_version" : "0.9.4",
-    "git_commit" : "88d11c39262ea9952e2f2f119194b1e499e5efc3",
+    "git_commit" : "ef44f4d20ee76b6720fdb475ed633469add1869d",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-33-g88d11c3"
+    "git_tag" : "v0.1.1-35-gef44f4d"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/io/publish/.config.vsh.yaml
+++ b/target/nextflow/io/publish/.config.vsh.yaml
@@ -222,9 +222,9 @@ build_info:
  output: "target/nextflow/io/publish"
  executable: "target/nextflow/io/publish/main.nf"
  viash_version: "0.9.4"
-  git_commit: "88d11c39262ea9952e2f2f119194b1e499e5efc3"
+  git_commit: "ef44f4d20ee76b6720fdb475ed633469add1869d"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-33-g88d11c3"
+  git_tag: "v0.1.1-35-gef44f4d"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/nextflow/io/publish/main.nf
+++ b/target/nextflow/io/publish/main.nf
@@ -3302,9 +3302,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish",
    "viash_version" : "0.9.4",
-    "git_commit" : "88d11c39262ea9952e2f2f119194b1e499e5efc3",
+    "git_commit" : "ef44f4d20ee76b6720fdb475ed633469add1869d",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-33-g88d11c3"
+    "git_tag" : "v0.1.1-35-gef44f4d"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/io/untar/.config.vsh.yaml
+++ b/target/nextflow/io/untar/.config.vsh.yaml
@@ -159,9 +159,9 @@ build_info:
  output: "target/nextflow/io/untar"
  executable: "target/nextflow/io/untar/main.nf"
  viash_version: "0.9.4"
-  git_commit: "88d11c39262ea9952e2f2f119194b1e499e5efc3"
+  git_commit: "ef44f4d20ee76b6720fdb475ed633469add1869d"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-33-g88d11c3"
+  git_tag: "v0.1.1-35-gef44f4d"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/nextflow/io/untar/main.nf
+++ b/target/nextflow/io/untar/main.nf
@@ -3232,9 +3232,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/untar",
    "viash_version" : "0.9.4",
-    "git_commit" : "88d11c39262ea9952e2f2f119194b1e499e5efc3",
+    "git_commit" : "ef44f4d20ee76b6720fdb475ed633469add1869d",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-33-g88d11c3"
+    "git_tag" : "v0.1.1-35-gef44f4d"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/runner/.config.vsh.yaml
+++ b/target/nextflow/runner/.config.vsh.yaml
@@ -214,9 +214,9 @@ build_info:
  output: "target/nextflow/runner"
  executable: "target/nextflow/runner/main.nf"
  viash_version: "0.9.4"
-  git_commit: "88d11c39262ea9952e2f2f119194b1e499e5efc3"
+  git_commit: "ef44f4d20ee76b6720fdb475ed633469add1869d"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-33-g88d11c3"
+  git_tag: "v0.1.1-35-gef44f4d"
  dependencies:
  - "target/nextflow/demultiplex"
  - "target/nextflow/io/publish"
--- a/target/nextflow/runner/main.nf
+++ b/target/nextflow/runner/main.nf
@@ -3296,9 +3296,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/runner",
    "viash_version" : "0.9.4",
-    "git_commit" : "88d11c39262ea9952e2f2f119194b1e499e5efc3",
+    "git_commit" : "ef44f4d20ee76b6720fdb475ed633469add1869d",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-33-g88d11c3"
+    "git_tag" : "v0.1.1-35-gef44f4d"
  },
  "package_config" : {
    "name" : "demultiplex",
@@ -3393,7 +3393,8 @@ workflow run_wf {
          state_to_pass
        },
        toState: { id, result, state ->
-          state + result
+          // Duplicate the results under its own key, makes it easier to access later.
+          state + result + [ to_return: result ]
        },
      )
      | publish.run(
@@ -3426,7 +3427,7 @@ workflow run_wf {
            output_demultiplexer_logs: demultiplexer_logs_output,
          ]
        },
-        toState: { id, result, state -> [:] },
+        toState: { id, result, state -> [ fastq_output: state.to_return.output ] },
        directives: [
          publishDir: [
            path: "${params.publish_dir}", 
@@ -3449,7 +3450,7 @@ def get_version(input) {
  def yamlSlurper = new groovy.yaml.YamlSlurper()
  def loaded_viash_config = yamlSlurper.parse(inputFile)
  def version = (loaded_viash_config.version) ? loaded_viash_config.version : "unknown_version"
-  println("Version to be used: ${version}")
+  println("Version of demultiplex to be used: ${version}")
  return version
 }