Build branch outflow with version outflow (4245b40)

Build pipeline: viash-hub.demultiplex.outflow-f8tvg Source commit: 4245b40c8f Source message: Fix path to _viash.yaml [no_run_base_tests,no_run_nxf_tests]
2024-12-10 14:58:00 +00:00
parent d1913fc8b9
commit f6d898cb00
23 changed files with 75 additions and 72 deletions
--- a/nextflow.config
+++ b/nextflow.config
@@ -10,4 +10,3 @@ process {
  }
 }

-
--- a/src/runner/main.nf
+++ b/src/runner/main.nf
@@ -1,6 +1,6 @@
 def date = new Date().format('yyyyMMdd_hhmmss')

-def viash_config = java.nio.file.Paths.get("$projectDir/../../").toAbsolutePath().normalize().toString() + "/_viash.yaml"
+def viash_config = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString() + "/_viash.yaml"
 def version = get_version(file(viash_config).text)

 workflow run_wf {
@@ -24,10 +24,17 @@ workflow run_wf {
        fromState: { id, state ->
          def id1 = (params.add_date_time) ? "${id}_${date}" : id
          def id2 = (params.add_workflow_id) ? "${id1}_demultiplex_${version}" : id1
+
          def fastq_output_1 = (id == "run") ? state.fastq_output : "${id2}/" + state.fastq_output
          def falco_output_1 = (id == "run") ? state.falco_output : "${id2}/" + state.falco_output
          def multiqc_output_1 = (id == "run") ? state.multiqc_output : "${id2}/" + state.multiqc_output
-          println("Publising to ${params.publish_dir}/${id2}")
+
+          if (id == "run") {
+            println("Publising to ${params.publish_dir}")
+          } else {
+            println("Publising to ${params.publish_dir}/${id2}")
+          }
+
          [
            input: state.output,
            input_falco: state.output_falco,
--- a/src/runner/nextflow.config
+++ b/src/runner/nextflow.config
@@ -2,15 +2,5 @@ manifest {
  nextflowVersion = '!>=20.12.1-edge'
 }

-params {
-  rootDir = java.nio.file.Paths.get("$projectDir/../../").toAbsolutePath().normalize().toString()
-}
-
-process {
-  withName: publishStatesProc {
-    publishDir = [ enabled: false ]
-  }
-}
-
 // include common settings
 includeConfig("${params.rootDir}/src/config/labels.config")
--- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
@@ -141,9 +141,9 @@ build_info:
  output: "target/executable/io/interop_summary_to_csv"
  executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
  viash_version: "0.9.0"
-  git_commit: "850924de0ce1af49300d7f0b3dbe620e4f97c916"
-  git_remote: "https://x-access-token:ghs_In7H7ob9B5hTOzNDr8gE6y2z2kDr5e3ZuuxO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-16-g850924d"
+  git_commit: "4245b40c8f598c3ed1f977a8f07633c94db034b8"
+  git_remote: "https://x-access-token:ghs_sB7wMG2xwNdg7QnND7N1smsoVpwFO11EH6hM@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-17-g4245b40"
 package_config:
  name: "demultiplex"
  version: "outflow"
--- a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
+++ b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
@@ -470,9 +470,9 @@ 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="2024-12-10T14:26:52Z"
+LABEL org.opencontainers.image.created="2024-12-10T14:52:35Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="850924de0ce1af49300d7f0b3dbe620e4f97c916"
+LABEL org.opencontainers.image.revision="4245b40c8f598c3ed1f977a8f07633c94db034b8"
 LABEL org.opencontainers.image.version="outflow"

 VIASHDOCKER
--- a/target/executable/io/publish/.config.vsh.yaml
+++ b/target/executable/io/publish/.config.vsh.yaml
@@ -169,9 +169,9 @@ build_info:
  output: "target/executable/io/publish"
  executable: "target/executable/io/publish/publish"
  viash_version: "0.9.0"
-  git_commit: "850924de0ce1af49300d7f0b3dbe620e4f97c916"
-  git_remote: "https://x-access-token:ghs_In7H7ob9B5hTOzNDr8gE6y2z2kDr5e3ZuuxO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-16-g850924d"
+  git_commit: "4245b40c8f598c3ed1f977a8f07633c94db034b8"
+  git_remote: "https://x-access-token:ghs_sB7wMG2xwNdg7QnND7N1smsoVpwFO11EH6hM@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-17-g4245b40"
 package_config:
  name: "demultiplex"
  version: "outflow"
--- a/target/executable/io/publish/publish
+++ b/target/executable/io/publish/publish
@@ -479,9 +479,9 @@ FROM debian:stable-20220912
 ENTRYPOINT []
 RUN apt update && apt install -y procps
 LABEL org.opencontainers.image.description="Companion container for running component io publish"
-LABEL org.opencontainers.image.created="2024-12-10T14:26:52Z"
+LABEL org.opencontainers.image.created="2024-12-10T14:52:35Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="850924de0ce1af49300d7f0b3dbe620e4f97c916"
+LABEL org.opencontainers.image.revision="4245b40c8f598c3ed1f977a8f07633c94db034b8"
 LABEL org.opencontainers.image.version="outflow"

 VIASHDOCKER
--- a/target/executable/io/untar/.config.vsh.yaml
+++ b/target/executable/io/untar/.config.vsh.yaml
@@ -148,9 +148,9 @@ build_info:
  output: "target/executable/io/untar"
  executable: "target/executable/io/untar/untar"
  viash_version: "0.9.0"
-  git_commit: "850924de0ce1af49300d7f0b3dbe620e4f97c916"
-  git_remote: "https://x-access-token:ghs_In7H7ob9B5hTOzNDr8gE6y2z2kDr5e3ZuuxO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-16-g850924d"
+  git_commit: "4245b40c8f598c3ed1f977a8f07633c94db034b8"
+  git_remote: "https://x-access-token:ghs_sB7wMG2xwNdg7QnND7N1smsoVpwFO11EH6hM@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-17-g4245b40"
 package_config:
  name: "demultiplex"
  version: "outflow"
--- a/target/executable/io/untar/untar
+++ b/target/executable/io/untar/untar
@@ -476,9 +476,9 @@ 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="2024-12-10T14:26:52Z"
+LABEL org.opencontainers.image.created="2024-12-10T14:52:35Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="850924de0ce1af49300d7f0b3dbe620e4f97c916"
+LABEL org.opencontainers.image.revision="4245b40c8f598c3ed1f977a8f07633c94db034b8"
 LABEL org.opencontainers.image.version="outflow"

 VIASHDOCKER
--- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
+++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
@@ -139,9 +139,9 @@ build_info:
  output: "target/nextflow/dataflow/combine_samples"
  executable: "target/nextflow/dataflow/combine_samples/main.nf"
  viash_version: "0.9.0"
-  git_commit: "850924de0ce1af49300d7f0b3dbe620e4f97c916"
-  git_remote: "https://x-access-token:ghs_In7H7ob9B5hTOzNDr8gE6y2z2kDr5e3ZuuxO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-16-g850924d"
+  git_commit: "4245b40c8f598c3ed1f977a8f07633c94db034b8"
+  git_remote: "https://x-access-token:ghs_sB7wMG2xwNdg7QnND7N1smsoVpwFO11EH6hM@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-17-g4245b40"
 package_config:
  name: "demultiplex"
  version: "outflow"
--- a/target/nextflow/dataflow/combine_samples/main.nf
+++ b/target/nextflow/dataflow/combine_samples/main.nf
@@ -2972,9 +2972,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/combine_samples",
    "viash_version" : "0.9.0",
-    "git_commit" : "850924de0ce1af49300d7f0b3dbe620e4f97c916",
-    "git_remote" : "https://x-access-token:ghs_In7H7ob9B5hTOzNDr8gE6y2z2kDr5e3ZuuxO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-16-g850924d"
+    "git_commit" : "4245b40c8f598c3ed1f977a8f07633c94db034b8",
+    "git_remote" : "https://x-access-token:ghs_sB7wMG2xwNdg7QnND7N1smsoVpwFO11EH6hM@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-17-g4245b40"
  },
  "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
@@ -133,9 +133,9 @@ build_info:
  output: "target/nextflow/dataflow/gather_fastqs_and_validate"
  executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
  viash_version: "0.9.0"
-  git_commit: "850924de0ce1af49300d7f0b3dbe620e4f97c916"
-  git_remote: "https://x-access-token:ghs_In7H7ob9B5hTOzNDr8gE6y2z2kDr5e3ZuuxO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-16-g850924d"
+  git_commit: "4245b40c8f598c3ed1f977a8f07633c94db034b8"
+  git_remote: "https://x-access-token:ghs_sB7wMG2xwNdg7QnND7N1smsoVpwFO11EH6hM@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-17-g4245b40"
 package_config:
  name: "demultiplex"
  version: "outflow"
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
@@ -2965,9 +2965,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
    "viash_version" : "0.9.0",
-    "git_commit" : "850924de0ce1af49300d7f0b3dbe620e4f97c916",
-    "git_remote" : "https://x-access-token:ghs_In7H7ob9B5hTOzNDr8gE6y2z2kDr5e3ZuuxO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-16-g850924d"
+    "git_commit" : "4245b40c8f598c3ed1f977a8f07633c94db034b8",
+    "git_remote" : "https://x-access-token:ghs_sB7wMG2xwNdg7QnND7N1smsoVpwFO11EH6hM@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-17-g4245b40"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/demultiplex/.config.vsh.yaml
+++ b/target/nextflow/demultiplex/.config.vsh.yaml
@@ -220,9 +220,9 @@ build_info:
  output: "target/nextflow/demultiplex"
  executable: "target/nextflow/demultiplex/main.nf"
  viash_version: "0.9.0"
-  git_commit: "850924de0ce1af49300d7f0b3dbe620e4f97c916"
-  git_remote: "https://x-access-token:ghs_In7H7ob9B5hTOzNDr8gE6y2z2kDr5e3ZuuxO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-16-g850924d"
+  git_commit: "4245b40c8f598c3ed1f977a8f07633c94db034b8"
+  git_remote: "https://x-access-token:ghs_sB7wMG2xwNdg7QnND7N1smsoVpwFO11EH6hM@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-17-g4245b40"
  dependencies:
  - "target/nextflow/io/untar"
  - "target/nextflow/dataflow/gather_fastqs_and_validate"
--- a/target/nextflow/demultiplex/main.nf
+++ b/target/nextflow/demultiplex/main.nf
@@ -3088,9 +3088,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/demultiplex",
    "viash_version" : "0.9.0",
-    "git_commit" : "850924de0ce1af49300d7f0b3dbe620e4f97c916",
-    "git_remote" : "https://x-access-token:ghs_In7H7ob9B5hTOzNDr8gE6y2z2kDr5e3ZuuxO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-16-g850924d"
+    "git_commit" : "4245b40c8f598c3ed1f977a8f07633c94db034b8",
+    "git_remote" : "https://x-access-token:ghs_sB7wMG2xwNdg7QnND7N1smsoVpwFO11EH6hM@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-17-g4245b40"
  },
  "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
@@ -141,9 +141,9 @@ build_info:
  output: "target/nextflow/io/interop_summary_to_csv"
  executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
  viash_version: "0.9.0"
-  git_commit: "850924de0ce1af49300d7f0b3dbe620e4f97c916"
-  git_remote: "https://x-access-token:ghs_In7H7ob9B5hTOzNDr8gE6y2z2kDr5e3ZuuxO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-16-g850924d"
+  git_commit: "4245b40c8f598c3ed1f977a8f07633c94db034b8"
+  git_remote: "https://x-access-token:ghs_sB7wMG2xwNdg7QnND7N1smsoVpwFO11EH6hM@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-17-g4245b40"
 package_config:
  name: "demultiplex"
  version: "outflow"
--- a/target/nextflow/io/interop_summary_to_csv/main.nf
+++ b/target/nextflow/io/interop_summary_to_csv/main.nf
@@ -2977,9 +2977,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/interop_summary_to_csv",
    "viash_version" : "0.9.0",
-    "git_commit" : "850924de0ce1af49300d7f0b3dbe620e4f97c916",
-    "git_remote" : "https://x-access-token:ghs_In7H7ob9B5hTOzNDr8gE6y2z2kDr5e3ZuuxO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-16-g850924d"
+    "git_commit" : "4245b40c8f598c3ed1f977a8f07633c94db034b8",
+    "git_remote" : "https://x-access-token:ghs_sB7wMG2xwNdg7QnND7N1smsoVpwFO11EH6hM@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-17-g4245b40"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/io/publish/.config.vsh.yaml
+++ b/target/nextflow/io/publish/.config.vsh.yaml
@@ -169,9 +169,9 @@ build_info:
  output: "target/nextflow/io/publish"
  executable: "target/nextflow/io/publish/main.nf"
  viash_version: "0.9.0"
-  git_commit: "850924de0ce1af49300d7f0b3dbe620e4f97c916"
-  git_remote: "https://x-access-token:ghs_In7H7ob9B5hTOzNDr8gE6y2z2kDr5e3ZuuxO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-16-g850924d"
+  git_commit: "4245b40c8f598c3ed1f977a8f07633c94db034b8"
+  git_remote: "https://x-access-token:ghs_sB7wMG2xwNdg7QnND7N1smsoVpwFO11EH6hM@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-17-g4245b40"
 package_config:
  name: "demultiplex"
  version: "outflow"
--- a/target/nextflow/io/publish/main.nf
+++ b/target/nextflow/io/publish/main.nf
@@ -3011,9 +3011,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish",
    "viash_version" : "0.9.0",
-    "git_commit" : "850924de0ce1af49300d7f0b3dbe620e4f97c916",
-    "git_remote" : "https://x-access-token:ghs_In7H7ob9B5hTOzNDr8gE6y2z2kDr5e3ZuuxO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-16-g850924d"
+    "git_commit" : "4245b40c8f598c3ed1f977a8f07633c94db034b8",
+    "git_remote" : "https://x-access-token:ghs_sB7wMG2xwNdg7QnND7N1smsoVpwFO11EH6hM@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-17-g4245b40"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/io/untar/.config.vsh.yaml
+++ b/target/nextflow/io/untar/.config.vsh.yaml
@@ -148,9 +148,9 @@ build_info:
  output: "target/nextflow/io/untar"
  executable: "target/nextflow/io/untar/main.nf"
  viash_version: "0.9.0"
-  git_commit: "850924de0ce1af49300d7f0b3dbe620e4f97c916"
-  git_remote: "https://x-access-token:ghs_In7H7ob9B5hTOzNDr8gE6y2z2kDr5e3ZuuxO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-16-g850924d"
+  git_commit: "4245b40c8f598c3ed1f977a8f07633c94db034b8"
+  git_remote: "https://x-access-token:ghs_sB7wMG2xwNdg7QnND7N1smsoVpwFO11EH6hM@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-17-g4245b40"
 package_config:
  name: "demultiplex"
  version: "outflow"
--- a/target/nextflow/io/untar/main.nf
+++ b/target/nextflow/io/untar/main.nf
@@ -2989,9 +2989,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/untar",
    "viash_version" : "0.9.0",
-    "git_commit" : "850924de0ce1af49300d7f0b3dbe620e4f97c916",
-    "git_remote" : "https://x-access-token:ghs_In7H7ob9B5hTOzNDr8gE6y2z2kDr5e3ZuuxO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-16-g850924d"
+    "git_commit" : "4245b40c8f598c3ed1f977a8f07633c94db034b8",
+    "git_remote" : "https://x-access-token:ghs_sB7wMG2xwNdg7QnND7N1smsoVpwFO11EH6hM@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-17-g4245b40"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/runner/.config.vsh.yaml
+++ b/target/nextflow/runner/.config.vsh.yaml
@@ -156,9 +156,9 @@ build_info:
  output: "target/nextflow/runner"
  executable: "target/nextflow/runner/main.nf"
  viash_version: "0.9.0"
-  git_commit: "850924de0ce1af49300d7f0b3dbe620e4f97c916"
-  git_remote: "https://x-access-token:ghs_In7H7ob9B5hTOzNDr8gE6y2z2kDr5e3ZuuxO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-16-g850924d"
+  git_commit: "4245b40c8f598c3ed1f977a8f07633c94db034b8"
+  git_remote: "https://x-access-token:ghs_sB7wMG2xwNdg7QnND7N1smsoVpwFO11EH6hM@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-17-g4245b40"
  dependencies:
  - "target/nextflow/demultiplex"
  - "target/nextflow/io/publish"
--- a/target/nextflow/runner/main.nf
+++ b/target/nextflow/runner/main.nf
@@ -3003,9 +3003,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/runner",
    "viash_version" : "0.9.0",
-    "git_commit" : "850924de0ce1af49300d7f0b3dbe620e4f97c916",
-    "git_remote" : "https://x-access-token:ghs_In7H7ob9B5hTOzNDr8gE6y2z2kDr5e3ZuuxO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-16-g850924d"
+    "git_commit" : "4245b40c8f598c3ed1f977a8f07633c94db034b8",
+    "git_remote" : "https://x-access-token:ghs_sB7wMG2xwNdg7QnND7N1smsoVpwFO11EH6hM@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-17-g4245b40"
  },
  "package_config" : {
    "name" : "demultiplex",
@@ -3053,7 +3053,7 @@ include { publish } from "${meta.resources_dir}/../../nextflow/io/publish/main.n
 // user-provided Nextflow code
 def date = new Date().format('yyyyMMdd_hhmmss')

-def viash_config = java.nio.file.Paths.get("$projectDir/../../").toAbsolutePath().normalize().toString() + "/_viash.yaml"
+def viash_config = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString() + "/_viash.yaml"
 def version = get_version(file(viash_config).text)

 workflow run_wf {
@@ -3077,10 +3077,17 @@ workflow run_wf {
        fromState: { id, state ->
          def id1 = (params.add_date_time) ? "${id}_${date}" : id
          def id2 = (params.add_workflow_id) ? "${id1}_demultiplex_${version}" : id1
+
          def fastq_output_1 = (id == "run") ? state.fastq_output : "${id2}/" + state.fastq_output
          def falco_output_1 = (id == "run") ? state.falco_output : "${id2}/" + state.falco_output
          def multiqc_output_1 = (id == "run") ? state.multiqc_output : "${id2}/" + state.multiqc_output
-          println("Publising to ${params.publish_dir}/${id2}")
+
+          if (id == "run") {
+            println("Publising to ${params.publish_dir}")
+          } else {
+            println("Publising to ${params.publish_dir}/${id2}")
+          }
+
          [
            input: state.output,
            input_falco: state.output_falco,