Build branch main with version main (0acfda6)

Build pipeline: viash-hub.demultiplex.main-zmw5v Source commit: 0acfda628d Source message: Ignore lines starting with '#' in run information file (#39)
2025-03-20 20:56:23 +00:00
parent d521259fcf
commit 26f9bf6da2
22 changed files with 50 additions and 44 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,9 @@
+# demultiplex v0.3.7
+
+## Minor updates
+
+* Ignore lines starting with '#' when parsing run information CSV (PR #39).
+
 # demultiplex v0.3.6

 ## Minor updates
--- a/src/dataflow/gather_fastqs_and_validate/main.nf
+++ b/src/dataflow/gather_fastqs_and_validate/main.nf
@@ -17,8 +17,8 @@ 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()) {
-            // skip empty line
+          if (csv_items.isEmpty() || csv_items[0].startsWith("#")) {
+            // skip empty or commented line 
            return
          }
          def possible_header = csv_items[0]
--- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
@@ -146,9 +146,9 @@ 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: "55699d24c0ff8d88e572ccc1a5ebc40217bb9524"
+  git_commit: "0acfda628d38430a7cdc21acf52878703b3b4bfc"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-19-g55699d2"
+  git_tag: "v0.1.1-20-g0acfda6"
 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
@@ -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="2025-03-20T19:30:15Z"
+LABEL org.opencontainers.image.created="2025-03-20T20:31:40Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="55699d24c0ff8d88e572ccc1a5ebc40217bb9524"
+LABEL org.opencontainers.image.revision="0acfda628d38430a7cdc21acf52878703b3b4bfc"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/io/publish/.config.vsh.yaml
+++ b/target/executable/io/publish/.config.vsh.yaml
@@ -196,9 +196,9 @@ build_info:
  output: "target/executable/io/publish"
  executable: "target/executable/io/publish/publish"
  viash_version: "0.9.0"
-  git_commit: "55699d24c0ff8d88e572ccc1a5ebc40217bb9524"
+  git_commit: "0acfda628d38430a7cdc21acf52878703b3b4bfc"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-19-g55699d2"
+  git_tag: "v0.1.1-20-g0acfda6"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/executable/io/publish/publish
+++ b/target/executable/io/publish/publish
@@ -490,9 +490,9 @@ 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="2025-03-20T19:30:15Z"
+LABEL org.opencontainers.image.created="2025-03-20T20:31:40Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="55699d24c0ff8d88e572ccc1a5ebc40217bb9524"
+LABEL org.opencontainers.image.revision="0acfda628d38430a7cdc21acf52878703b3b4bfc"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/io/untar/.config.vsh.yaml
+++ b/target/executable/io/untar/.config.vsh.yaml
@@ -153,9 +153,9 @@ build_info:
  output: "target/executable/io/untar"
  executable: "target/executable/io/untar/untar"
  viash_version: "0.9.0"
-  git_commit: "55699d24c0ff8d88e572ccc1a5ebc40217bb9524"
+  git_commit: "0acfda628d38430a7cdc21acf52878703b3b4bfc"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-19-g55699d2"
+  git_tag: "v0.1.1-20-g0acfda6"
 package_config:
  name: "demultiplex"
  version: "main"
--- 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="2025-03-20T19:30:14Z"
+LABEL org.opencontainers.image.created="2025-03-20T20:31:40Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="55699d24c0ff8d88e572ccc1a5ebc40217bb9524"
+LABEL org.opencontainers.image.revision="0acfda628d38430a7cdc21acf52878703b3b4bfc"
 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
@@ -162,9 +162,9 @@ build_info:
  output: "target/nextflow/dataflow/combine_samples"
  executable: "target/nextflow/dataflow/combine_samples/main.nf"
  viash_version: "0.9.0"
-  git_commit: "55699d24c0ff8d88e572ccc1a5ebc40217bb9524"
+  git_commit: "0acfda628d38430a7cdc21acf52878703b3b4bfc"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-19-g55699d2"
+  git_tag: "v0.1.1-20-g0acfda6"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/nextflow/dataflow/combine_samples/main.nf
+++ b/target/nextflow/dataflow/combine_samples/main.nf
@@ -3000,9 +3000,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/combine_samples",
    "viash_version" : "0.9.0",
-    "git_commit" : "55699d24c0ff8d88e572ccc1a5ebc40217bb9524",
+    "git_commit" : "0acfda628d38430a7cdc21acf52878703b3b4bfc",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-19-g55699d2"
+    "git_tag" : "v0.1.1-20-g0acfda6"
  },
  "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
@@ -138,9 +138,9 @@ 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: "55699d24c0ff8d88e572ccc1a5ebc40217bb9524"
+  git_commit: "0acfda628d38430a7cdc21acf52878703b3b4bfc"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-19-g55699d2"
+  git_tag: "v0.1.1-20-g0acfda6"
 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
@@ -2973,9 +2973,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
    "viash_version" : "0.9.0",
-    "git_commit" : "55699d24c0ff8d88e572ccc1a5ebc40217bb9524",
+    "git_commit" : "0acfda628d38430a7cdc21acf52878703b3b4bfc",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-19-g55699d2"
+    "git_tag" : "v0.1.1-20-g0acfda6"
  },
  "package_config" : {
    "name" : "demultiplex",
@@ -3038,8 +3038,8 @@ 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()) {
-            // skip empty line
+          if (csv_items.isEmpty() || csv_items[0].startsWith("#")) {
+            // skip empty or commented line 
            return
          }
          def possible_header = csv_items[0]
--- a/target/nextflow/demultiplex/.config.vsh.yaml
+++ b/target/nextflow/demultiplex/.config.vsh.yaml
@@ -244,9 +244,9 @@ build_info:
  output: "target/nextflow/demultiplex"
  executable: "target/nextflow/demultiplex/main.nf"
  viash_version: "0.9.0"
-  git_commit: "55699d24c0ff8d88e572ccc1a5ebc40217bb9524"
+  git_commit: "0acfda628d38430a7cdc21acf52878703b3b4bfc"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-19-g55699d2"
+  git_tag: "v0.1.1-20-g0acfda6"
  dependencies:
  - "target/nextflow/io/untar"
  - "target/nextflow/dataflow/gather_fastqs_and_validate"
--- a/target/nextflow/demultiplex/main.nf
+++ b/target/nextflow/demultiplex/main.nf
@@ -3120,9 +3120,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/demultiplex",
    "viash_version" : "0.9.0",
-    "git_commit" : "55699d24c0ff8d88e572ccc1a5ebc40217bb9524",
+    "git_commit" : "0acfda628d38430a7cdc21acf52878703b3b4bfc",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-19-g55699d2"
+    "git_tag" : "v0.1.1-20-g0acfda6"
  },
  "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
@@ -146,9 +146,9 @@ 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: "55699d24c0ff8d88e572ccc1a5ebc40217bb9524"
+  git_commit: "0acfda628d38430a7cdc21acf52878703b3b4bfc"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-19-g55699d2"
+  git_tag: "v0.1.1-20-g0acfda6"
 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
@@ -2985,9 +2985,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/interop_summary_to_csv",
    "viash_version" : "0.9.0",
-    "git_commit" : "55699d24c0ff8d88e572ccc1a5ebc40217bb9524",
+    "git_commit" : "0acfda628d38430a7cdc21acf52878703b3b4bfc",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-19-g55699d2"
+    "git_tag" : "v0.1.1-20-g0acfda6"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/io/publish/.config.vsh.yaml
+++ b/target/nextflow/io/publish/.config.vsh.yaml
@@ -196,9 +196,9 @@ build_info:
  output: "target/nextflow/io/publish"
  executable: "target/nextflow/io/publish/main.nf"
  viash_version: "0.9.0"
-  git_commit: "55699d24c0ff8d88e572ccc1a5ebc40217bb9524"
+  git_commit: "0acfda628d38430a7cdc21acf52878703b3b4bfc"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-19-g55699d2"
+  git_tag: "v0.1.1-20-g0acfda6"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/nextflow/io/publish/main.nf
+++ b/target/nextflow/io/publish/main.nf
@@ -3044,9 +3044,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish",
    "viash_version" : "0.9.0",
-    "git_commit" : "55699d24c0ff8d88e572ccc1a5ebc40217bb9524",
+    "git_commit" : "0acfda628d38430a7cdc21acf52878703b3b4bfc",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-19-g55699d2"
+    "git_tag" : "v0.1.1-20-g0acfda6"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/io/untar/.config.vsh.yaml
+++ b/target/nextflow/io/untar/.config.vsh.yaml
@@ -153,9 +153,9 @@ build_info:
  output: "target/nextflow/io/untar"
  executable: "target/nextflow/io/untar/main.nf"
  viash_version: "0.9.0"
-  git_commit: "55699d24c0ff8d88e572ccc1a5ebc40217bb9524"
+  git_commit: "0acfda628d38430a7cdc21acf52878703b3b4bfc"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-19-g55699d2"
+  git_tag: "v0.1.1-20-g0acfda6"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/nextflow/io/untar/main.nf
+++ b/target/nextflow/io/untar/main.nf
@@ -2997,9 +2997,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/untar",
    "viash_version" : "0.9.0",
-    "git_commit" : "55699d24c0ff8d88e572ccc1a5ebc40217bb9524",
+    "git_commit" : "0acfda628d38430a7cdc21acf52878703b3b4bfc",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-19-g55699d2"
+    "git_tag" : "v0.1.1-20-g0acfda6"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/runner/.config.vsh.yaml
+++ b/target/nextflow/runner/.config.vsh.yaml
@@ -192,9 +192,9 @@ build_info:
  output: "target/nextflow/runner"
  executable: "target/nextflow/runner/main.nf"
  viash_version: "0.9.0"
-  git_commit: "55699d24c0ff8d88e572ccc1a5ebc40217bb9524"
+  git_commit: "0acfda628d38430a7cdc21acf52878703b3b4bfc"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-19-g55699d2"
+  git_tag: "v0.1.1-20-g0acfda6"
  dependencies:
  - "target/nextflow/demultiplex"
  - "target/nextflow/io/publish"
--- a/target/nextflow/runner/main.nf
+++ b/target/nextflow/runner/main.nf
@@ -3040,9 +3040,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/runner",
    "viash_version" : "0.9.0",
-    "git_commit" : "55699d24c0ff8d88e572ccc1a5ebc40217bb9524",
+    "git_commit" : "0acfda628d38430a7cdc21acf52878703b3b4bfc",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-19-g55699d2"
+    "git_tag" : "v0.1.1-20-g0acfda6"
  },
  "package_config" : {
    "name" : "demultiplex",