From 26f9bf6da22b28f4046345865b69c81c176861b6 Mon Sep 17 00:00:00 2001
From: CI <toni@data-intuitive.com>
Date: Thu, 20 Mar 2025 20:56:23 +0000
Subject: [PATCH] Build branch main with version main (0acfda6)

Build pipeline: viash-hub.demultiplex.main-zmw5v

Source commit: https://github.com/viash-hub/demultiplex/commit/0acfda628d38430a7cdc21acf52878703b3b4bfc

Source message: Ignore lines starting with '#' in run information file (#39)
---
 CHANGELOG.md                                              | 6 ++++++
 src/dataflow/gather_fastqs_and_validate/main.nf           | 4 ++--
 .../executable/io/interop_summary_to_csv/.config.vsh.yaml | 4 ++--
 .../io/interop_summary_to_csv/interop_summary_to_csv      | 4 ++--
 target/executable/io/publish/.config.vsh.yaml             | 4 ++--
 target/executable/io/publish/publish                      | 4 ++--
 target/executable/io/untar/.config.vsh.yaml               | 4 ++--
 target/executable/io/untar/untar                          | 4 ++--
 target/nextflow/dataflow/combine_samples/.config.vsh.yaml | 4 ++--
 target/nextflow/dataflow/combine_samples/main.nf          | 4 ++--
 .../dataflow/gather_fastqs_and_validate/.config.vsh.yaml  | 4 ++--
 .../nextflow/dataflow/gather_fastqs_and_validate/main.nf  | 8 ++++----
 target/nextflow/demultiplex/.config.vsh.yaml              | 4 ++--
 target/nextflow/demultiplex/main.nf                       | 4 ++--
 .../nextflow/io/interop_summary_to_csv/.config.vsh.yaml   | 4 ++--
 target/nextflow/io/interop_summary_to_csv/main.nf         | 4 ++--
 target/nextflow/io/publish/.config.vsh.yaml               | 4 ++--
 target/nextflow/io/publish/main.nf                        | 4 ++--
 target/nextflow/io/untar/.config.vsh.yaml                 | 4 ++--
 target/nextflow/io/untar/main.nf                          | 4 ++--
 target/nextflow/runner/.config.vsh.yaml                   | 4 ++--
 target/nextflow/runner/main.nf                            | 4 ++--
 22 files changed, 50 insertions(+), 44 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 960ad4a..41be392 100644
--- 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
diff --git a/src/dataflow/gather_fastqs_and_validate/main.nf b/src/dataflow/gather_fastqs_and_validate/main.nf
index 98ee102..6d4d925 100644
--- 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]
diff --git a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
index 090988f..da8f78c 100644
--- 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"
diff --git a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
index 179995e..502baa7 100755
--- 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
diff --git a/target/executable/io/publish/.config.vsh.yaml b/target/executable/io/publish/.config.vsh.yaml
index 4d027fb..abf6f7f 100644
--- 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"
diff --git a/target/executable/io/publish/publish b/target/executable/io/publish/publish
index 763d0ed..30694a6 100755
--- 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
diff --git a/target/executable/io/untar/.config.vsh.yaml b/target/executable/io/untar/.config.vsh.yaml
index 44cbc0f..8a3be3c 100644
--- 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"
diff --git a/target/executable/io/untar/untar b/target/executable/io/untar/untar
index a236a65..3e1fd18 100755
--- 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
diff --git a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
index beab819..76d7a0f 100644
--- 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"
diff --git a/target/nextflow/dataflow/combine_samples/main.nf b/target/nextflow/dataflow/combine_samples/main.nf
index 436f930..3621ae9 100644
--- 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",
diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
index 23a932a..1b2698a 100644
--- 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"
diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
index 1ee728e..44aa2fe 100644
--- 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]
diff --git a/target/nextflow/demultiplex/.config.vsh.yaml b/target/nextflow/demultiplex/.config.vsh.yaml
index 0b530f9..3c9a318 100644
--- 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"
diff --git a/target/nextflow/demultiplex/main.nf b/target/nextflow/demultiplex/main.nf
index de1cb63..a0399e2 100644
--- 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",
diff --git a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
index dd91b04..d596c84 100644
--- 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"
diff --git a/target/nextflow/io/interop_summary_to_csv/main.nf b/target/nextflow/io/interop_summary_to_csv/main.nf
index a7b9fe6..51a8f5e 100644
--- 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",
diff --git a/target/nextflow/io/publish/.config.vsh.yaml b/target/nextflow/io/publish/.config.vsh.yaml
index a956635..19d084b 100644
--- 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"
diff --git a/target/nextflow/io/publish/main.nf b/target/nextflow/io/publish/main.nf
index f7dd834..b3954cf 100644
--- 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",
diff --git a/target/nextflow/io/untar/.config.vsh.yaml b/target/nextflow/io/untar/.config.vsh.yaml
index 05cc022..a39c61f 100644
--- 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"
diff --git a/target/nextflow/io/untar/main.nf b/target/nextflow/io/untar/main.nf
index 820f910..ac9f7ce 100644
--- 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",
diff --git a/target/nextflow/runner/.config.vsh.yaml b/target/nextflow/runner/.config.vsh.yaml
index 7036ae0..0595a3a 100644
--- 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"
diff --git a/target/nextflow/runner/main.nf b/target/nextflow/runner/main.nf
index 1cb785f..bfe653f 100644
--- 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",