From 33e99f842db6959acf68c65595f5105a4bb79f21 Mon Sep 17 00:00:00 2001
From: CI <toni@data-intuitive.com>
Date: Fri, 10 Jan 2025 15:13:29 +0000
Subject: [PATCH] Build branch copycomplete_check with version
 copycomplete_check (4d8c825)

Build pipeline: viash-hub.demultiplex.copycomplete-check-6k5m4

Source commit: https://github.com/viash-hub/demultiplex/commit/4d8c825fdf075218611913f59ab92fd85043b499

Source message: Update CHANGELOG
---
 CHANGELOG.md                                               | 7 +++++++
 .../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   | 4 ++--
 target/nextflow/demultiplex/.config.vsh.yaml               | 4 ++--
 target/nextflow/demultiplex/main.nf                        | 4 ++--
 target/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 ++--
 21 files changed, 47 insertions(+), 40 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 68ac6c0..387da3e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,10 @@
+# demultiplex v0.3.5
+
+## Minor updates
+
+* In case Illumina data is detected in the input folder, check for the presence of the 'copyComplete.txt' file.
+  This check can be disabled using `--skip_copycomplete_check` (PR #34).
+
 # demultiplex v0.3.4
 
 ## Minor updates
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 5a93d41..a1bcc62 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: "d1416b59c493c554210dc608b4e60fcca6ce1665"
+  git_commit: "4d8c825fdf075218611913f59ab92fd85043b499"
   git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-15-gd1416b5"
+  git_tag: "v0.1.1-16-g4d8c825"
 package_config:
   name: "demultiplex"
   version: "copycomplete_check"
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 14a14c3..4169afb 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="2025-01-10T14:42:21Z"
+LABEL org.opencontainers.image.created="2025-01-10T14:59:08Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="d1416b59c493c554210dc608b4e60fcca6ce1665"
+LABEL org.opencontainers.image.revision="4d8c825fdf075218611913f59ab92fd85043b499"
 LABEL org.opencontainers.image.version="copycomplete_check"
 
 VIASHDOCKER
diff --git a/target/executable/io/publish/.config.vsh.yaml b/target/executable/io/publish/.config.vsh.yaml
index a52f14c..a3837af 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: "d1416b59c493c554210dc608b4e60fcca6ce1665"
+  git_commit: "4d8c825fdf075218611913f59ab92fd85043b499"
   git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-15-gd1416b5"
+  git_tag: "v0.1.1-16-g4d8c825"
 package_config:
   name: "demultiplex"
   version: "copycomplete_check"
diff --git a/target/executable/io/publish/publish b/target/executable/io/publish/publish
index f600699..b7b6486 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="2025-01-10T14:42:21Z"
+LABEL org.opencontainers.image.created="2025-01-10T14:59:08Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="d1416b59c493c554210dc608b4e60fcca6ce1665"
+LABEL org.opencontainers.image.revision="4d8c825fdf075218611913f59ab92fd85043b499"
 LABEL org.opencontainers.image.version="copycomplete_check"
 
 VIASHDOCKER
diff --git a/target/executable/io/untar/.config.vsh.yaml b/target/executable/io/untar/.config.vsh.yaml
index b965a77..cf61171 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: "d1416b59c493c554210dc608b4e60fcca6ce1665"
+  git_commit: "4d8c825fdf075218611913f59ab92fd85043b499"
   git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-15-gd1416b5"
+  git_tag: "v0.1.1-16-g4d8c825"
 package_config:
   name: "demultiplex"
   version: "copycomplete_check"
diff --git a/target/executable/io/untar/untar b/target/executable/io/untar/untar
index 99a57df..6226438 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="2025-01-10T14:42:22Z"
+LABEL org.opencontainers.image.created="2025-01-10T14:59:08Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="d1416b59c493c554210dc608b4e60fcca6ce1665"
+LABEL org.opencontainers.image.revision="4d8c825fdf075218611913f59ab92fd85043b499"
 LABEL org.opencontainers.image.version="copycomplete_check"
 
 VIASHDOCKER
diff --git a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
index 70a3970..fc99c3d 100644
--- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
+++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
@@ -144,9 +144,9 @@ build_info:
   output: "target/nextflow/dataflow/combine_samples"
   executable: "target/nextflow/dataflow/combine_samples/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d1416b59c493c554210dc608b4e60fcca6ce1665"
+  git_commit: "4d8c825fdf075218611913f59ab92fd85043b499"
   git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-15-gd1416b5"
+  git_tag: "v0.1.1-16-g4d8c825"
 package_config:
   name: "demultiplex"
   version: "copycomplete_check"
diff --git a/target/nextflow/dataflow/combine_samples/main.nf b/target/nextflow/dataflow/combine_samples/main.nf
index 8da5dde..3cfe775 100644
--- a/target/nextflow/dataflow/combine_samples/main.nf
+++ b/target/nextflow/dataflow/combine_samples/main.nf
@@ -2980,9 +2980,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/dataflow/combine_samples",
     "viash_version" : "0.9.0",
-    "git_commit" : "d1416b59c493c554210dc608b4e60fcca6ce1665",
+    "git_commit" : "4d8c825fdf075218611913f59ab92fd85043b499",
     "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-15-gd1416b5"
+    "git_tag" : "v0.1.1-16-g4d8c825"
   },
   "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 db5bcf5..673509b 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: "d1416b59c493c554210dc608b4e60fcca6ce1665"
+  git_commit: "4d8c825fdf075218611913f59ab92fd85043b499"
   git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-15-gd1416b5"
+  git_tag: "v0.1.1-16-g4d8c825"
 package_config:
   name: "demultiplex"
   version: "copycomplete_check"
diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
index 0a6a2ff..57a01a0 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" : "d1416b59c493c554210dc608b4e60fcca6ce1665",
+    "git_commit" : "4d8c825fdf075218611913f59ab92fd85043b499",
     "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-15-gd1416b5"
+    "git_tag" : "v0.1.1-16-g4d8c825"
   },
   "package_config" : {
     "name" : "demultiplex",
diff --git a/target/nextflow/demultiplex/.config.vsh.yaml b/target/nextflow/demultiplex/.config.vsh.yaml
index 32b1206..314785f 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: "d1416b59c493c554210dc608b4e60fcca6ce1665"
+  git_commit: "4d8c825fdf075218611913f59ab92fd85043b499"
   git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-15-gd1416b5"
+  git_tag: "v0.1.1-16-g4d8c825"
   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 1cd1227..755a281 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" : "d1416b59c493c554210dc608b4e60fcca6ce1665",
+    "git_commit" : "4d8c825fdf075218611913f59ab92fd85043b499",
     "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-15-gd1416b5"
+    "git_tag" : "v0.1.1-16-g4d8c825"
   },
   "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 2179c5b..ec03767 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: "d1416b59c493c554210dc608b4e60fcca6ce1665"
+  git_commit: "4d8c825fdf075218611913f59ab92fd85043b499"
   git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-15-gd1416b5"
+  git_tag: "v0.1.1-16-g4d8c825"
 package_config:
   name: "demultiplex"
   version: "copycomplete_check"
diff --git a/target/nextflow/io/interop_summary_to_csv/main.nf b/target/nextflow/io/interop_summary_to_csv/main.nf
index efa00e9..aa4fd1b 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" : "d1416b59c493c554210dc608b4e60fcca6ce1665",
+    "git_commit" : "4d8c825fdf075218611913f59ab92fd85043b499",
     "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-15-gd1416b5"
+    "git_tag" : "v0.1.1-16-g4d8c825"
   },
   "package_config" : {
     "name" : "demultiplex",
diff --git a/target/nextflow/io/publish/.config.vsh.yaml b/target/nextflow/io/publish/.config.vsh.yaml
index ed0a91f..688b22e 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: "d1416b59c493c554210dc608b4e60fcca6ce1665"
+  git_commit: "4d8c825fdf075218611913f59ab92fd85043b499"
   git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-15-gd1416b5"
+  git_tag: "v0.1.1-16-g4d8c825"
 package_config:
   name: "demultiplex"
   version: "copycomplete_check"
diff --git a/target/nextflow/io/publish/main.nf b/target/nextflow/io/publish/main.nf
index cd1902a..56b73ca 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" : "d1416b59c493c554210dc608b4e60fcca6ce1665",
+    "git_commit" : "4d8c825fdf075218611913f59ab92fd85043b499",
     "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-15-gd1416b5"
+    "git_tag" : "v0.1.1-16-g4d8c825"
   },
   "package_config" : {
     "name" : "demultiplex",
diff --git a/target/nextflow/io/untar/.config.vsh.yaml b/target/nextflow/io/untar/.config.vsh.yaml
index dde5567..23cf9d8 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: "d1416b59c493c554210dc608b4e60fcca6ce1665"
+  git_commit: "4d8c825fdf075218611913f59ab92fd85043b499"
   git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-15-gd1416b5"
+  git_tag: "v0.1.1-16-g4d8c825"
 package_config:
   name: "demultiplex"
   version: "copycomplete_check"
diff --git a/target/nextflow/io/untar/main.nf b/target/nextflow/io/untar/main.nf
index 4ab9cb5..bed9e44 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" : "d1416b59c493c554210dc608b4e60fcca6ce1665",
+    "git_commit" : "4d8c825fdf075218611913f59ab92fd85043b499",
     "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-15-gd1416b5"
+    "git_tag" : "v0.1.1-16-g4d8c825"
   },
   "package_config" : {
     "name" : "demultiplex",
diff --git a/target/nextflow/runner/.config.vsh.yaml b/target/nextflow/runner/.config.vsh.yaml
index 8bb9059..e73819e 100644
--- a/target/nextflow/runner/.config.vsh.yaml
+++ b/target/nextflow/runner/.config.vsh.yaml
@@ -184,9 +184,9 @@ build_info:
   output: "target/nextflow/runner"
   executable: "target/nextflow/runner/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d1416b59c493c554210dc608b4e60fcca6ce1665"
+  git_commit: "4d8c825fdf075218611913f59ab92fd85043b499"
   git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-15-gd1416b5"
+  git_tag: "v0.1.1-16-g4d8c825"
   dependencies:
   - "target/nextflow/demultiplex"
   - "target/nextflow/io/publish"
diff --git a/target/nextflow/runner/main.nf b/target/nextflow/runner/main.nf
index 514c87e..6062c60 100644
--- a/target/nextflow/runner/main.nf
+++ b/target/nextflow/runner/main.nf
@@ -3029,9 +3029,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/runner",
     "viash_version" : "0.9.0",
-    "git_commit" : "d1416b59c493c554210dc608b4e60fcca6ce1665",
+    "git_commit" : "4d8c825fdf075218611913f59ab92fd85043b499",
     "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-15-gd1416b5"
+    "git_tag" : "v0.1.1-16-g4d8c825"
   },
   "package_config" : {
     "name" : "demultiplex",