Build branch main with version main (45accaa)

Build pipeline: viash-hub.demultiplex.main-ghkns Source commit: 45accaa50e Source message: Avoid empty csv entries when parsing sample information (#29)
2024-12-11 18:06:57 +00:00
parent 2121a3ac1c
commit 6be5d38b03
22 changed files with 71 additions and 59 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,9 @@
+# demultiplex v0.3.2
+
+# Bug fixes
+
+* Ignore empty CSV entries when parsing sample information (PR #29).
+
 # demultiplex v0.3.1

 # Minor updates
--- a/src/dataflow/gather_fastqs_and_validate/main.nf
+++ b/src/dataflow/gather_fastqs_and_validate/main.nf
@@ -50,7 +50,10 @@ workflow run_wf {
              println "Found sample names column '${csv_items[sample_id_column_index]}'."
              return
            }
-            samples += csv_items[sample_id_column_index]
+            def candidate_sample_id = csv_items[sample_id_column_index]
+            if (candidate_sample_id?.trim()) { // Don't add empty csv entries.
+              samples += csv_items[sample_id_column_index]
+            }
          }
          // This return is important! (If 'true' is returned, the parsing stops.)
          return 
--- 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: "5c096fce4015435019d81e2cc524a478f4034adc"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-10-g5c096fc"
+  git_commit: "45accaa50e52c6b29c78259995293789f345c80d"
+  git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-11-g45accaa"
 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="2024-12-11T15:28:43Z"
+LABEL org.opencontainers.image.created="2024-12-11T17:49:17Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="5c096fce4015435019d81e2cc524a478f4034adc"
+LABEL org.opencontainers.image.revision="45accaa50e52c6b29c78259995293789f345c80d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/io/publish/.config.vsh.yaml
+++ b/target/executable/io/publish/.config.vsh.yaml
@@ -170,9 +170,9 @@ build_info:
  output: "target/executable/io/publish"
  executable: "target/executable/io/publish/publish"
  viash_version: "0.9.0"
-  git_commit: "5c096fce4015435019d81e2cc524a478f4034adc"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-10-g5c096fc"
+  git_commit: "45accaa50e52c6b29c78259995293789f345c80d"
+  git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-11-g45accaa"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/executable/io/publish/publish
+++ b/target/executable/io/publish/publish
@@ -482,9 +482,9 @@ 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="2024-12-11T15:28:44Z"
+LABEL org.opencontainers.image.created="2024-12-11T17:49:17Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="5c096fce4015435019d81e2cc524a478f4034adc"
+LABEL org.opencontainers.image.revision="45accaa50e52c6b29c78259995293789f345c80d"
 LABEL org.opencontainers.image.version="main"

 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: "5c096fce4015435019d81e2cc524a478f4034adc"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-10-g5c096fc"
+  git_commit: "45accaa50e52c6b29c78259995293789f345c80d"
+  git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-11-g45accaa"
 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="2024-12-11T15:28:44Z"
+LABEL org.opencontainers.image.created="2024-12-11T17:49:18Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="5c096fce4015435019d81e2cc524a478f4034adc"
+LABEL org.opencontainers.image.revision="45accaa50e52c6b29c78259995293789f345c80d"
 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
@@ -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: "5c096fce4015435019d81e2cc524a478f4034adc"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-10-g5c096fc"
+  git_commit: "45accaa50e52c6b29c78259995293789f345c80d"
+  git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-11-g45accaa"
 package_config:
  name: "demultiplex"
  version: "main"
--- 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" : "5c096fce4015435019d81e2cc524a478f4034adc",
-    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-10-g5c096fc"
+    "git_commit" : "45accaa50e52c6b29c78259995293789f345c80d",
+    "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-11-g45accaa"
  },
  "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: "5c096fce4015435019d81e2cc524a478f4034adc"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-10-g5c096fc"
+  git_commit: "45accaa50e52c6b29c78259995293789f345c80d"
+  git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-11-g45accaa"
 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
@@ -2965,9 +2965,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
    "viash_version" : "0.9.0",
-    "git_commit" : "5c096fce4015435019d81e2cc524a478f4034adc",
-    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-10-g5c096fc"
+    "git_commit" : "45accaa50e52c6b29c78259995293789f345c80d",
+    "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-11-g45accaa"
  },
  "package_config" : {
    "name" : "demultiplex",
@@ -3063,7 +3063,10 @@ workflow run_wf {
              println "Found sample names column '${csv_items[sample_id_column_index]}'."
              return
            }
-            samples += csv_items[sample_id_column_index]
+            def candidate_sample_id = csv_items[sample_id_column_index]
+            if (candidate_sample_id?.trim()) { // Don't add empty csv entries.
+              samples += csv_items[sample_id_column_index]
+            }
          }
          // This return is important! (If 'true' is returned, the parsing stops.)
          return 
--- 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: "5c096fce4015435019d81e2cc524a478f4034adc"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-10-g5c096fc"
+  git_commit: "45accaa50e52c6b29c78259995293789f345c80d"
+  git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-11-g45accaa"
  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" : "5c096fce4015435019d81e2cc524a478f4034adc",
-    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-10-g5c096fc"
+    "git_commit" : "45accaa50e52c6b29c78259995293789f345c80d",
+    "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-11-g45accaa"
  },
  "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: "5c096fce4015435019d81e2cc524a478f4034adc"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-10-g5c096fc"
+  git_commit: "45accaa50e52c6b29c78259995293789f345c80d"
+  git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-11-g45accaa"
 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
@@ -2977,9 +2977,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/interop_summary_to_csv",
    "viash_version" : "0.9.0",
-    "git_commit" : "5c096fce4015435019d81e2cc524a478f4034adc",
-    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-10-g5c096fc"
+    "git_commit" : "45accaa50e52c6b29c78259995293789f345c80d",
+    "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-11-g45accaa"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/io/publish/.config.vsh.yaml
+++ b/target/nextflow/io/publish/.config.vsh.yaml
@@ -170,9 +170,9 @@ build_info:
  output: "target/nextflow/io/publish"
  executable: "target/nextflow/io/publish/main.nf"
  viash_version: "0.9.0"
-  git_commit: "5c096fce4015435019d81e2cc524a478f4034adc"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-10-g5c096fc"
+  git_commit: "45accaa50e52c6b29c78259995293789f345c80d"
+  git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-11-g45accaa"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/nextflow/io/publish/main.nf
+++ b/target/nextflow/io/publish/main.nf
@@ -3012,9 +3012,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish",
    "viash_version" : "0.9.0",
-    "git_commit" : "5c096fce4015435019d81e2cc524a478f4034adc",
-    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-10-g5c096fc"
+    "git_commit" : "45accaa50e52c6b29c78259995293789f345c80d",
+    "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-11-g45accaa"
  },
  "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: "5c096fce4015435019d81e2cc524a478f4034adc"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-10-g5c096fc"
+  git_commit: "45accaa50e52c6b29c78259995293789f345c80d"
+  git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-11-g45accaa"
 package_config:
  name: "demultiplex"
  version: "main"
--- 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" : "5c096fce4015435019d81e2cc524a478f4034adc",
-    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-10-g5c096fc"
+    "git_commit" : "45accaa50e52c6b29c78259995293789f345c80d",
+    "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-11-g45accaa"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/runner/.config.vsh.yaml
+++ b/target/nextflow/runner/.config.vsh.yaml
@@ -182,9 +182,9 @@ build_info:
  output: "target/nextflow/runner"
  executable: "target/nextflow/runner/main.nf"
  viash_version: "0.9.0"
-  git_commit: "5c096fce4015435019d81e2cc524a478f4034adc"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-10-g5c096fc"
+  git_commit: "45accaa50e52c6b29c78259995293789f345c80d"
+  git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-11-g45accaa"
  dependencies:
  - "target/nextflow/demultiplex"
  - "target/nextflow/io/publish"
--- a/target/nextflow/runner/main.nf
+++ b/target/nextflow/runner/main.nf
@@ -3027,9 +3027,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/runner",
    "viash_version" : "0.9.0",
-    "git_commit" : "5c096fce4015435019d81e2cc524a478f4034adc",
-    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-10-g5c096fc"
+    "git_commit" : "45accaa50e52c6b29c78259995293789f345c80d",
+    "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-11-g45accaa"
  },
  "package_config" : {
    "name" : "demultiplex",