Build branch main with version main (a311a12)

Build pipeline: viash-hub.demultiplex.main-7bh8g Source commit: a311a12056 Source message: Update integration tests (#18) * Updated test data (version) and pointer + variable * Add resources_test argument in unit test
2024-10-08 12:39:21 +00:00
parent e52e4f7724
commit 0e5d645386
17 changed files with 70 additions and 67 deletions
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -8,8 +8,8 @@ links:
  repository: https://github.com/viash-hub/demultiplex
 info:
  test_resources:
-    - path: https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz
-      dest: test_resources
+    - path: gs://viash-hub-test-data/demultiplex/v2/
+      dest: testData

 viash_version: 0.9.0

--- a/src/demultiplex/integration_tests.sh
+++ b/src/demultiplex/integration_tests.sh
@@ -13,4 +13,5 @@ nextflow run . \
  -profile docker,no_publish \
  -entry test_wf \
  -c src/config/tests.config \
+  --resources_test https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/ \
  -resume
--- a/src/demultiplex/test.nf
+++ b/src/demultiplex/test.nf
@@ -2,13 +2,15 @@ nextflow.enable.dsl=2

 include { demultiplex } from params.rootDir + "/target/nextflow/demultiplex/main.nf"

+params.resources_test = params.rootDir + "/testData/"
+
 workflow test_wf {
  output_ch = Channel.fromList([
        [
          // sample_sheet: resources_test.resolve("bcl_convert_samplesheet.csv"),
          // input: resources_test.resolve("iseq-DI/"),
          //sample_sheet: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/SampleSheet.csv",
-          input: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz",
+          input: params.resources_test + "200624_A00834_0183_BHMTFYDRXX.tar.gz",
          publish_dir: "output_dir/",
        ]
      ])
--- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
@@ -141,17 +141,17 @@ 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: "aca8016d742c72e4badc2fc91a40b8f7f1290010"
-  git_remote: "https://x-access-token:ghs_iapdCPeFvCi4LG9kGlxTAK6B1ovFxM2rf4WE@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-1-gaca8016"
+  git_commit: "a311a12056e0dbcfa8103ab0a4f6c7350f2f4c4e"
+  git_remote: "https://x-access-token:ghs_I5gscIGc0N3NRaJ8ljNMSCb4w56xXA2xlViM@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-2-ga311a12"
 package_config:
  name: "demultiplex"
  version: "main"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
-    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
-      dest: "test_resources"
+    - path: "gs://viash-hub-test-data/demultiplex/v2/"
+      dest: "testData"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- 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="2024-09-17T15:18:53Z"
+LABEL org.opencontainers.image.created="2024-10-08T12:19:34Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="aca8016d742c72e4badc2fc91a40b8f7f1290010"
+LABEL org.opencontainers.image.revision="a311a12056e0dbcfa8103ab0a4f6c7350f2f4c4e"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/io/untar/.config.vsh.yaml
+++ b/target/executable/io/untar/.config.vsh.yaml
@@ -148,17 +148,17 @@ build_info:
  output: "target/executable/io/untar"
  executable: "target/executable/io/untar/untar"
  viash_version: "0.9.0"
-  git_commit: "aca8016d742c72e4badc2fc91a40b8f7f1290010"
-  git_remote: "https://x-access-token:ghs_iapdCPeFvCi4LG9kGlxTAK6B1ovFxM2rf4WE@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-1-gaca8016"
+  git_commit: "a311a12056e0dbcfa8103ab0a4f6c7350f2f4c4e"
+  git_remote: "https://x-access-token:ghs_I5gscIGc0N3NRaJ8ljNMSCb4w56xXA2xlViM@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-2-ga311a12"
 package_config:
  name: "demultiplex"
  version: "main"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
-    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
-      dest: "test_resources"
+    - path: "gs://viash-hub-test-data/demultiplex/v2/"
+      dest: "testData"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- 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="2024-09-17T15:18:53Z"
+LABEL org.opencontainers.image.created="2024-10-08T12:19:34Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="aca8016d742c72e4badc2fc91a40b8f7f1290010"
+LABEL org.opencontainers.image.revision="a311a12056e0dbcfa8103ab0a4f6c7350f2f4c4e"
 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
@@ -139,17 +139,17 @@ build_info:
  output: "target/nextflow/dataflow/combine_samples"
  executable: "target/nextflow/dataflow/combine_samples/main.nf"
  viash_version: "0.9.0"
-  git_commit: "aca8016d742c72e4badc2fc91a40b8f7f1290010"
-  git_remote: "https://x-access-token:ghs_iapdCPeFvCi4LG9kGlxTAK6B1ovFxM2rf4WE@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-1-gaca8016"
+  git_commit: "a311a12056e0dbcfa8103ab0a4f6c7350f2f4c4e"
+  git_remote: "https://x-access-token:ghs_I5gscIGc0N3NRaJ8ljNMSCb4w56xXA2xlViM@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-2-ga311a12"
 package_config:
  name: "demultiplex"
  version: "main"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
-    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
-      dest: "test_resources"
+    - path: "gs://viash-hub-test-data/demultiplex/v2/"
+      dest: "testData"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- 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" : "aca8016d742c72e4badc2fc91a40b8f7f1290010",
-    "git_remote" : "https://x-access-token:ghs_iapdCPeFvCi4LG9kGlxTAK6B1ovFxM2rf4WE@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-1-gaca8016"
+    "git_commit" : "a311a12056e0dbcfa8103ab0a4f6c7350f2f4c4e",
+    "git_remote" : "https://x-access-token:ghs_I5gscIGc0N3NRaJ8ljNMSCb4w56xXA2xlViM@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-2-ga311a12"
  },
  "package_config" : {
    "name" : "demultiplex",
@@ -2983,8 +2983,8 @@ meta = [
    "info" : {
      "test_resources" : [
        {
-          "path" : "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz",
-          "dest" : "test_resources"
+          "path" : "gs://viash-hub-test-data/demultiplex/v2/",
+          "dest" : "testData"
        }
      ]
    },
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
@@ -133,17 +133,17 @@ 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: "aca8016d742c72e4badc2fc91a40b8f7f1290010"
-  git_remote: "https://x-access-token:ghs_iapdCPeFvCi4LG9kGlxTAK6B1ovFxM2rf4WE@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-1-gaca8016"
+  git_commit: "a311a12056e0dbcfa8103ab0a4f6c7350f2f4c4e"
+  git_remote: "https://x-access-token:ghs_I5gscIGc0N3NRaJ8ljNMSCb4w56xXA2xlViM@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-2-ga311a12"
 package_config:
  name: "demultiplex"
  version: "main"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
-    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
-      dest: "test_resources"
+    - path: "gs://viash-hub-test-data/demultiplex/v2/"
+      dest: "testData"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- 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" : "aca8016d742c72e4badc2fc91a40b8f7f1290010",
-    "git_remote" : "https://x-access-token:ghs_iapdCPeFvCi4LG9kGlxTAK6B1ovFxM2rf4WE@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-1-gaca8016"
+    "git_commit" : "a311a12056e0dbcfa8103ab0a4f6c7350f2f4c4e",
+    "git_remote" : "https://x-access-token:ghs_I5gscIGc0N3NRaJ8ljNMSCb4w56xXA2xlViM@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-2-ga311a12"
  },
  "package_config" : {
    "name" : "demultiplex",
@@ -2976,8 +2976,8 @@ meta = [
    "info" : {
      "test_resources" : [
        {
-          "path" : "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz",
-          "dest" : "test_resources"
+          "path" : "gs://viash-hub-test-data/demultiplex/v2/",
+          "dest" : "testData"
        }
      ]
    },
--- a/target/nextflow/demultiplex/.config.vsh.yaml
+++ b/target/nextflow/demultiplex/.config.vsh.yaml
@@ -186,9 +186,9 @@ build_info:
  output: "target/nextflow/demultiplex"
  executable: "target/nextflow/demultiplex/main.nf"
  viash_version: "0.9.0"
-  git_commit: "aca8016d742c72e4badc2fc91a40b8f7f1290010"
-  git_remote: "https://x-access-token:ghs_iapdCPeFvCi4LG9kGlxTAK6B1ovFxM2rf4WE@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-1-gaca8016"
+  git_commit: "a311a12056e0dbcfa8103ab0a4f6c7350f2f4c4e"
+  git_remote: "https://x-access-token:ghs_I5gscIGc0N3NRaJ8ljNMSCb4w56xXA2xlViM@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-2-ga311a12"
  dependencies:
  - "target/nextflow/io/untar"
  - "target/nextflow/dataflow/gather_fastqs_and_validate"
@@ -203,8 +203,8 @@ package_config:
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
-    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
-      dest: "test_resources"
+    - path: "gs://viash-hub-test-data/demultiplex/v2/"
+      dest: "testData"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/nextflow/demultiplex/main.nf
+++ b/target/nextflow/demultiplex/main.nf
@@ -3049,9 +3049,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/demultiplex",
    "viash_version" : "0.9.0",
-    "git_commit" : "aca8016d742c72e4badc2fc91a40b8f7f1290010",
-    "git_remote" : "https://x-access-token:ghs_iapdCPeFvCi4LG9kGlxTAK6B1ovFxM2rf4WE@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-1-gaca8016"
+    "git_commit" : "a311a12056e0dbcfa8103ab0a4f6c7350f2f4c4e",
+    "git_remote" : "https://x-access-token:ghs_I5gscIGc0N3NRaJ8ljNMSCb4w56xXA2xlViM@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-2-ga311a12"
  },
  "package_config" : {
    "name" : "demultiplex",
@@ -3060,8 +3060,8 @@ meta = [
    "info" : {
      "test_resources" : [
        {
-          "path" : "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz",
-          "dest" : "test_resources"
+          "path" : "gs://viash-hub-test-data/demultiplex/v2/",
+          "dest" : "testData"
        }
      ]
    },
--- a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
@@ -141,17 +141,17 @@ 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: "aca8016d742c72e4badc2fc91a40b8f7f1290010"
-  git_remote: "https://x-access-token:ghs_iapdCPeFvCi4LG9kGlxTAK6B1ovFxM2rf4WE@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-1-gaca8016"
+  git_commit: "a311a12056e0dbcfa8103ab0a4f6c7350f2f4c4e"
+  git_remote: "https://x-access-token:ghs_I5gscIGc0N3NRaJ8ljNMSCb4w56xXA2xlViM@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-2-ga311a12"
 package_config:
  name: "demultiplex"
  version: "main"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
-    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
-      dest: "test_resources"
+    - path: "gs://viash-hub-test-data/demultiplex/v2/"
+      dest: "testData"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- 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" : "aca8016d742c72e4badc2fc91a40b8f7f1290010",
-    "git_remote" : "https://x-access-token:ghs_iapdCPeFvCi4LG9kGlxTAK6B1ovFxM2rf4WE@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-1-gaca8016"
+    "git_commit" : "a311a12056e0dbcfa8103ab0a4f6c7350f2f4c4e",
+    "git_remote" : "https://x-access-token:ghs_I5gscIGc0N3NRaJ8ljNMSCb4w56xXA2xlViM@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-2-ga311a12"
  },
  "package_config" : {
    "name" : "demultiplex",
@@ -2988,8 +2988,8 @@ meta = [
    "info" : {
      "test_resources" : [
        {
-          "path" : "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz",
-          "dest" : "test_resources"
+          "path" : "gs://viash-hub-test-data/demultiplex/v2/",
+          "dest" : "testData"
        }
      ]
    },
--- a/target/nextflow/io/untar/.config.vsh.yaml
+++ b/target/nextflow/io/untar/.config.vsh.yaml
@@ -148,17 +148,17 @@ build_info:
  output: "target/nextflow/io/untar"
  executable: "target/nextflow/io/untar/main.nf"
  viash_version: "0.9.0"
-  git_commit: "aca8016d742c72e4badc2fc91a40b8f7f1290010"
-  git_remote: "https://x-access-token:ghs_iapdCPeFvCi4LG9kGlxTAK6B1ovFxM2rf4WE@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-1-gaca8016"
+  git_commit: "a311a12056e0dbcfa8103ab0a4f6c7350f2f4c4e"
+  git_remote: "https://x-access-token:ghs_I5gscIGc0N3NRaJ8ljNMSCb4w56xXA2xlViM@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-2-ga311a12"
 package_config:
  name: "demultiplex"
  version: "main"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
-    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
-      dest: "test_resources"
+    - path: "gs://viash-hub-test-data/demultiplex/v2/"
+      dest: "testData"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- 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" : "aca8016d742c72e4badc2fc91a40b8f7f1290010",
-    "git_remote" : "https://x-access-token:ghs_iapdCPeFvCi4LG9kGlxTAK6B1ovFxM2rf4WE@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-1-gaca8016"
+    "git_commit" : "a311a12056e0dbcfa8103ab0a4f6c7350f2f4c4e",
+    "git_remote" : "https://x-access-token:ghs_I5gscIGc0N3NRaJ8ljNMSCb4w56xXA2xlViM@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-2-ga311a12"
  },
  "package_config" : {
    "name" : "demultiplex",
@@ -3000,8 +3000,8 @@ meta = [
    "info" : {
      "test_resources" : [
        {
-          "path" : "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz",
-          "dest" : "test_resources"
+          "path" : "gs://viash-hub-test-data/demultiplex/v2/",
+          "dest" : "testData"
        }
      ]
    },