diff --git a/_viash.yaml b/_viash.yaml index b3a09d4..5229d3a 100644 --- 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 diff --git a/src/demultiplex/integration_tests.sh b/src/demultiplex/integration_tests.sh index 1042753..5d01dcd 100755 --- 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 diff --git a/src/demultiplex/test.nf b/src/demultiplex/test.nf index c46a438..922fb81 100644 --- 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/", ] ]) 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 04160e4..a513d54 100644 --- 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" 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 1c57d0f..bbc8ad5 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="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 diff --git a/target/executable/io/untar/.config.vsh.yaml b/target/executable/io/untar/.config.vsh.yaml index 112bbef..7e5eb0b 100644 --- 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" diff --git a/target/executable/io/untar/untar b/target/executable/io/untar/untar index 9597c62..41f8df7 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="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 diff --git a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml index c89f60f..4e428eb 100644 --- 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" diff --git a/target/nextflow/dataflow/combine_samples/main.nf b/target/nextflow/dataflow/combine_samples/main.nf index c5641f1..5562d8d 100644 --- 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" } ] }, 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 bba9007..5b5c3f7 100644 --- 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" diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf index 005fcfc..e7a67e6 100644 --- 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" } ] }, diff --git a/target/nextflow/demultiplex/.config.vsh.yaml b/target/nextflow/demultiplex/.config.vsh.yaml index f5bfbcb..8be1d88 100644 --- 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" diff --git a/target/nextflow/demultiplex/main.nf b/target/nextflow/demultiplex/main.nf index 51078b2..76b2e55 100644 --- 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" } ] }, 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 19d4abf..0a9c4e8 100644 --- 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" diff --git a/target/nextflow/io/interop_summary_to_csv/main.nf b/target/nextflow/io/interop_summary_to_csv/main.nf index d87c321..d4e482b 100644 --- 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" } ] }, diff --git a/target/nextflow/io/untar/.config.vsh.yaml b/target/nextflow/io/untar/.config.vsh.yaml index 99e7054..6c9838a 100644 --- 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" diff --git a/target/nextflow/io/untar/main.nf b/target/nextflow/io/untar/main.nf index 6d8565b..fd0b271 100644 --- 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" } ] },