diff --git a/CHANGELOG.md b/CHANGELOG.md index 7608e8d..ba6ac9f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,8 +1,4 @@ -# demultiplex v0.2.0 - -## Breaking changes - -* `demultiplex` workflow: renamed `sample_sheet` argument to `run_information` (PR #24) +# demultiplex v0.3.0 ## Major updates @@ -34,6 +30,12 @@ The default structure in the output directory is: The `$publish_dir` variable corresponds to the argument provided with `--publish-dir`. The `date-time-stamp` is generated by the workflow based on when it was launched and is thus guaranteed to be unique. +# demultiplex v0.2.0 + +## Breaking changes + +* `demultiplex` workflow: renamed `sample_sheet` argument to `run_information` (PR #24) + ## New features * Add support for `bases2fastq` demultiplexer (PR #24) 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 fd9e33b..a114fbf 100644 --- 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: "64a371e168472c987d9ec61b0373b0e28762dfcd" - git_remote: "https://x-access-token:ghs_NEnBDPGgmRYfKlNL6VeMqiNleTP4aC2s2yz6@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-7-g64a371e" + git_commit: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f" + git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-8-gb7e30f3" 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 c269a9e..4e01eb6 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="2024-12-11T08:48:31Z" +LABEL org.opencontainers.image.created="2024-12-11T09:14:04Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="64a371e168472c987d9ec61b0373b0e28762dfcd" +LABEL org.opencontainers.image.revision="b7e30f394e7a4ae7a51961ade824e24ffe718e1f" 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 aa17ed8..d223b52 100644 --- 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: "64a371e168472c987d9ec61b0373b0e28762dfcd" - git_remote: "https://x-access-token:ghs_NEnBDPGgmRYfKlNL6VeMqiNleTP4aC2s2yz6@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-7-g64a371e" + git_commit: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f" + git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-8-gb7e30f3" package_config: name: "demultiplex" version: "main" diff --git a/target/executable/io/publish/publish b/target/executable/io/publish/publish index a32e36e..b504a92 100755 --- 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="2024-12-11T08:48:32Z" +LABEL org.opencontainers.image.created="2024-12-11T09:14:04Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="64a371e168472c987d9ec61b0373b0e28762dfcd" +LABEL org.opencontainers.image.revision="b7e30f394e7a4ae7a51961ade824e24ffe718e1f" 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 eae7313..d944c73 100644 --- 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: "64a371e168472c987d9ec61b0373b0e28762dfcd" - git_remote: "https://x-access-token:ghs_NEnBDPGgmRYfKlNL6VeMqiNleTP4aC2s2yz6@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-7-g64a371e" + git_commit: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f" + git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-8-gb7e30f3" package_config: name: "demultiplex" version: "main" diff --git a/target/executable/io/untar/untar b/target/executable/io/untar/untar index 36307c9..e31208c 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="2024-12-11T08:48:32Z" +LABEL org.opencontainers.image.created="2024-12-11T09:14:04Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="64a371e168472c987d9ec61b0373b0e28762dfcd" +LABEL org.opencontainers.image.revision="b7e30f394e7a4ae7a51961ade824e24ffe718e1f" 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 84611e4..4c51bfd 100644 --- 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: "64a371e168472c987d9ec61b0373b0e28762dfcd" - git_remote: "https://x-access-token:ghs_NEnBDPGgmRYfKlNL6VeMqiNleTP4aC2s2yz6@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-7-g64a371e" + git_commit: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f" + git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-8-gb7e30f3" 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 73d766c..bca0dd1 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" : "64a371e168472c987d9ec61b0373b0e28762dfcd", - "git_remote" : "https://x-access-token:ghs_NEnBDPGgmRYfKlNL6VeMqiNleTP4aC2s2yz6@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-7-g64a371e" + "git_commit" : "b7e30f394e7a4ae7a51961ade824e24ffe718e1f", + "git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-8-gb7e30f3" }, "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 ad0bbf5..c841bfa 100644 --- 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: "64a371e168472c987d9ec61b0373b0e28762dfcd" - git_remote: "https://x-access-token:ghs_NEnBDPGgmRYfKlNL6VeMqiNleTP4aC2s2yz6@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-7-g64a371e" + git_commit: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f" + git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-8-gb7e30f3" 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 9d4fedc..15151cd 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" : "64a371e168472c987d9ec61b0373b0e28762dfcd", - "git_remote" : "https://x-access-token:ghs_NEnBDPGgmRYfKlNL6VeMqiNleTP4aC2s2yz6@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-7-g64a371e" + "git_commit" : "b7e30f394e7a4ae7a51961ade824e24ffe718e1f", + "git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-8-gb7e30f3" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/demultiplex/.config.vsh.yaml b/target/nextflow/demultiplex/.config.vsh.yaml index 011c578..1cd4813 100644 --- 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: "64a371e168472c987d9ec61b0373b0e28762dfcd" - git_remote: "https://x-access-token:ghs_NEnBDPGgmRYfKlNL6VeMqiNleTP4aC2s2yz6@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-7-g64a371e" + git_commit: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f" + git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-8-gb7e30f3" 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 a38178a..c85ab94 100644 --- 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" : "64a371e168472c987d9ec61b0373b0e28762dfcd", - "git_remote" : "https://x-access-token:ghs_NEnBDPGgmRYfKlNL6VeMqiNleTP4aC2s2yz6@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-7-g64a371e" + "git_commit" : "b7e30f394e7a4ae7a51961ade824e24ffe718e1f", + "git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-8-gb7e30f3" }, "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 0dc39db..72fe8c8 100644 --- 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: "64a371e168472c987d9ec61b0373b0e28762dfcd" - git_remote: "https://x-access-token:ghs_NEnBDPGgmRYfKlNL6VeMqiNleTP4aC2s2yz6@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-7-g64a371e" + git_commit: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f" + git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-8-gb7e30f3" 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 f7a3b2e..ae56c22 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" : "64a371e168472c987d9ec61b0373b0e28762dfcd", - "git_remote" : "https://x-access-token:ghs_NEnBDPGgmRYfKlNL6VeMqiNleTP4aC2s2yz6@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-7-g64a371e" + "git_commit" : "b7e30f394e7a4ae7a51961ade824e24ffe718e1f", + "git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-8-gb7e30f3" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/io/publish/.config.vsh.yaml b/target/nextflow/io/publish/.config.vsh.yaml index 451f805..e0d50c8 100644 --- 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: "64a371e168472c987d9ec61b0373b0e28762dfcd" - git_remote: "https://x-access-token:ghs_NEnBDPGgmRYfKlNL6VeMqiNleTP4aC2s2yz6@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-7-g64a371e" + git_commit: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f" + git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-8-gb7e30f3" package_config: name: "demultiplex" version: "main" diff --git a/target/nextflow/io/publish/main.nf b/target/nextflow/io/publish/main.nf index 029a10a..f8f1591 100644 --- 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" : "64a371e168472c987d9ec61b0373b0e28762dfcd", - "git_remote" : "https://x-access-token:ghs_NEnBDPGgmRYfKlNL6VeMqiNleTP4aC2s2yz6@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-7-g64a371e" + "git_commit" : "b7e30f394e7a4ae7a51961ade824e24ffe718e1f", + "git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-8-gb7e30f3" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/io/untar/.config.vsh.yaml b/target/nextflow/io/untar/.config.vsh.yaml index 4739546..a7c9326 100644 --- 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: "64a371e168472c987d9ec61b0373b0e28762dfcd" - git_remote: "https://x-access-token:ghs_NEnBDPGgmRYfKlNL6VeMqiNleTP4aC2s2yz6@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-7-g64a371e" + git_commit: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f" + git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-8-gb7e30f3" package_config: name: "demultiplex" version: "main" diff --git a/target/nextflow/io/untar/main.nf b/target/nextflow/io/untar/main.nf index 52b2fd7..3aa78d8 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" : "64a371e168472c987d9ec61b0373b0e28762dfcd", - "git_remote" : "https://x-access-token:ghs_NEnBDPGgmRYfKlNL6VeMqiNleTP4aC2s2yz6@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-7-g64a371e" + "git_commit" : "b7e30f394e7a4ae7a51961ade824e24ffe718e1f", + "git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-8-gb7e30f3" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/runner/.config.vsh.yaml b/target/nextflow/runner/.config.vsh.yaml index 8dcb8cc..6b3d2ee 100644 --- a/target/nextflow/runner/.config.vsh.yaml +++ b/target/nextflow/runner/.config.vsh.yaml @@ -156,9 +156,9 @@ build_info: output: "target/nextflow/runner" executable: "target/nextflow/runner/main.nf" viash_version: "0.9.0" - git_commit: "64a371e168472c987d9ec61b0373b0e28762dfcd" - git_remote: "https://x-access-token:ghs_NEnBDPGgmRYfKlNL6VeMqiNleTP4aC2s2yz6@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-7-g64a371e" + git_commit: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f" + git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-8-gb7e30f3" dependencies: - "target/nextflow/demultiplex" - "target/nextflow/io/publish" diff --git a/target/nextflow/runner/main.nf b/target/nextflow/runner/main.nf index f92e662..794a0af 100644 --- a/target/nextflow/runner/main.nf +++ b/target/nextflow/runner/main.nf @@ -3003,9 +3003,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/runner", "viash_version" : "0.9.0", - "git_commit" : "64a371e168472c987d9ec61b0373b0e28762dfcd", - "git_remote" : "https://x-access-token:ghs_NEnBDPGgmRYfKlNL6VeMqiNleTP4aC2s2yz6@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-7-g64a371e" + "git_commit" : "b7e30f394e7a4ae7a51961ade824e24ffe718e1f", + "git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-8-gb7e30f3" }, "package_config" : { "name" : "demultiplex",