From 214329783f6718efd7f953c5e2bca957bd31c224 Mon Sep 17 00:00:00 2001 From: CI Date: Tue, 5 Aug 2025 11:20:53 +0000 Subject: [PATCH] Build branch main with version main (0d4c458) Build pipeline: viash-hub.demultiplex.main-zst7j Source commit: https://github.com/viash-hub/demultiplex/commit/0d4c4584f0d18ab18c21e7d71c43b8deed2c4805 Source message: Only publish transfer_complete.txt file when the exit code is 0 (#58) --- CHANGELOG.md | 6 ++++++ src/runner/main.nf | 6 ++++-- .../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 ++-- .../nextflow/dataflow/combine_samples/.config.vsh.yaml | 4 ++-- target/nextflow/dataflow/combine_samples/main.nf | 4 ++-- .../gather_fastqs_and_validate/.config.vsh.yaml | 4 ++-- .../dataflow/gather_fastqs_and_validate/main.nf | 4 ++-- target/nextflow/demultiplex/.config.vsh.yaml | 4 ++-- target/nextflow/demultiplex/main.nf | 4 ++-- target/nextflow/detect_demultiplexer/.config.vsh.yaml | 4 ++-- target/nextflow/detect_demultiplexer/main.nf | 4 ++-- .../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 | 10 ++++++---- 24 files changed, 58 insertions(+), 48 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 37c8da9..85b2aa7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,9 @@ +# demultiplex v0.4.4 + +## Bug fixes + +* Only add the `transfer_complete.txt` files when the exitcode for the workflow is 0 (PR #58) + # demultiplex v0.4.3 ## Minor changes diff --git a/src/runner/main.nf b/src/runner/main.nf index 78cba99..a97a5bd 100644 --- a/src/runner/main.nf +++ b/src/runner/main.nf @@ -73,8 +73,10 @@ workflow run_wf { // Alternatively setOnComplete could be used to add actions, but that only adds them at the end of the list (which is executed in order). // The 'completed.txt' file must be created before the onComplete of the integration tests are run, so we need to prepend to the list. workflow.onCompleteActions.add(0, { - def complete_file = file("${params.publish_dir}/${prefix}/transfer_completed.txt") - complete_file.text = "" // This will create a file when it does not exist. + if (workflow.exitStatus == 0) { + def complete_file = file("${params.publish_dir}/${prefix}/transfer_completed.txt") + complete_file.text = "" // This will create a file when it does not exist. + } }) [ 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 5900431..a89f08f 100644 --- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml +++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml @@ -160,9 +160,9 @@ build_info: output: "target/executable/io/interop_summary_to_csv" executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv" viash_version: "0.9.4" - git_commit: "76a469a0dde244672cd700cb70ea7a874b2fb6ee" + git_commit: "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-36-g76a469a" + git_tag: "v0.1.1-37-g0d4c458" 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 775c997..549d820 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 @@ -454,9 +454,9 @@ 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="2025-07-29T09:06:08Z" +LABEL org.opencontainers.image.created="2025-08-05T10:55:23Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="76a469a0dde244672cd700cb70ea7a874b2fb6ee" +LABEL org.opencontainers.image.revision="0d4c4584f0d18ab18c21e7d71c43b8deed2c4805" 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 8ec43d0..cb85b92 100644 --- a/target/executable/io/publish/.config.vsh.yaml +++ b/target/executable/io/publish/.config.vsh.yaml @@ -222,9 +222,9 @@ build_info: output: "target/executable/io/publish" executable: "target/executable/io/publish/publish" viash_version: "0.9.4" - git_commit: "76a469a0dde244672cd700cb70ea7a874b2fb6ee" + git_commit: "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-36-g76a469a" + git_tag: "v0.1.1-37-g0d4c458" package_config: name: "demultiplex" version: "main" diff --git a/target/executable/io/publish/publish b/target/executable/io/publish/publish index e8cb029..8bee7da 100755 --- a/target/executable/io/publish/publish +++ b/target/executable/io/publish/publish @@ -450,9 +450,9 @@ 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="2025-07-29T09:06:07Z" +LABEL org.opencontainers.image.created="2025-08-05T10:55:23Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="76a469a0dde244672cd700cb70ea7a874b2fb6ee" +LABEL org.opencontainers.image.revision="0d4c4584f0d18ab18c21e7d71c43b8deed2c4805" 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 2844eb5..cabf8c0 100644 --- a/target/executable/io/untar/.config.vsh.yaml +++ b/target/executable/io/untar/.config.vsh.yaml @@ -159,9 +159,9 @@ build_info: output: "target/executable/io/untar" executable: "target/executable/io/untar/untar" viash_version: "0.9.4" - git_commit: "76a469a0dde244672cd700cb70ea7a874b2fb6ee" + git_commit: "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-36-g76a469a" + git_tag: "v0.1.1-37-g0d4c458" package_config: name: "demultiplex" version: "main" diff --git a/target/executable/io/untar/untar b/target/executable/io/untar/untar index 1eb0897..bab2a13 100755 --- a/target/executable/io/untar/untar +++ b/target/executable/io/untar/untar @@ -450,9 +450,9 @@ 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="2025-07-29T09:06:07Z" +LABEL org.opencontainers.image.created="2025-08-05T10:55:23Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="76a469a0dde244672cd700cb70ea7a874b2fb6ee" +LABEL org.opencontainers.image.revision="0d4c4584f0d18ab18c21e7d71c43b8deed2c4805" 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 f60e5cc..5dd7843 100644 --- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml +++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml @@ -168,9 +168,9 @@ build_info: output: "target/nextflow/dataflow/combine_samples" executable: "target/nextflow/dataflow/combine_samples/main.nf" viash_version: "0.9.4" - git_commit: "76a469a0dde244672cd700cb70ea7a874b2fb6ee" + git_commit: "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-36-g76a469a" + git_tag: "v0.1.1-37-g0d4c458" 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 d97ed1a..60c6c94 100644 --- a/target/nextflow/dataflow/combine_samples/main.nf +++ b/target/nextflow/dataflow/combine_samples/main.nf @@ -3235,9 +3235,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/dataflow/combine_samples", "viash_version" : "0.9.4", - "git_commit" : "76a469a0dde244672cd700cb70ea7a874b2fb6ee", + "git_commit" : "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-36-g76a469a" + "git_tag" : "v0.1.1-37-g0d4c458" }, "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 18ccd84..cb6dae6 100644 --- a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml +++ b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml @@ -159,9 +159,9 @@ build_info: output: "target/nextflow/dataflow/gather_fastqs_and_validate" executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf" viash_version: "0.9.4" - git_commit: "76a469a0dde244672cd700cb70ea7a874b2fb6ee" + git_commit: "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-36-g76a469a" + git_tag: "v0.1.1-37-g0d4c458" 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 f7d818d..e221cbf 100644 --- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf +++ b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf @@ -3232,9 +3232,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/dataflow/gather_fastqs_and_validate", "viash_version" : "0.9.4", - "git_commit" : "76a469a0dde244672cd700cb70ea7a874b2fb6ee", + "git_commit" : "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-36-g76a469a" + "git_tag" : "v0.1.1-37-g0d4c458" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/demultiplex/.config.vsh.yaml b/target/nextflow/demultiplex/.config.vsh.yaml index 7db3410..4085773 100644 --- a/target/nextflow/demultiplex/.config.vsh.yaml +++ b/target/nextflow/demultiplex/.config.vsh.yaml @@ -268,9 +268,9 @@ build_info: output: "target/nextflow/demultiplex" executable: "target/nextflow/demultiplex/main.nf" viash_version: "0.9.4" - git_commit: "76a469a0dde244672cd700cb70ea7a874b2fb6ee" + git_commit: "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-36-g76a469a" + git_tag: "v0.1.1-37-g0d4c458" 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 7ea5b0d..1280069 100644 --- a/target/nextflow/demultiplex/main.nf +++ b/target/nextflow/demultiplex/main.nf @@ -3380,9 +3380,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/demultiplex", "viash_version" : "0.9.4", - "git_commit" : "76a469a0dde244672cd700cb70ea7a874b2fb6ee", + "git_commit" : "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-36-g76a469a" + "git_tag" : "v0.1.1-37-g0d4c458" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/detect_demultiplexer/.config.vsh.yaml b/target/nextflow/detect_demultiplexer/.config.vsh.yaml index 2200b42..12941ab 100644 --- a/target/nextflow/detect_demultiplexer/.config.vsh.yaml +++ b/target/nextflow/detect_demultiplexer/.config.vsh.yaml @@ -168,9 +168,9 @@ build_info: output: "target/nextflow/detect_demultiplexer" executable: "target/nextflow/detect_demultiplexer/main.nf" viash_version: "0.9.4" - git_commit: "76a469a0dde244672cd700cb70ea7a874b2fb6ee" + git_commit: "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-36-g76a469a" + git_tag: "v0.1.1-37-g0d4c458" package_config: name: "demultiplex" version: "main" diff --git a/target/nextflow/detect_demultiplexer/main.nf b/target/nextflow/detect_demultiplexer/main.nf index 1e27990..c8f7fa8 100644 --- a/target/nextflow/detect_demultiplexer/main.nf +++ b/target/nextflow/detect_demultiplexer/main.nf @@ -3224,9 +3224,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/detect_demultiplexer", "viash_version" : "0.9.4", - "git_commit" : "76a469a0dde244672cd700cb70ea7a874b2fb6ee", + "git_commit" : "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-36-g76a469a" + "git_tag" : "v0.1.1-37-g0d4c458" }, "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 cbd0bd3..d32529d 100644 --- a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml +++ b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml @@ -160,9 +160,9 @@ build_info: output: "target/nextflow/io/interop_summary_to_csv" executable: "target/nextflow/io/interop_summary_to_csv/main.nf" viash_version: "0.9.4" - git_commit: "76a469a0dde244672cd700cb70ea7a874b2fb6ee" + git_commit: "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-36-g76a469a" + git_tag: "v0.1.1-37-g0d4c458" 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 6e90cf4..2a8793d 100644 --- a/target/nextflow/io/interop_summary_to_csv/main.nf +++ b/target/nextflow/io/interop_summary_to_csv/main.nf @@ -3233,9 +3233,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/interop_summary_to_csv", "viash_version" : "0.9.4", - "git_commit" : "76a469a0dde244672cd700cb70ea7a874b2fb6ee", + "git_commit" : "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-36-g76a469a" + "git_tag" : "v0.1.1-37-g0d4c458" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/io/publish/.config.vsh.yaml b/target/nextflow/io/publish/.config.vsh.yaml index c23030c..733ba84 100644 --- a/target/nextflow/io/publish/.config.vsh.yaml +++ b/target/nextflow/io/publish/.config.vsh.yaml @@ -222,9 +222,9 @@ build_info: output: "target/nextflow/io/publish" executable: "target/nextflow/io/publish/main.nf" viash_version: "0.9.4" - git_commit: "76a469a0dde244672cd700cb70ea7a874b2fb6ee" + git_commit: "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-36-g76a469a" + git_tag: "v0.1.1-37-g0d4c458" package_config: name: "demultiplex" version: "main" diff --git a/target/nextflow/io/publish/main.nf b/target/nextflow/io/publish/main.nf index bae2236..f3e07dc 100644 --- a/target/nextflow/io/publish/main.nf +++ b/target/nextflow/io/publish/main.nf @@ -3302,9 +3302,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish", "viash_version" : "0.9.4", - "git_commit" : "76a469a0dde244672cd700cb70ea7a874b2fb6ee", + "git_commit" : "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-36-g76a469a" + "git_tag" : "v0.1.1-37-g0d4c458" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/io/untar/.config.vsh.yaml b/target/nextflow/io/untar/.config.vsh.yaml index c24da77..f404e88 100644 --- a/target/nextflow/io/untar/.config.vsh.yaml +++ b/target/nextflow/io/untar/.config.vsh.yaml @@ -159,9 +159,9 @@ build_info: output: "target/nextflow/io/untar" executable: "target/nextflow/io/untar/main.nf" viash_version: "0.9.4" - git_commit: "76a469a0dde244672cd700cb70ea7a874b2fb6ee" + git_commit: "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-36-g76a469a" + git_tag: "v0.1.1-37-g0d4c458" package_config: name: "demultiplex" version: "main" diff --git a/target/nextflow/io/untar/main.nf b/target/nextflow/io/untar/main.nf index 68b4dba..8487fa9 100644 --- a/target/nextflow/io/untar/main.nf +++ b/target/nextflow/io/untar/main.nf @@ -3232,9 +3232,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/untar", "viash_version" : "0.9.4", - "git_commit" : "76a469a0dde244672cd700cb70ea7a874b2fb6ee", + "git_commit" : "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-36-g76a469a" + "git_tag" : "v0.1.1-37-g0d4c458" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/runner/.config.vsh.yaml b/target/nextflow/runner/.config.vsh.yaml index 338286c..2fb2360 100644 --- a/target/nextflow/runner/.config.vsh.yaml +++ b/target/nextflow/runner/.config.vsh.yaml @@ -214,9 +214,9 @@ build_info: output: "target/nextflow/runner" executable: "target/nextflow/runner/main.nf" viash_version: "0.9.4" - git_commit: "76a469a0dde244672cd700cb70ea7a874b2fb6ee" + git_commit: "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-36-g76a469a" + git_tag: "v0.1.1-37-g0d4c458" dependencies: - "target/nextflow/demultiplex" - "target/nextflow/io/publish" diff --git a/target/nextflow/runner/main.nf b/target/nextflow/runner/main.nf index 60734a5..cd372f4 100644 --- a/target/nextflow/runner/main.nf +++ b/target/nextflow/runner/main.nf @@ -3296,9 +3296,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/runner", "viash_version" : "0.9.4", - "git_commit" : "76a469a0dde244672cd700cb70ea7a874b2fb6ee", + "git_commit" : "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-36-g76a469a" + "git_tag" : "v0.1.1-37-g0d4c458" }, "package_config" : { "name" : "demultiplex", @@ -3419,8 +3419,10 @@ workflow run_wf { // Alternatively setOnComplete could be used to add actions, but that only adds them at the end of the list (which is executed in order). // The 'completed.txt' file must be created before the onComplete of the integration tests are run, so we need to prepend to the list. workflow.onCompleteActions.add(0, { - def complete_file = file("${params.publish_dir}/${prefix}/transfer_completed.txt") - complete_file.text = "" // This will create a file when it does not exist. + if (workflow.exitStatus == 0) { + def complete_file = file("${params.publish_dir}/${prefix}/transfer_completed.txt") + complete_file.text = "" // This will create a file when it does not exist. + } }) [