diff --git a/src/check_resources/config.vsh.yaml b/src/check_resources/config.vsh.yaml index beae54a..923e613 100644 --- a/src/check_resources/config.vsh.yaml +++ b/src/check_resources/config.vsh.yaml @@ -1,5 +1,16 @@ name: check_resources -description: Check for available resources on the system. +description: | + Check for available resources on the system. + + This component is only useful when working with persistent storage environments + where all workflow steps execute on the same instance or share the same + storage volume. That is, running thus component on e.g. AWS Batch or + other cloud-based systems will not work as expected, since each step + can run on a different instance and resources will not be shared. + + For distributed environments, consider integrating resource checks directly + into the components that will actually consume the storage, rather than + using this standalone check. argument_groups: - name: Inputs diff --git a/target/executable/bgzip/.config.vsh.yaml b/target/executable/bgzip/.config.vsh.yaml index e583a94..a54c570 100644 --- a/target/executable/bgzip/.config.vsh.yaml +++ b/target/executable/bgzip/.config.vsh.yaml @@ -228,7 +228,7 @@ build_info: output: "target/executable/bgzip" executable: "target/executable/bgzip/bgzip" viash_version: "0.9.4" - git_commit: "cfc11db17dde3001289ba6d31c1172dbee58091b" + git_commit: "c27e41c13e2c3d367a8279a03eab6464ac758b65" git_remote: "https://github.com/viash-hub/toolbox" package_config: name: "toolbox" diff --git a/target/executable/bgzip/bgzip b/target/executable/bgzip/bgzip index 97cfd73..4ad14f9 100755 --- a/target/executable/bgzip/bgzip +++ b/target/executable/bgzip/bgzip @@ -448,9 +448,9 @@ ENTRYPOINT [] RUN bgzip -h | grep 'Version:' 2>&1 | sed 's/Version:\s\(.*\)/bgzip: "\1"/' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component bgzip" -LABEL org.opencontainers.image.created="2025-06-24T09:06:13Z" +LABEL org.opencontainers.image.created="2025-06-25T08:37:52Z" LABEL org.opencontainers.image.source="https://github.com/samtools/htslib" -LABEL org.opencontainers.image.revision="cfc11db17dde3001289ba6d31c1172dbee58091b" +LABEL org.opencontainers.image.revision="c27e41c13e2c3d367a8279a03eab6464ac758b65" LABEL org.opencontainers.image.version="check-resources" VIASHDOCKER diff --git a/target/executable/check_resources/.config.vsh.yaml b/target/executable/check_resources/.config.vsh.yaml index 2e8ab15..fea8979 100644 --- a/target/executable/check_resources/.config.vsh.yaml +++ b/target/executable/check_resources/.config.vsh.yaml @@ -51,7 +51,14 @@ resources: - type: "bash_script" path: "script.sh" is_executable: true -description: "Check for available resources on the system." +description: "Check for available resources on the system.\n\nThis component is only\ + \ useful when working with persistent storage environments\nwhere all workflow steps\ + \ execute on the same instance or share the same\nstorage volume. That is, running\ + \ thus component on e.g. AWS Batch or\nother cloud-based systems will not work as\ + \ expected, since each step\ncan run on a different instance and resources will\ + \ not be shared.\n\nFor distributed environments, consider integrating resource\ + \ checks directly\ninto the components that will actually consume the storage, rather\ + \ than\nusing this standalone check.\n" test_resources: - type: "bash_script" path: "test.sh" @@ -150,7 +157,7 @@ build_info: output: "target/executable/check_resources" executable: "target/executable/check_resources/check_resources" viash_version: "0.9.4" - git_commit: "cfc11db17dde3001289ba6d31c1172dbee58091b" + git_commit: "c27e41c13e2c3d367a8279a03eab6464ac758b65" git_remote: "https://github.com/viash-hub/toolbox" package_config: name: "toolbox" diff --git a/target/executable/check_resources/check_resources b/target/executable/check_resources/check_resources index f8c9563..0971af8 100755 --- a/target/executable/check_resources/check_resources +++ b/target/executable/check_resources/check_resources @@ -446,9 +446,9 @@ function ViashDockerfile { FROM bash:latest ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component check_resources" -LABEL org.opencontainers.image.created="2025-06-24T09:06:13Z" +LABEL org.opencontainers.image.created="2025-06-25T08:37:51Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/toolbox" -LABEL org.opencontainers.image.revision="cfc11db17dde3001289ba6d31c1172dbee58091b" +LABEL org.opencontainers.image.revision="c27e41c13e2c3d367a8279a03eab6464ac758b65" LABEL org.opencontainers.image.version="check-resources" VIASHDOCKER @@ -570,6 +570,16 @@ function ViashHelp { echo "" echo "Check for available resources on the system." echo "" + echo "This component is only useful when working with persistent storage environments" + echo "where all workflow steps execute on the same instance or share the same" + echo "storage volume. That is, running thus component on e.g. AWS Batch or" + echo "other cloud-based systems will not work as expected, since each step" + echo "can run on a different instance and resources will not be shared." + echo "" + echo "For distributed environments, consider integrating resource checks directly" + echo "into the components that will actually consume the storage, rather than" + echo "using this standalone check." + echo "" echo "Inputs:" echo " --tmp_space_required" echo " type: integer" diff --git a/target/executable/yq/.config.vsh.yaml b/target/executable/yq/.config.vsh.yaml index 265a263..01f4965 100644 --- a/target/executable/yq/.config.vsh.yaml +++ b/target/executable/yq/.config.vsh.yaml @@ -258,7 +258,7 @@ build_info: output: "target/executable/yq" executable: "target/executable/yq/yq" viash_version: "0.9.4" - git_commit: "cfc11db17dde3001289ba6d31c1172dbee58091b" + git_commit: "c27e41c13e2c3d367a8279a03eab6464ac758b65" git_remote: "https://github.com/viash-hub/toolbox" package_config: name: "toolbox" diff --git a/target/executable/yq/yq b/target/executable/yq/yq index cb321a4..4364d9f 100755 --- a/target/executable/yq/yq +++ b/target/executable/yq/yq @@ -450,9 +450,9 @@ RUN apk add --no-cache bash yq-go RUN /usr/bin/yq --version | sed 's/.*version\sv\(.*\)/yq: "\1"/' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component yq" -LABEL org.opencontainers.image.created="2025-06-24T09:06:13Z" +LABEL org.opencontainers.image.created="2025-06-25T08:37:52Z" LABEL org.opencontainers.image.source="https://github.com/mikefarah/yq" -LABEL org.opencontainers.image.revision="cfc11db17dde3001289ba6d31c1172dbee58091b" +LABEL org.opencontainers.image.revision="c27e41c13e2c3d367a8279a03eab6464ac758b65" LABEL org.opencontainers.image.version="check-resources" VIASHDOCKER diff --git a/target/nextflow/bgzip/.config.vsh.yaml b/target/nextflow/bgzip/.config.vsh.yaml index a738ca8..0cf265d 100644 --- a/target/nextflow/bgzip/.config.vsh.yaml +++ b/target/nextflow/bgzip/.config.vsh.yaml @@ -228,7 +228,7 @@ build_info: output: "target/nextflow/bgzip" executable: "target/nextflow/bgzip/main.nf" viash_version: "0.9.4" - git_commit: "cfc11db17dde3001289ba6d31c1172dbee58091b" + git_commit: "c27e41c13e2c3d367a8279a03eab6464ac758b65" git_remote: "https://github.com/viash-hub/toolbox" package_config: name: "toolbox" diff --git a/target/nextflow/bgzip/main.nf b/target/nextflow/bgzip/main.nf index d611f1b..a82149d 100644 --- a/target/nextflow/bgzip/main.nf +++ b/target/nextflow/bgzip/main.nf @@ -3317,7 +3317,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bgzip", "viash_version" : "0.9.4", - "git_commit" : "cfc11db17dde3001289ba6d31c1172dbee58091b", + "git_commit" : "c27e41c13e2c3d367a8279a03eab6464ac758b65", "git_remote" : "https://github.com/viash-hub/toolbox" }, "package_config" : { diff --git a/target/nextflow/check_resources/.config.vsh.yaml b/target/nextflow/check_resources/.config.vsh.yaml index 06ed9ff..87c5ffe 100644 --- a/target/nextflow/check_resources/.config.vsh.yaml +++ b/target/nextflow/check_resources/.config.vsh.yaml @@ -51,7 +51,14 @@ resources: - type: "bash_script" path: "script.sh" is_executable: true -description: "Check for available resources on the system." +description: "Check for available resources on the system.\n\nThis component is only\ + \ useful when working with persistent storage environments\nwhere all workflow steps\ + \ execute on the same instance or share the same\nstorage volume. That is, running\ + \ thus component on e.g. AWS Batch or\nother cloud-based systems will not work as\ + \ expected, since each step\ncan run on a different instance and resources will\ + \ not be shared.\n\nFor distributed environments, consider integrating resource\ + \ checks directly\ninto the components that will actually consume the storage, rather\ + \ than\nusing this standalone check.\n" test_resources: - type: "bash_script" path: "test.sh" @@ -150,7 +157,7 @@ build_info: output: "target/nextflow/check_resources" executable: "target/nextflow/check_resources/main.nf" viash_version: "0.9.4" - git_commit: "cfc11db17dde3001289ba6d31c1172dbee58091b" + git_commit: "c27e41c13e2c3d367a8279a03eab6464ac758b65" git_remote: "https://github.com/viash-hub/toolbox" package_config: name: "toolbox" diff --git a/target/nextflow/check_resources/main.nf b/target/nextflow/check_resources/main.nf index 6768065..215e5f8 100644 --- a/target/nextflow/check_resources/main.nf +++ b/target/nextflow/check_resources/main.nf @@ -3100,7 +3100,7 @@ meta = [ "is_executable" : true } ], - "description" : "Check for available resources on the system.", + "description" : "Check for available resources on the system.\n\nThis component is only useful when working with persistent storage environments\nwhere all workflow steps execute on the same instance or share the same\nstorage volume. That is, running thus component on e.g. AWS Batch or\nother cloud-based systems will not work as expected, since each step\ncan run on a different instance and resources will not be shared.\n\nFor distributed environments, consider integrating resource checks directly\ninto the components that will actually consume the storage, rather than\nusing this standalone check.\n", "test_resources" : [ { "type" : "bash_script", @@ -3216,7 +3216,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/check_resources", "viash_version" : "0.9.4", - "git_commit" : "cfc11db17dde3001289ba6d31c1172dbee58091b", + "git_commit" : "c27e41c13e2c3d367a8279a03eab6464ac758b65", "git_remote" : "https://github.com/viash-hub/toolbox" }, "package_config" : { diff --git a/target/nextflow/check_resources/nextflow.config b/target/nextflow/check_resources/nextflow.config index 63271d8..bf4c7a3 100644 --- a/target/nextflow/check_resources/nextflow.config +++ b/target/nextflow/check_resources/nextflow.config @@ -3,7 +3,7 @@ manifest { mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' version = 'check-resources' - description = 'Check for available resources on the system.' + description = 'Check for available resources on the system.\n\nThis component is only useful when working with persistent storage environments\nwhere all workflow steps execute on the same instance or share the same\nstorage volume. That is, running thus component on e.g. AWS Batch or\nother cloud-based systems will not work as expected, since each step\ncan run on a different instance and resources will not be shared.\n\nFor distributed environments, consider integrating resource checks directly\ninto the components that will actually consume the storage, rather than\nusing this standalone check.\n' } process.container = 'nextflow/bash:latest' diff --git a/target/nextflow/check_resources/nextflow_schema.json b/target/nextflow/check_resources/nextflow_schema.json index 5b52cca..13d3ec5 100644 --- a/target/nextflow/check_resources/nextflow_schema.json +++ b/target/nextflow/check_resources/nextflow_schema.json @@ -1,7 +1,7 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", "title": "check_resources", - "description": "Check for available resources on the system.", + "description": "Check for available resources on the system.\n\nThis component is only useful when working with persistent storage environments\nwhere all workflow steps execute on the same instance or share the same\nstorage volume. That is, running thus component on e.g. AWS Batch or\nother cloud-based systems will not work as expected, since each step\ncan run on a different instance and resources will not be shared.\n\nFor distributed environments, consider integrating resource checks directly\ninto the components that will actually consume the storage, rather than\nusing this standalone check.\n", "type": "object", "$defs": { "inputs": { diff --git a/target/nextflow/yq/.config.vsh.yaml b/target/nextflow/yq/.config.vsh.yaml index 1c28764..6695fd9 100644 --- a/target/nextflow/yq/.config.vsh.yaml +++ b/target/nextflow/yq/.config.vsh.yaml @@ -258,7 +258,7 @@ build_info: output: "target/nextflow/yq" executable: "target/nextflow/yq/main.nf" viash_version: "0.9.4" - git_commit: "cfc11db17dde3001289ba6d31c1172dbee58091b" + git_commit: "c27e41c13e2c3d367a8279a03eab6464ac758b65" git_remote: "https://github.com/viash-hub/toolbox" package_config: name: "toolbox" diff --git a/target/nextflow/yq/main.nf b/target/nextflow/yq/main.nf index ef4f984..0d47958 100644 --- a/target/nextflow/yq/main.nf +++ b/target/nextflow/yq/main.nf @@ -3330,7 +3330,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/yq", "viash_version" : "0.9.4", - "git_commit" : "cfc11db17dde3001289ba6d31c1172dbee58091b", + "git_commit" : "c27e41c13e2c3d367a8279a03eab6464ac758b65", "git_remote" : "https://github.com/viash-hub/toolbox" }, "package_config" : {