From 28b0e0579cfea61d655fe411c51eeb612efb012c Mon Sep 17 00:00:00 2001 From: Vasu Jaganath Date: Wed, 14 Oct 2026 16:13:37 -0400 Subject: [PATCH 1/2] fix: pull the rebuilt tool images from vjaganat90 bbbcdownload has failed since 2026-10-14: polusai/bbbc-download-plugin:0.1.0-dev1 (Ubuntu 20.04, a 2022 CA bundle) does not trust the certificate chain data.broadinstitute.org now serves. The seven images are rebuilt from their PolusAI/image-tools sources (precompute-slide-tool from PolusAI/image-tools#571) on the newest base images with fresh CA certificates, under the tools' own image names and dev-bumped versions, so they can be re-tagged to polusai/ unchanged. The file-renaming, montage and basic-flatfield plugin images give way to the image-tools tools. precompute-slide-tool 1.7.3-dev1 drops preadator, whose worker initializer reads its name with a zero-timeout queue get and breaks the process pool under load: 11/300 runs of 1.7.3-dev0 failed with 12 runs at once on the BBBC001 data, 0/300 of 1.7.3-dev1. --- cwl_adapters/basic-flatfield-estimation.cwl | 2 +- cwl_adapters/bbbcdownload.cwl | 2 +- cwl_adapters/file-renaming.cwl | 2 +- cwl_adapters/image_assembler.cwl | 2 +- cwl_adapters/montage.cwl | 2 +- cwl_adapters/ome-converter.cwl | 2 +- cwl_adapters/precompute_slide.cwl | 2 +- 7 files changed, 7 insertions(+), 7 deletions(-) diff --git a/cwl_adapters/basic-flatfield-estimation.cwl b/cwl_adapters/basic-flatfield-estimation.cwl index 85c18ea..6e68a1e 100644 --- a/cwl_adapters/basic-flatfield-estimation.cwl +++ b/cwl_adapters/basic-flatfield-estimation.cwl @@ -10,7 +10,7 @@ doc: |- requirements: DockerRequirement: - dockerPull: polusai/basic-flatfield-estimation-plugin:2.1.1 + dockerPull: vjaganat90/basic-flatfield-estimation-tool:2.1.6-dev0 # See https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement InitialWorkDirRequirement: listing: diff --git a/cwl_adapters/bbbcdownload.cwl b/cwl_adapters/bbbcdownload.cwl index 9fba292..8b4e617 100644 --- a/cwl_adapters/bbbcdownload.cwl +++ b/cwl_adapters/bbbcdownload.cwl @@ -9,7 +9,7 @@ doc: |- requirements: DockerRequirement: - dockerPull: polusai/bbbc-download-plugin:0.1.0-dev1 + dockerPull: vjaganat90/bbbc-download-plugin:0.1.1-dev1 # See https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement InitialWorkDirRequirement: listing: diff --git a/cwl_adapters/file-renaming.cwl b/cwl_adapters/file-renaming.cwl index 29628cd..ff2cc33 100644 --- a/cwl_adapters/file-renaming.cwl +++ b/cwl_adapters/file-renaming.cwl @@ -9,7 +9,7 @@ doc: |- requirements: DockerRequirement: - dockerPull: polusai/file-renaming-plugin:0.2.1-dev0 # NOTE: 0.2.3 not pushed yet + dockerPull: vjaganat90/file-renaming-tool:0.2.6-dev0 # See https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement InitialWorkDirRequirement: listing: diff --git a/cwl_adapters/image_assembler.cwl b/cwl_adapters/image_assembler.cwl index 1b4b1f0..f023c67 100644 --- a/cwl_adapters/image_assembler.cwl +++ b/cwl_adapters/image_assembler.cwl @@ -10,7 +10,7 @@ doc: |- requirements: DockerRequirement: - dockerPull: polusai/image-assembler-tool:1.4.3 + dockerPull: vjaganat90/image-assembler-tool:1.4.4-dev0 # See https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement InitialWorkDirRequirement: listing: diff --git a/cwl_adapters/montage.cwl b/cwl_adapters/montage.cwl index bc90bb0..1b5b1db 100644 --- a/cwl_adapters/montage.cwl +++ b/cwl_adapters/montage.cwl @@ -10,7 +10,7 @@ doc: |- requirements: DockerRequirement: - dockerPull: polusai/montage-plugin:0.5.0 + dockerPull: vjaganat90/montage-tool:0.5.3-dev0 # See https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement InitialWorkDirRequirement: listing: diff --git a/cwl_adapters/ome-converter.cwl b/cwl_adapters/ome-converter.cwl index 88d1b83..5d7d2e8 100644 --- a/cwl_adapters/ome-converter.cwl +++ b/cwl_adapters/ome-converter.cwl @@ -10,7 +10,7 @@ doc: |- requirements: DockerRequirement: - dockerPull: polusai/ome-converter-tool:0.3.3-dev4 + dockerPull: vjaganat90/ome-converter-tool:0.3.5-dev0 # See https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement InitialWorkDirRequirement: listing: diff --git a/cwl_adapters/precompute_slide.cwl b/cwl_adapters/precompute_slide.cwl index c90ad4d..34a870e 100644 --- a/cwl_adapters/precompute_slide.cwl +++ b/cwl_adapters/precompute_slide.cwl @@ -10,7 +10,7 @@ doc: |- requirements: DockerRequirement: - dockerPull: polusai/precompute-slide-tool:1.7.3-dev0 + dockerPull: vjaganat90/precompute-slide-tool:1.7.3-dev1 # See https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement InitialWorkDirRequirement: listing: From 3f4aa55e18898408f39203b1fe3ed3bd26158169 Mon Sep 17 00:00:00 2001 From: Vasu Jaganath Date: Wed, 14 Oct 2026 16:13:44 -0400 Subject: [PATCH 2/2] fix: file-renaming's mapDirectory is a flag file-renaming-tool takes --mapDirectory as a boolean flag where file-renaming-plugin took raw, map or nothing, so any string value is now an unexpected extra argument. The bbbc workflows leave it unset. --- cwl_adapters/file-renaming.cwl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cwl_adapters/file-renaming.cwl b/cwl_adapters/file-renaming.cwl index ff2cc33..3813f19 100644 --- a/cwl_adapters/file-renaming.cwl +++ b/cwl_adapters/file-renaming.cwl @@ -31,7 +31,7 @@ inputs: mapDirectory: inputBinding: prefix: --mapDirectory - type: string? # enum: raw, map, default + type: boolean? # file-renaming-tool: a flag; the plugin took raw, map or nothing preview: label: Generate a JSON file describing what the outputs should be