From b36db58b40dddc4bb10b458c9d8e26500975bf72 Mon Sep 17 00:00:00 2001 From: Florian Wuennemann Date: Mon, 18 Dec 2023 14:00:41 +0000 Subject: [PATCH 1/4] Changed prefix naming for CLAHE to prevent file overlap. --- conf/modules.config | 7 ++++++- null/pipeline_info/execution_trace_2023-12-18_13-37-29.txt | 1 + 2 files changed, 7 insertions(+), 1 deletion(-) create mode 100644 null/pipeline_info/execution_trace_2023-12-18_13-37-29.txt diff --git a/conf/modules.config b/conf/modules.config index a8eea3d..ce4d82f 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -162,7 +162,12 @@ process { } withName: "CLAHE" { - ext.prefix = { "${meta.id}_${image.name.split("\\.")[0]}_clahe" } + ext.prefix = { + def name = image.name + // Remove the last extension for all files + def base = name.lastIndexOf('.') != -1 ? name[0..name.lastIndexOf('.') - 1] : name + return "${meta.id}_${base}_clahe" + } ext.when = { !params.skip_clahe } ext.args = [ "", params.clahe_pyramid_tile ? "--tile-size ${params.clahe_pyramid_tile}" : "", diff --git a/null/pipeline_info/execution_trace_2023-12-18_13-37-29.txt b/null/pipeline_info/execution_trace_2023-12-18_13-37-29.txt new file mode 100644 index 0000000..6b739ac --- /dev/null +++ b/null/pipeline_info/execution_trace_2023-12-18_13-37-29.txt @@ -0,0 +1 @@ +task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar From 5ae7dd67bd898aa009e9e90a0b770f325aa70427 Mon Sep 17 00:00:00 2001 From: Florian Wuennemann Date: Mon, 18 Dec 2023 14:02:11 +0000 Subject: [PATCH 2/4] Updated Changelog. --- CHANGELOG.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 098a749..aad04cc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## v1.0.1dev - [2023.12.18] + +### `Fixed` + +- Changed file prefix used in CLAHE to prevent file naming collisions if user used dots in filenames + ## v1.0.1dev - [2023.12.15] ### `Added` From 15a615260b3ce55c8e484ba89e5ec50f1467468c Mon Sep 17 00:00:00 2001 From: Florian Wuennemann Date: Mon, 18 Dec 2023 15:10:23 +0100 Subject: [PATCH 3/4] Delete null/pipeline_info/execution_trace_2023-12-18_13-37-29.txt --- null/pipeline_info/execution_trace_2023-12-18_13-37-29.txt | 1 - 1 file changed, 1 deletion(-) delete mode 100644 null/pipeline_info/execution_trace_2023-12-18_13-37-29.txt diff --git a/null/pipeline_info/execution_trace_2023-12-18_13-37-29.txt b/null/pipeline_info/execution_trace_2023-12-18_13-37-29.txt deleted file mode 100644 index 6b739ac..0000000 --- a/null/pipeline_info/execution_trace_2023-12-18_13-37-29.txt +++ /dev/null @@ -1 +0,0 @@ -task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar From 6967c9213218951921cfe9494b1c567ec7925d21 Mon Sep 17 00:00:00 2001 From: Florian Wuennemann Date: Mon, 18 Dec 2023 15:11:24 +0100 Subject: [PATCH 4/4] Update conf/modules.config MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> --- conf/modules.config | 1 - 1 file changed, 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index ce4d82f..6359aed 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -164,7 +164,6 @@ process { withName: "CLAHE" { ext.prefix = { def name = image.name - // Remove the last extension for all files def base = name.lastIndexOf('.') != -1 ? name[0..name.lastIndexOf('.') - 1] : name return "${meta.id}_${base}_clahe" }