From 1111cac0e0dbe4b6a2dd1bdbba9e5ebe7688955f Mon Sep 17 00:00:00 2001 From: Mohammed Faizal Eeman Mootor <68152431+Faizal-Eeman@users.noreply.github.com> Date: Fri, 15 Mar 2024 14:57:17 -0700 Subject: [PATCH] Release 5.0.0 (#136) * bump version to v5.0.0 * Update CHANGELOG.md * Update README * Closes #92 - Improve CNV calling description * update configtest-F16.json to reflect version bump * Update README --------- Co-authored-by: Mootor --- CHANGELOG.md | 4 ++++ README.md | 4 ++-- nextflow.config | 2 +- test/configtest-F16.json | 12 ++++++------ 4 files changed, 13 insertions(+), 9 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1ac7ec34..edd62e64 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,10 @@ All notable changes to the call-gSV pipeline. --- ## [Unreleased] + +--- + +## [5.0.0] - 2024-03-15 ### Added - Add PlantUML diagram - Add configtest-F16 for nextflow pipeline test diff --git a/README.md b/README.md index 74af33ea..7fd9d4bb 100644 --- a/README.md +++ b/README.md @@ -116,7 +116,7 @@ Currently the following filters are applied by Delly when calling SVs. Parameter ### 2. Calling Copy Number Variants -The second step of the pipeline identifies any found CNVs. To do this, Delly requires an aligned and sorted BAM file and BAM index as an input, as well as the BCF output from the initial SV calling (to refine breakpoints) and a mappability map. Any CNVs identified are annotated and output as a single BCF file. +The second step of the pipeline identifies CNVs. To do this, Delly requires an aligned and sorted BAM file, as well as the BCF output from the SV calling step (to refine breakpoints) and a mappability map. Any CNVs identified are annotated and output as a single BCF file. Currently the following filters are applied by Delly when calling CNVs. Parameters with a "call-gSV default" can be updated in the sample specific nextflow [config](config/template.config) file.
@@ -307,7 +307,7 @@ The pipeline-call-gSV is licensed under the GNU General Public License version 2 The pipeline-call-gSV takes BAM and BCF files and utilizes Delly to call/regenotype gSV/gCNV. -Copyright (C) 2021-2022 University of California Los Angeles ("Boutros Lab") All rights reserved. +Copyright (C) 2021-2024 University of California Los Angeles ("Boutros Lab") All rights reserved. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. diff --git a/nextflow.config b/nextflow.config index e694ebf7..da8faf21 100644 --- a/nextflow.config +++ b/nextflow.config @@ -4,5 +4,5 @@ manifest { name = 'call-gSV' author = 'Yu Pan, Tim Sanders, Yael Berkovich, Mohammed Faizal Eeman Mootor' description = 'A pipeline to call germline structural variants utilizing Delly and Manta' - version = '5.0.0-rc.1' + version = '5.0.0' } diff --git a/test/configtest-F16.json b/test/configtest-F16.json index 0884bbe7..8d1b03ba 100644 --- a/test/configtest-F16.json +++ b/test/configtest-F16.json @@ -41,7 +41,7 @@ "author": "Yu Pan, Tim Sanders, Yael Berkovich, Mohammed Faizal Eeman Mootor", "description": "A pipeline to call germline structural variants utilizing Delly and Manta", "name": "call-gSV", - "version": "5.0.0-rc.1" + "version": "5.0.0" }, "params": { "GCNV": "gCNV", @@ -70,7 +70,7 @@ ] } }, - "log_output_dir": "/tmp/test-only-outputs/call-gSV-5.0.0-rc.1/8675309/log-call-gSV-5.0.0-rc.1-19970704T165655Z", + "log_output_dir": "/tmp/test-only-outputs/call-gSV-5.0.0/8675309/log-call-gSV-5.0.0-19970704T165655Z", "manta_version": "1.6.0", "map_qual": "20", "mappability_map": "/hot/ref/tool-specific-input/Delly/GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.r101.s501.blacklist.gz", @@ -79,7 +79,7 @@ "min_cpus": "1", "min_memory": "1 MB", "output_dir": "/tmp/test-only-outputs", - "output_dir_base": "/tmp/test-only-outputs/call-gSV-5.0.0-rc.1/8675309", + "output_dir_base": "/tmp/test-only-outputs/call-gSV-5.0.0/8675309", "pipeval_version": "4.0.0-rc.2", "proc_resource_params": { "call_gCNV_Delly": { @@ -503,15 +503,15 @@ }, "report": { "enabled": true, - "file": "/tmp/test-only-outputs/call-gSV-5.0.0-rc.1/8675309/log-call-gSV-5.0.0-rc.1-19970704T165655Z/nextflow-log/report.html" + "file": "/tmp/test-only-outputs/call-gSV-5.0.0/8675309/log-call-gSV-5.0.0-19970704T165655Z/nextflow-log/report.html" }, "timeline": { "enabled": true, - "file": "/tmp/test-only-outputs/call-gSV-5.0.0-rc.1/8675309/log-call-gSV-5.0.0-rc.1-19970704T165655Z/nextflow-log/timeline.html" + "file": "/tmp/test-only-outputs/call-gSV-5.0.0/8675309/log-call-gSV-5.0.0-19970704T165655Z/nextflow-log/timeline.html" }, "trace": { "enabled": true, - "file": "/tmp/test-only-outputs/call-gSV-5.0.0-rc.1/8675309/log-call-gSV-5.0.0-rc.1-19970704T165655Z/nextflow-log/trace.txt" + "file": "/tmp/test-only-outputs/call-gSV-5.0.0/8675309/log-call-gSV-5.0.0-19970704T165655Z/nextflow-log/trace.txt" }, "tz": "sun.util.calendar.ZoneInfo[id=\"UTC\",offset=0,dstSavings=0,useDaylight=false,transitions=0,lastRule=null]", "workDir": "/scratch/300935",