From 2040581fad4c97be033a90ea4a71a4943e945438 Mon Sep 17 00:00:00 2001 From: Yash Patel <86321070+yashpatel6@users.noreply.github.com> Date: Wed, 13 Mar 2024 10:39:22 -0700 Subject: [PATCH] Release `v1.0.0` (#58) * Bump version in CHANGELOG * Bump version in nextflow.config * Update test paths * Update expected changes in tests --------- Co-authored-by: Nicholas Wiltsie --- CHANGELOG.md | 4 ++++ nextflow.config | 4 ++-- nftest.yml | 8 ++++---- test/configtest-F16.json | 14 +++++++------- test/configtest-F32.json | 14 +++++++------- 5 files changed, 24 insertions(+), 20 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6d320c93..f4332a55 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,10 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm --- ## [Unreleased] + +--- + +## [1.0.0] - 2024-03-13 ### [Added] - Sort BAMs before merging for consistent order of output BAM @PG header lines - Add NFTest case diff --git a/nextflow.config b/nextflow.config index 4e0b71d7..233728e6 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,7 +1,7 @@ // Metadata manifest { name = 'recalibrate-BAM' - author = 'Yash Patel' + author = 'Yash Patel, Nicholas Wiltsie' description = 'Nextflow pipeline to perform Indel Realignment and Base Quality Score Recalibration' - version = '1.0.0-rc.4' + version = '1.0.0' } diff --git a/nftest.yml b/nftest.yml index afb39192..e15a7fa9 100644 --- a/nftest.yml +++ b/nftest.yml @@ -12,15 +12,15 @@ cases: skip: false verbose: true asserts: - - actual: recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/GATK-4.2.4.1/output/BWA-MEM2-2.2.1_GATK-4.2.4.1_A-mini_S2-v1.1.5.bam + - actual: recalibrate-BAM-*/TWGSAMIN000001/GATK-*/output/BWA-MEM2-*_GATK-*_A-mini_S2-v1.1.5.bam expect: /hot/software/pipeline/pipeline-recalibrate-BAM/Nextflow/development/output/BWA-MEM2-2.2.1_GATK-4.2.4.1_A-mini_S2-v1.1.5.bam method: md5 - - actual: recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/GATK-4.2.4.1/output/BWA-MEM2-2.2.1_GATK-4.2.4.1_A-mini_S2-v1.1.5.bam.bai + - actual: recalibrate-BAM-*/TWGSAMIN000001/GATK-*/output/BWA-MEM2-*_GATK-*_A-mini_S2-v1.1.5.bam.bai expect: /hot/software/pipeline/pipeline-recalibrate-BAM/Nextflow/development/output/BWA-MEM2-2.2.1_GATK-4.2.4.1_A-mini_S2-v1.1.5.bam.bai method: md5 - - actual: recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/GATK-4.2.4.1/output/BWA-MEM2-2.2.1_GATK-4.2.4.1_A-mini_S2-v1.1.5.bam.sha512 + - actual: recalibrate-BAM-*/TWGSAMIN000001/GATK-*/output/BWA-MEM2-*_GATK-*_A-mini_S2-v1.1.5.bam.sha512 expect: /hot/software/pipeline/pipeline-recalibrate-BAM/Nextflow/development/output/BWA-MEM2-2.2.1_GATK-4.2.4.1_A-mini_S2-v1.1.5.bam.sha512 method: md5 - - actual: recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/GATK-4.2.4.1/output/BWA-MEM2-2.2.1_GATK-4.2.4.1_A-mini_S2-v1.1.5.bam.bai.sha512 + - actual: recalibrate-BAM-*/TWGSAMIN000001/GATK-*/output/BWA-MEM2-*_GATK-*_A-mini_S2-v1.1.5.bam.bai.sha512 expect: /hot/software/pipeline/pipeline-recalibrate-BAM/Nextflow/development/output/BWA-MEM2-2.2.1_GATK-4.2.4.1_A-mini_S2-v1.1.5.bam.bai.sha512 method: md5 diff --git a/test/configtest-F16.json b/test/configtest-F16.json index fb7614dc..77b1c0a4 100644 --- a/test/configtest-F16.json +++ b/test/configtest-F16.json @@ -36,10 +36,10 @@ "uid_and_gid": "-u $(id -u):$(id -g)" }, "manifest": { - "author": "Yash Patel", + "author": "Yash Patel, Nicholas Wiltsie", "description": "Nextflow pipeline to perform Indel Realignment and Base Quality Score Recalibration", "name": "recalibrate-BAM", - "version": "1.0.0-rc.4" + "version": "1.0.0" }, "params": { "aligner": "BWA-MEM2-2.2.1", @@ -74,7 +74,7 @@ "is_DOC_run": false, "is_emit_original_quals": true, "is_targeted": false, - "log_output_dir": "/tmp/outputs/recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-rc.4-19970704T165655Z", + "log_output_dir": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z", "max_cpus": "16", "max_memory": "31 GB", "metapipeline_delete_input_bams": false, @@ -85,7 +85,7 @@ "min_cpus": "1", "min_memory": "1 MB", "output_dir": "/tmp/outputs", - "output_dir_base": "/tmp/outputs/recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/GATK-4.2.4.1", + "output_dir_base": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/GATK-4.2.4.1", "parallelize_by_chromosome": true, "patient_id": "TWGSAMIN000001", "picard_version": "2.26.10", @@ -414,15 +414,15 @@ }, "report": { "enabled": true, - "file": "/tmp/outputs/recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-rc.4-19970704T165655Z/nextflow-log/report.html" + "file": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z/nextflow-log/report.html" }, "timeline": { "enabled": true, - "file": "/tmp/outputs/recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-rc.4-19970704T165655Z/nextflow-log/timeline.html" + "file": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z/nextflow-log/timeline.html" }, "trace": { "enabled": true, - "file": "/tmp/outputs/recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-rc.4-19970704T165655Z/nextflow-log/trace.txt" + "file": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z/nextflow-log/trace.txt" }, "workDir": "/scratch/851543" } diff --git a/test/configtest-F32.json b/test/configtest-F32.json index 41bc7284..1fbe66b5 100644 --- a/test/configtest-F32.json +++ b/test/configtest-F32.json @@ -36,10 +36,10 @@ "uid_and_gid": "-u $(id -u):$(id -g)" }, "manifest": { - "author": "Yash Patel", + "author": "Yash Patel, Nicholas Wiltsie", "description": "Nextflow pipeline to perform Indel Realignment and Base Quality Score Recalibration", "name": "recalibrate-BAM", - "version": "1.0.0-rc.4" + "version": "1.0.0" }, "params": { "aligner": "BWA-MEM2-2.2.1", @@ -74,7 +74,7 @@ "is_DOC_run": false, "is_emit_original_quals": true, "is_targeted": false, - "log_output_dir": "/tmp/outputs/recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-rc.4-19970704T165655Z", + "log_output_dir": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z", "max_cpus": "32", "max_memory": "64 GB", "metapipeline_delete_input_bams": false, @@ -85,7 +85,7 @@ "min_cpus": "1", "min_memory": "1 MB", "output_dir": "/tmp/outputs", - "output_dir_base": "/tmp/outputs/recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/GATK-4.2.4.1", + "output_dir_base": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/GATK-4.2.4.1", "parallelize_by_chromosome": true, "patient_id": "TWGSAMIN000001", "picard_version": "2.26.10", @@ -414,15 +414,15 @@ }, "report": { "enabled": true, - "file": "/tmp/outputs/recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-rc.4-19970704T165655Z/nextflow-log/report.html" + "file": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z/nextflow-log/report.html" }, "timeline": { "enabled": true, - "file": "/tmp/outputs/recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-rc.4-19970704T165655Z/nextflow-log/timeline.html" + "file": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z/nextflow-log/timeline.html" }, "trace": { "enabled": true, - "file": "/tmp/outputs/recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-rc.4-19970704T165655Z/nextflow-log/trace.txt" + "file": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z/nextflow-log/trace.txt" }, "workDir": "/scratch/851543" }