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Release v1.0.0 (#58)
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* Bump version in CHANGELOG

* Bump version in nextflow.config

* Update test paths

* Update expected changes in tests

---------

Co-authored-by: Nicholas Wiltsie <[email protected]>
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yashpatel6 and nwiltsie authored Mar 13, 2024
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -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
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4 changes: 2 additions & 2 deletions nextflow.config
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@@ -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'
}
8 changes: 4 additions & 4 deletions nftest.yml
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Expand Up @@ -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
14 changes: 7 additions & 7 deletions test/configtest-F16.json
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -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,
Expand All @@ -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",
Expand Down Expand Up @@ -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"
}
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14 changes: 7 additions & 7 deletions test/configtest-F32.json
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -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,
Expand All @@ -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",
Expand Down Expand Up @@ -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"
}
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