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Release 10.0.0 (#301)
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* Bump version for release

* Fix typo

* Update version in config test

* Add requirements to README

* Remove use of bl-base docker image

* Update CHANGELOG

* Update CHANGELOG.md

Co-authored-by: Takafumi Yamaguchi <[email protected]>

---------

Co-authored-by: Takafumi Yamaguchi <[email protected]>
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yashpatel6 and tyamaguchi-ucla authored Apr 1, 2024
1 parent 82dda1c commit 76c63a1
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Showing 7 changed files with 16 additions and 12 deletions.
6 changes: 5 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -8,10 +8,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [Unreleased]

## [10.0.0] - 2024-03-29
### Added
- Add Action to generate documentation in GitHub Pages
- Add Action to run Nextflow configuration regression tests
- Add setup_docker_cpus method
- Add `setup_docker_cpus` method
### Removed
- Remove old `bl-base` Docker image

## [10.0.0-rc.1] - 2024-01-24
### Changed
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3 changes: 3 additions & 0 deletions README.md
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Expand Up @@ -27,6 +27,9 @@ The pipeline should be run **WITH A SINGLE SAMPLE AT A TIME**. Otherwise resourc

## How To Run

**Requirements**
Currently supported Nextflow versions: `23.04.2`

Below is a summary of how to run the pipeline. See [here](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3197004/How+to+run+a+nextflow+pipeline) for full instructions.

Pipelines should be run **WITH A SINGLE SAMPLE AT TIME**. Otherwise resource allocation and Nextflow errors could cause the pipeline to fail.
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1 change: 0 additions & 1 deletion config/default.config
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Expand Up @@ -26,7 +26,6 @@ params {
docker_image_bwa_and_samtools = "${-> params.docker_container_registry}/bwa-mem2_samtools-1.12:2.2.1"
docker_image_hisat2_and_samtools = "${-> params.docker_container_registry}/hisat2_samtools-1.12:2.2.1"
docker_image_picardtools = "${-> params.docker_container_registry}/picard:3.0.0"
docker_image_sha512sum = "${-> params.docker_container_registry}/bl-base:1.1.0"
docker_image_validate = "${-> params.docker_container_registry}/pipeval:${params.pipeval_version}"
docker_image_gatk = "broadinstitute/gatk:4.2.4.1"
docker_image_samtools = "${-> params.docker_container_registry}/samtools:1.17"
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1 change: 0 additions & 1 deletion main.nf
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Expand Up @@ -38,7 +38,6 @@ log.info """\
- BWA-MEM2: ${params.aligner.contains("BWA-MEM2") ? params.docker_image_bwa_and_samtools : "None"}
- HISAT2: ${params.aligner.contains("HISAT2") ? params.docker_image_hisat2_and_samtools : "None"}
- Picard Tools: ${params.docker_image_picardtools}
- sha512sum: ${params.docker_image_sha512sum}
- validate: ${params.docker_image_validate}
- GATK: ${params.docker_image_gatk}
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2 changes: 1 addition & 1 deletion module/check_512sum.nf
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@@ -1,6 +1,6 @@
// produce checksum for the bam and bam index
process generate_sha512sum {
container params.docker_image_sha512sum
container params.docker_image_validate

publishDir path: "${checksum_output_dir}",
mode: "copy",
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -2,5 +2,5 @@ manifest {
name = "align-DNA"
author = "Benjamin Carlin; Chenghao Zhu; Aaron Holmes; Yash Patel; Nicole Zeltser; Jieun Oh; Jaron Arbet"
description = "alignment pipeline for paired fastqs DNA samples"
version = "10.0.0-rc.1"
version = "10.0.0"
}
13 changes: 6 additions & 7 deletions test/configtest-F16.json
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Expand Up @@ -34,7 +34,7 @@
"author": "Benjamin Carlin; Chenghao Zhu; Aaron Holmes; Yash Patel; Nicole Zeltser; Jieun Oh; Jaron Arbet",
"description": "alignment pipeline for paired fastqs DNA samples",
"name": "align-DNA",
"version": "10.0.0-rc.1"
"version": "10.0.0"
},
"params": {
"aligner": [
Expand All @@ -51,7 +51,6 @@
"docker_image_hisat2_and_samtools": "ghcr.io/uclahs-cds/hisat2_samtools-1.12:2.2.1",
"docker_image_picardtools": "ghcr.io/uclahs-cds/picard:3.0.0",
"docker_image_samtools": "ghcr.io/uclahs-cds/samtools:1.17",
"docker_image_sha512sum": "ghcr.io/uclahs-cds/bl-base:1.1.0",
"docker_image_validate": "ghcr.io/uclahs-cds/pipeval:4.0.0-rc.2",
"enable_spark": false,
"gatk_command_mem_diff": "5 GB",
Expand All @@ -72,15 +71,15 @@
}
]
},
"log_output_dir": "/tmp/outputs/align-DNA-10.0.0-rc.1/a_mini_n2_picard/log-align-DNA-10.0.0-rc.1-19970704T165655Z/",
"log_output_dir": "/tmp/outputs/align-DNA-10.0.0/a_mini_n2_picard/log-align-DNA-10.0.0-19970704T165655Z/",
"make_duplicates": true,
"mark_duplicates": true,
"max_cpus": "16",
"max_memory": "31 GB",
"min_cpus": "1",
"min_memory": "1 MB",
"output_dir": "/tmp/outputs",
"output_dir_base": "/tmp/outputs/align-DNA-10.0.0-rc.1/a_mini_n2_picard",
"output_dir_base": "/tmp/outputs/align-DNA-10.0.0/a_mini_n2_picard",
"pipeval_version": "4.0.0-rc.2",
"proc_resource_params": {
"align_DNA_BWA_MEM2": {
Expand Down Expand Up @@ -283,15 +282,15 @@
},
"report": {
"enabled": true,
"file": "/tmp/outputs/align-DNA-10.0.0-rc.1/a_mini_n2_picard/log-align-DNA-10.0.0-rc.1-19970704T165655Z//nextflow-log/report.html"
"file": "/tmp/outputs/align-DNA-10.0.0/a_mini_n2_picard/log-align-DNA-10.0.0-19970704T165655Z//nextflow-log/report.html"
},
"timeline": {
"enabled": true,
"file": "/tmp/outputs/align-DNA-10.0.0-rc.1/a_mini_n2_picard/log-align-DNA-10.0.0-rc.1-19970704T165655Z//nextflow-log/timeline.html"
"file": "/tmp/outputs/align-DNA-10.0.0/a_mini_n2_picard/log-align-DNA-10.0.0-19970704T165655Z//nextflow-log/timeline.html"
},
"trace": {
"enabled": true,
"file": "/tmp/outputs/align-DNA-10.0.0-rc.1/a_mini_n2_picard/log-align-DNA-10.0.0-rc.1-19970704T165655Z//nextflow-log/trace.txt"
"file": "/tmp/outputs/align-DNA-10.0.0/a_mini_n2_picard/log-align-DNA-10.0.0-19970704T165655Z//nextflow-log/trace.txt"
},
"workDir": "/scratch/8543"
}
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