Release 10.0.0 (#301)

* 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]>
uclahs-cds · Apr 1, 2024 · 76c63a1 · 76c63a1
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -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

diff --git a/README.md b/README.md
@@ -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.

diff --git a/config/default.config b/config/default.config
@@ -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"

diff --git a/main.nf b/main.nf
@@ -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}
 

diff --git a/module/check_512sum.nf b/module/check_512sum.nf
@@ -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",

diff --git a/nextflow.config b/nextflow.config
@@ -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"
     }
diff --git a/test/configtest-F16.json b/test/configtest-F16.json
@@ -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": [
@@ -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",
@@ -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": {
@@ -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"
   }