diff --git a/CHANGELOG.md b/CHANGELOG.md index de0ec91..bc90f33 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,12 +4,13 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [unreleased] +## [v2.5.0] ### Changed -- Reconciled workflow with wf-template v5.3.1 +- Reconciled workflow with wf-template v5.3.2 - Update Spectre to v0.3.2, which includes support for calling CNVs in hg19 data. - ClinVar version in SnpEff container updated to version 20241103. - Hidden additional options in MinKNOW for a simplified user experience. +- Improved performance of readStats process by updating to bamstats 0.19.1. ### Added - `--spectre_args` may be used to provide custom arguments to the Spectre process. ### Fixed diff --git a/base.config b/base.config index 1d2e3c8..6506708 100644 --- a/base.config +++ b/base.config @@ -1,4 +1,5 @@ params { + out_dir = "output" wf { // container sha e2l_base_tag = "sha2b856c1f358ddf1576217a336bc0e9864b6dc0ed" @@ -9,7 +10,7 @@ params { str_tag = "shadd2f2963fe39351d4e0d6fa3ca54e1064c6ec057" spectre_tag = "sha42472d37a5a992c3ee27894a23dce5e2fff66d27" snpeff_tag = "shab01c188f11ca9ce53d186fe22111eeac52409523" - common_sha = "shad28e55140f75a68f59bbecc74e880aeab16ab158" + common_sha = "shaf15f9d80aba72c20e3e71f84869619873a56b8af" } } diff --git a/lib/common.nf b/lib/common.nf index 3a8568d..745b892 100644 --- a/lib/common.nf +++ b/lib/common.nf @@ -2,6 +2,8 @@ import groovy.json.JsonBuilder process getParams { label "wf_common" + publishDir "${params.out_dir}", mode: 'copy', pattern: "params.json" + cache false cpus 1 memory "2 GB" output: diff --git a/nextflow.config b/nextflow.config index 78d0df9..6370723 100755 --- a/nextflow.config +++ b/nextflow.config @@ -13,8 +13,6 @@ params { aws_image_prefix = null aws_queue = null - out_dir = "output" - // feature flags snp = false sv = false @@ -31,7 +29,6 @@ params { bam = null ref = null bed = null - out_dir = "output" bam_min_coverage = 20 downsample_coverage = false downsample_coverage_target = 60 @@ -144,7 +141,7 @@ manifest { description = 'SNV calling, SV calling, modified base calling, CNV calling, and STR genotyping of human samples.' mainScript = 'main.nf' nextflowVersion = '>=23.04.2' - version = '2.4.1' + version = '2.5.0' } epi2melabs {