Merge branch 'cw-5311' into 'dev'

v2.5.0 See merge request epi2melabs/workflows/wf-human-variation!350
epi2me-labs · Dec 3, 2024 · e7d07fc · e7d07fc
2 parents 99aa46f + 193ccae
commit e7d07fc
Show file tree

Hide file tree

Showing 4 changed files with 8 additions and 7 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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 {