Merge pull request #366 from drpatelh/fixes

Final pre-release fixes

Author: drpatelh

CHANGELOG.md

@@ -3,7 +3,20 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[2.6](https://github.com/nf-core/viralrecon/releases/tag/2.6)] - 2023-03-17
+## [[2.6.0](https://github.com/nf-core/viralrecon/releases/tag/2.6.0)] - 2023-03-23
+
+### Credits
+
+Special thanks to the following for their code contributions to the release:
+
+- [Friederike Hanssen](https://github.com/FriederikeHanssen)
+- [Hugo Tavares](https://github.com/tavareshugo)
+- [Matthew Wells](https://github.com/mattheww95)
+- [Maxime Garcia](https://github.com/maxulysse)
+- [Phil Ewels](https://github.com/ewels)
+- [Sara Monzón](https://github.com/saramonzon)
+
+Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
 
 ### Enhancements & fixes
 

modules.json

@@ -42,7 +42,7 @@
                     },
                     "bcftools/norm": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "bcad95fb35e567ad25840d3297c3e17eff211a3a",
                         "installed_by": ["modules"]
                     },
                     "bcftools/query": {
@@ -142,7 +142,7 @@
                     },
                     "kraken2/kraken2": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "7c695e0147df1157413e06246d9b0094617d3e6b",
                         "installed_by": ["modules"]
                     },
                     "minia": {
@@ -177,13 +177,13 @@
                     },
                     "picard/collectmultiplemetrics": {
                         "branch": "master",
-                        "git_sha": "2f88b26e9804b99e98f7cd08e74c3f88288a3358",
+                        "git_sha": "75027bf77472b1f4fd2cdd7e46f83119dfb0f2c6",
                         "installed_by": ["modules"]
                     },
                     "picard/markduplicates": {
                         "branch": "master",
-                        "git_sha": "2f88b26e9804b99e98f7cd08e74c3f88288a3358",
-                        "installed_by": ["bam_markduplicates_picard", "modules"]
+                        "git_sha": "75027bf77472b1f4fd2cdd7e46f83119dfb0f2c6",
+                        "installed_by": ["modules", "bam_markduplicates_picard"]
                     },
                     "plasmidid": {
                         "branch": "master",
@@ -266,7 +266,7 @@
                 "nf-core": {
                     "bam_markduplicates_picard": {
                         "branch": "master",
-                        "git_sha": "6daac2bc63f4847e0c7cc661f4f5b043ac13faaf",
+                        "git_sha": "6f1697c121719dedde9e0537b6ed6a9cb8c13583",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_sort_stats_samtools": {
@@ -276,7 +276,7 @@
                     },
                     "bam_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "92eb5091ae5368a60cda58b3a0ced8b36d715b0f",
+                        "git_sha": "b4b7f89e7fd6d2293f0c176213f710e0bcdaf19e",
                         "installed_by": ["bam_sort_stats_samtools", "bam_markduplicates_picard"]
                     },
                     "fastq_align_bowtie2": {

modules/nf-core/bcftools/norm/main.nf

@@ -255,7 +255,7 @@ manifest {
     description     = """Assembly and intrahost/low-frequency variant calling for viral samples"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '2.6'
+    version         = '2.6.0'
     doi             = 'https://doi.org/10.5281/zenodo.3901628'
 }
 

modules/nf-core/bcftools/norm/meta.yml

@@ -3,7 +3,7 @@
 //
 
 include { IVAR_TRIM               } from '../../modules/nf-core/ivar/trim/main'
-include { BAM_SORT_STATS_SAMTOOLS } from './bam_sort_stats_samtools/main'
+include { BAM_SORT_STATS_SAMTOOLS } from '../nf-core/bam_sort_stats_samtools/main'
 
 workflow BAM_TRIM_PRIMERS_IVAR {
     take: