Merge pull request #132 from nf-cmgg/dev

v2.0.6 Release PR

Author: matthdsm

.github/workflows/ci.yml

@@ -10,7 +10,7 @@ on:
 
 env:
   NXF_ANSI_LOG: false
-  NFT_VER: "0.8.4"
+  NFT_VER: "0.9.2"
   NFT_WORKDIR: "~"
   NFT_DIFF: "pdiff"
   NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
@@ -30,7 +30,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "24.10.0"
+          - "25.04.0"
         tags:
           - "modules/local/panelcoverage"
           - "subworkflows/local/bam_qc"

CHANGELOG.md

@@ -5,6 +5,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## dev
 
+## v2.0.6
+
+- Update bash options for nextflow version 25.04.2
+- Update `bcl-convert` module to 4.3.13
+- Update `bowtie2` module to 2.5.4
+- Update `multiqc` module to 1.29
+
 ## v2.0.5
 
 - Panel coverage will now run all genelists' coverage analysis in one process per sample

README.md

@@ -2,7 +2,7 @@
 
 [![GitHub Actions CI Status](https://github.com/nf-cmgg/preprocessing/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-cmgg/preprocessing/actions/workflows/ci.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-cmgg/preprocessing/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-cmgg/preprocessing/actions/workflows/linting.yml)
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.10.0-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A525.04.0-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-cmgg/preprocessing/releases/tag/2.0.5/"
+  This report has been generated by the <a href="https://github.com/nf-cmgg/preprocessing/releases/tag/2.0.6/"
   target="_blank">nf-cmgg/preprocessing</a> analysis pipeline.
 report_section_order:
   "nf-cmgg-preprocessing-methods-description":

modules.json

@@ -7,12 +7,12 @@
                 "nf-core": {
                     "bcl2fastq": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["bcl_demultiplex"]
                     },
                     "bclconvert": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "27cceb2eb8aa959d4a8819caab886386a59a3789",
                         "installed_by": ["bcl_demultiplex", "modules"]
                     },
                     "biobambam/bamsormadup": {
@@ -23,25 +23,25 @@
                     },
                     "bowtie2/align": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "8864afe586537bf562eac7b83349c26207f3cb4d",
                         "installed_by": ["fastq_align_dna", "modules"],
                         "patch": "modules/nf-core/bowtie2/align/bowtie2-align.diff"
                     },
                     "bwa/mem": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "a29f18660f5e3748d44d6f716241e70c942c065d",
                         "installed_by": ["fastq_align_dna"],
                         "patch": "modules/nf-core/bwa/mem/bwa-mem.diff"
                     },
                     "bwamem2/mem": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "a29f18660f5e3748d44d6f716241e70c942c065d",
                         "installed_by": ["fastq_align_dna"],
                         "patch": "modules/nf-core/bwamem2/mem/bwamem2-mem.diff"
                     },
                     "dragmap/align": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "8864afe586537bf562eac7b83349c26207f3cb4d",
                         "installed_by": ["fastq_align_dna"],
                         "patch": "modules/nf-core/dragmap/align/dragmap-align.diff"
                     },
@@ -64,7 +64,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
+                        "git_sha": "471cf3ca1617271b9b6fea09ea2ebdee78b874de",
                         "installed_by": ["modules"]
                     },
                     "picard/collecthsmetrics": {
@@ -138,7 +138,7 @@
                     },
                     "snapaligner/align": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "77bdd7e1047d2abe21ae8d89acc295ea553ecbae",
                         "installed_by": ["fastq_align_dna", "modules"],
                         "patch": "modules/nf-core/snapaligner/align/snapaligner-align.diff"
                     },
@@ -154,12 +154,12 @@
                 "nf-core": {
                     "bcl_demultiplex": {
                         "branch": "master",
-                        "git_sha": "a6e6bec1b1da613b89a6c0a3a46713f880cf5aca",
+                        "git_sha": "27cceb2eb8aa959d4a8819caab886386a59a3789",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_align_dna": {
                         "branch": "master",
-                        "git_sha": "0fa40bbf85955171ec197334ac70a1197fba600d",
+                        "git_sha": "a29f18660f5e3748d44d6f716241e70c942c065d",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {