Merge pull request #104 from sanger-tol/dev

Release 1.1.6

.github/workflows/ci.yml

@@ -24,7 +24,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "22.10.1"
+          - "23.10.1"
           - "latest-everything"
     steps:
       - name: Check out pipeline code

CHANGELOG.md

@@ -3,6 +3,23 @@
 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).
 
+## [[1.1.6](https://github.com/sanger-tol/variantcalling/releases/tag/1.1.6)] - Shang Tang (patch 6) - [2025-02-10]
+
+### Enhancements & fixes
+
+- Allow DeepVariant and BCFtools to handle CSI files
+- Deal with genomes >4GB in Minimap
+
+### Software dependencies
+
+Note, since the pipeline is using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference. Only `Docker` or `Singularity` containers are supported, `conda` is not supported.
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| nextflow   | 22.10.1     | 23.10.1     |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present. </br> **NB:** Dependency has been **added** if just the new version information is present. </br> **NB:** Dependency has been **removed** if version information isn't present.
+
 ## [[1.1.5](https://github.com/sanger-tol/variantcalling/releases/tag/1.1.5)] - Shang Tang (patch 5) - [2025-01-14]
 
 ### Enhancements & fixes

README.md

@@ -2,7 +2,7 @@
 
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7890527-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7890527)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.10.1-23aa62.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/)
@@ -34,7 +34,7 @@ Steps involved:
 
 ## Quick Start
 
-1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`)
+1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=23.10.1`)
 
 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.
 

conf/modules.config

@@ -43,7 +43,7 @@ process {
         }
 
         withName: '.*:.*:ALIGN_PACBIO:MINIMAP2_ALIGN' {
-            ext.args = { "-ax map-hifi --cs=short -R ${meta.read_group}" }
+            ext.args = { "-ax map-hifi --cs=short -R ${meta.read_group} -I" + Math.ceil(meta2.genome_size/1e9) + 'G' }
         }
 
         withName: '.*:.*:ALIGN_PACBIO:SAMTOOLS_MERGE' {

modules.json

@@ -7,7 +7,13 @@
                 "nf-core": {
                     "bcftools/concat": {
                         "branch": "master",
-                        "git_sha": "d1e0ec7670fa77905a378627232566ce54c3c26d",
+                        "git_sha": "c807a63439b48f181523b9c943f5e51eaa805387",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/bcftools/concat/bcftools-concat.diff"
+                    },
+                    "bcftools/index": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "blast/blastn": {
@@ -28,7 +34,8 @@
                     "deepvariant/rundeepvariant": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/deepvariant/rundeepvariant/deepvariant-rundeepvariant.diff"
                     },
                     "gunzip": {
                         "branch": "master",