diff --git a/CHANGELOG.md b/CHANGELOG.md index 3d1c127..000352d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,7 +8,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added - New primer schemes; ARTIC V5.3.2 and Midnight IDT V2 ### Updated -- Nextclade & pangolin +- Nextclade bump to 2.14.0 +- Pangolin bump to 4.3 - For alt primers we take the largest region (Updated ARTIC code merges a canonical primer site with an alt site, producing an interval that encompasses both) ## [v0.3.29] diff --git a/main.nf b/main.nf index 0e4ad72..56e3db5 100644 --- a/main.nf +++ b/main.nf @@ -353,6 +353,9 @@ process pangolin { then pangolin --update fi + + # set cache for snakemake to prevent permission issuses + export XDG_CACHE_HOME=\$(pwd -P) pangolin --all-versions 2>&1 | sed 's/: /,/' > pangolin.version pangolin --threads ${task.cpus} $params._pangolin_options consensus.fasta diff --git a/nextflow.config b/nextflow.config index cc3d4ba..554d28e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -36,10 +36,9 @@ params { report_lineage = true report_coverage = true report_variant_summary = true - pangolin_version = "4.2" pangolin_options = null - nextclade_version = "2.11.0" nextclade_data_tag = null + nextclade_version = "2.14.0" update_data = false aws_image_prefix = null aws_queue = null @@ -61,8 +60,8 @@ params { ] common_sha = "sha0fa3896acb70eecc0d432c91a1516d596a87741c" container_sha = 'shaa5485f2d1c9085c23b266273556a4ce01e5e0dd9' - nextclade_sha = 'shaede3ca9a1b17c2a1d0696ef7ff8503ec167d5df9' - pangolin_sha = 'sha1266e6040bf6e9f02e569f0eba5011a17d47f7aa' + nextclade_sha = 'sha24df77bfdb05353178d9798d1edf87822ae84756' + pangolin_sha = 'sha983ccbd03506597918e5c99689eac6fcc84de431' } } diff --git a/nextflow_schema.json b/nextflow_schema.json index 5ba9df1..cbf7f76 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -219,18 +219,13 @@ "default": false, "description": "Update pangolin & Nextclade data at runtime." }, - "pangolin_version": { - "type": "string", - "default": "4.2", - "hidden": true - }, "pangolin_options": { "type": "string", "description": "Pass options to pangolin, use like this \"--analysis-mode fast --min-length 26000\"." }, "nextclade_version": { "type": "string", - "default": "2.11.0", + "default": "2.14.0", "hidden": true }, "nextclade_data_tag": {