diff --git a/CHANGELOG.md b/CHANGELOG.md index c60b36ee..bc5b6a4c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,30 +3,19 @@ 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). -## v1.0dev - [date] +## v0.1.0 - [date] Initial release of genomic-medicine-sweden/skierfe, created with the [nf-core](https://nf-co.re/) template. ### `Added` -- Added a switch to choose phasing software [#83](https://github.com/genomic-medicine-sweden/skierfe/pull/83) -- Added SNV annotation subworkflow to test profile [#75](https://github.com/genomic-medicine-sweden/skierfe/pull/75) -- Refactored conditionally required parameters validation [#69](https://github.com/genomic-medicine-sweden/skierfe/pull/69) -- Added CNV workflow to test profile [#68](https://github.com/genomic-medicine-sweden/skierfe/pull/68) -- Updated and rename output directories [#65](https://github.com/genomic-medicine-sweden/skierfe/pull/65) -- Updated GLNexus version [#58](https://github.com/genomic-medicine-sweden/skierfe/pull/58) -- Added uBAM support and multisample test [#51](https://github.com/genomic-medicine-sweden/skierfe/pull/51) -- Added Revio BAM test data [#50](https://github.com/genomic-medicine-sweden/skierfe/pull/50) -- Updated template to 2.13.1 [#38](https://github.com/genomic-medicine-sweden/skierfe/pull/38) -- Updated pipeline to run with a small test dataset [#35](https://github.com/genomic-medicine-sweden/skierfe/pull/35) -- Added test data and test profile [#33](https://github.com/genomic-medicine-sweden/skierfe/pull/33) - -### `Fixed` - -- Fix input file validation [#67](https://github.com/genomic-medicine-sweden/skierfe/pull/67) -- Fix BCFTools merge module inputs [#43](https://github.com/genomic-medicine-sweden/skierfe/pull/43) -- Fix Mosdepth input channel when run without a bed file [#66](https://github.com/genomic-medicine-sweden/skierfe/pull/66) - -### `Dependencies` - -### `Deprecated` +- Raw read QC with FastQC and FQCRS +- Align reads to reference with minimap2 +- Aligned read QC with cramino and mosdepth +- Call SNVs with DeepVariant and merge with GLNexus +- Annotate SNVs with echtvar and VEP +- Call SVs with Sniffles, tandem repeats with TRGT and CNVs with HiFiCNV +- Phase variants and haplotag reads with whatshap or HiPhase +- Create methylation pileups with modkit +- Assemble genomes with hifiasm +- Align assemly to reference and call variants with dipcall diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 63ae759e..cb0bb247 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,5 +1,5 @@ report_comment: > - This report has been generated by the genomic-medicine-sweden/skierfe + This report has been generated by the genomic-medicine-sweden/skierfe analysis pipeline. report_section_order: "genomic-medicine-sweden-skierfe-methods-description": diff --git a/nextflow.config b/nextflow.config index a41453fa..3b5c7d35 100644 --- a/nextflow.config +++ b/nextflow.config @@ -266,7 +266,7 @@ manifest { description = """Long-read variant calling pipeline""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '' + version = '0.1.0' doi = '' }