Merge pull request #83 from sanger-tol/doc

Updated the docs before release

CHANGELOG.md

@@ -3,6 +3,44 @@
 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).
 
+## [[1.2.0](https://github.com/sanger-tol/readmapping/releases/tag/1.2.0)] – Norwegian Ridgeback - [2023-12-20]
+
+### Enhancements & fixes
+
+- Restored recording read-groups (`@RG`) in the BAM/CRAM files.
+- Updated the CI procedure to use "sanger-tol" rather than "nf-core" names.
+- [crumble](https://github.com/jkbonfield/crumble) now used to compress the
+  PacBio HiFi alignments.
+- Execution statistics now under `pipeline_info/readmapping/` (to be consistent
+  with the other sanger-tol pipelines).
+- All resource requirements (memory, time, CPUs) now fit the actual usage. This
+  is achieved by automatically adjusting to the size of the input whenever
+  possible.
+- Added the `--use_work_dir_as_temp` parameter to make SAMTOOLS_COLLATE use its
+  work directory for temporary files instead of `$TMPDIR`. It can be used to avoid
+  leaving unwanted temporary files on a HPC.
+
+### Parameters
+
+| Old parameter | New parameter            |
+| ------------- | ------------------------ |
+|               | `--use_work_dir_as_temp` |
+
+> **NB:** Parameter has been **updated** if both old and new parameter information is present. </br> **NB:** Parameter has been **added** if just the new parameter information is present. </br> **NB:** Parameter has been **removed** if new parameter information isn't present.
+
+### 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.
+
+| Dependency | Old version     | New version   |
+| ---------- | --------------- | ------------- |
+| `blast`    | 2.12.0          | 2.13.0        |
+| `crumble`  |                 | 0.9.1         |
+| `samtools` | 1.14 and 1.16.1 | 1.14 and 1.17 |
+| `multiqc`  | 1.13            | 1.14          |
+
+> **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.
+
 ## [[1.1.0](https://github.com/sanger-tol/readmapping/releases/tag/1.1.0)] – Hebridean Black - [2023-03-16]
 
 ### Enhancements & fixes

nextflow.config

@@ -179,7 +179,7 @@ manifest {
     description     = 'Pipeline to map reads generated using different sequencing technologies against a genome assembly.'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '1.1.0'
+    version         = '1.2.0'
     doi             = '10.5281/zenodo.6563577'
 }