Merge pull request #152 from sanger-tol/Release-2.1.0

Release 2.1.0
sanger-tol · Dec 9, 2024 · e11e4a8 · e11e4a8
2 parents 5f89876 + e448f75
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -22,17 +22,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 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              |
-|-------------|--------------------------|--------------------------|
-| `agat`      |                          | 1.4.0                    |
-| `bedtools`   | 2.30.0                   | 2.31.1                  |
-| `busco`     | 5.5.0                    | 5.7.1                    | 
-| `cooler`    | 0.8.11                   | 0.9.2                    |
+| Dependency  | Old version                              | New version                              |
+| ----------- | ---------------------------------------- | ---------------------------------------- |
+| `agat`      |                                          | 1.4.0                                    |
+| `bedtools`  | 2.30.0                                   | 2.31.1                                   |
+| `busco`     | 5.5.0                                    | 5.7.1                                    |
+| `cooler`    | 0.8.11                                   | 0.9.2                                    |
 | `fastk`     | 427104ea91c78c3b8b8b49f1a7d6bbeaa869ba1c | 666652151335353eef2fcd58880bcef5bc2928e1 |
-| `gffread`   |                          | 0.12.7                   |
+| `gffread`   |                                          | 0.12.7                                   |
 | `merquryfk` | d00d98157618f4e8d1a9190026b19b471055b22e | 666652151335353eef2fcd58880bcef5bc2928e1 |
-| `multiqc`   | 1.14                     | 1.25.1                  |
-| `samtools`  | 1.17                     | 1.21                    |
+| `multiqc`   | 1.14                                     | 1.25.1                                   |
+| `samtools`  | 1.17                                     | 1.21                                     |
 
 > **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.
 
@@ -66,7 +66,6 @@ Note, since the pipeline is using Nextflow DSL2, each process will be run with i
 |               | --higlass_upload_directory |
 |               | --higlass_data_project_dir |
 
-
 ## [[1.2.2](https://github.com/sanger-tol/genomenote/releases/tag/1.2.2)] - Pyrenean Mountain Dog (patch 2) - [2024-09-10]
 
 ### Enhancements & fixes

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -12,6 +12,10 @@
 
 ## Pipeline tools
 
+- [AGAT](https://github.com/NBISweden/AGAT)
+
+  > Dainat J. AGAT: Another Gff Analysis Toolkit to handle annotations in any GTF/GFF format. (Version v1.4.0). Zenodo. https://www.doi.org/10.5281/zenodo.3552717
+
 - [BedTools](https://bedtools.readthedocs.io/en/latest/)
 
   > Quinlan, Aaron R., and Ira M. Hall. “BEDTools: A Flexible Suite of Utilities for Comparing Genomic Features.” Bioinformatics, vol. 26, no. 6, 2010, pp. 841–842., https://doi.org/10.1093/bioinformatics/btq033.
@@ -30,6 +34,10 @@
 
 - [FastK](https://github.com/thegenemyers/FASTK)
 
+- [GFFREAD](https://github.com/gpertea/gffread)
+
+  > Pertea G and Pertea M. "GFF Utilities: GffRead and GffCompare [version 1; peer review: 3 approved]". F1000Research 2020, 9:304 https://doi.org/10.12688/f1000research.23297.1
+
 - [MerquryFK](https://github.com/thegenemyers/MERQURY.FK)
 
 - [MultiQC](https://multiqc.info)

diff --git a/docs/usage.md b/docs/usage.md
@@ -30,7 +30,7 @@ You will need to supply the assembly accession for the genome you would like to
 
 ## Annotation input
 
-If you want to generate statistics on the set of proteins annotated for the assembly you will need to supply a GFF3 file of the predicted protein sequences. The assembly region names used in this file must match the assembly regions names used in the assembly fasta file provided with --fasta
+If you want to generate statistics on the geneset annotated for the assembly you will need to supply a GFF3 file of the predicted gene sequences. The assembly region names used in this file must match the assembly regions names used in the assembly fasta file provided with --fasta
 
 ```bash
 --annotation_set '[Path to annotation file :gff]

diff --git a/lib/Utils.groovy b/lib/Utils.groovy
@@ -22,7 +22,7 @@ class Utils {
 
         // Check that all channels are present
         // This channel list is ordered by required channel priority.
-        def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
+        def required_channels_in_order = ['conda-forge', 'bioconda']
         def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
 
         // Check that they are in the right order

diff --git a/nextflow.config b/nextflow.config
@@ -243,7 +243,7 @@ manifest {
     description     = """Creating standarised genome assembly publications"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version = '2.0.0'
+    version = '2.1.0'
     doi             = '10.5281/zenodo.7949384'
 }