Merge pull request #155 from sanger-tol/anaconda_purge

Anaconda purge (2.x.x)
sanger-tol · Dec 5, 2024 · 5f89876 · 5f89876
2 parents c4f45a0 + c4e97c3
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,39 @@
 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).
 
+## [[2.1.0](https://github.com/sanger-tol/genomenote/releases/tag/2.1.0)] - Pembroke Welsh Corgi [2024-12-05]
+
+### Enhancements & fixes
+
+- New annotation_statistics subworkfow which runs BUSCO in protein mode and generates some basic statistics on the the annotated gene set if provided with a GFF3 file of gene annotations using the `--annotation_set` option.
+- The genome_metadata subworkflow now queries Ensembl's GraphQL API to determine if Ensembl has released gene annotation for the assembly being processed.
+
+### Parameters
+
+| Old parameter | New parameter    |
+| ------------- | ---------------- |
+|               | --annotation_set |
+
+> **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. 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                    |
+| `fastk`     | 427104ea91c78c3b8b8b49f1a7d6bbeaa869ba1c | 666652151335353eef2fcd58880bcef5bc2928e1 |
+| `gffread`   |                          | 0.12.7                   |
+| `merquryfk` | d00d98157618f4e8d1a9190026b19b471055b22e | 666652151335353eef2fcd58880bcef5bc2928e1 |
+| `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.
+
 ## [[2.0.0](https://github.com/sanger-tol/genomenote/releases/tag/2.0.0)] - English Cocker Spaniel [2024-10-10]
 
 ### Enhancements & fixes
@@ -33,6 +66,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 |               | --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
@@ -48,9 +48,9 @@
 
 ## Software packaging/containerisation tools
 
-- [Anaconda](https://anaconda.com)
+- [Conda](https://conda.org/)
 
-  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
+  > conda contributors. conda: A system-level, binary package and environment manager running on all major operating systems and platforms. Computer software. https://github.com/conda/conda
 
 - [Bioconda](https://bioconda.github.io)
 

diff --git a/README.md b/README.md
@@ -4,7 +4,7 @@
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7949384-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7949384)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.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 conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=conda)](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/)
 [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/sanger-tol/genomenote)

diff --git a/conf/modules.config b/conf/modules.config
@@ -55,8 +55,8 @@ process {
         ext.args = { 'test' in workflow.profile.tokenize(',') ?
                         // Additional configuration to speed processes up during testing.
                         // Note: BUSCO *must* see the double-quotes around the parameters
-                        '--tar --metaeuk_parameters \'"-s=2"\' --metaeuk_rerun_parameters \'"-s=2"\''
-                    : '--tar' }
+                        '--tar --metaeuk --metaeuk_parameters \'"-s=2"\' --metaeuk_rerun_parameters \'"-s=2"\''
+                    : '--tar --metaeuk ' }
     }
 
     withName: "RESTRUCTUREBUSCODIR" {

diff --git a/conf/test_full.config b/conf/test_full.config
@@ -10,8 +10,6 @@
 ----------------------------------------------------------------------------------------
 */
 
-cleanup = true
-
 params {
     config_profile_name        = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'

diff --git a/modules.json b/modules.json
@@ -7,80 +7,80 @@
                 "nf-core": {
                     "agat/spstatistics": {
                         "branch": "master",
-                        "git_sha": "0a0b723d114e502207072603479b635dfbc2bf59",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "agat/sqstatbasic": {
                         "branch": "master",
-                        "git_sha": "0a0b723d114e502207072603479b635dfbc2bf59",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "bedtools/bamtobed": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
-                    "busco": {
+                    "busco/busco": {
                         "branch": "master",
-                        "git_sha": "e3126f437c336c826f242842fe51769cfce0ec2d",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"],
-                        "patch": "modules/nf-core/busco/busco.diff"
+                        "patch": "modules/nf-core/busco/busco/busco-busco.diff"
                     },
                     "cooler/cload": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "cooler/dump": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "cooler/zoomify": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "fastk/fastk": {
                         "branch": "master",
-                        "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/fastk/fastk/fastk-fastk.diff"
                     },
                     "gffread": {
                         "branch": "master",
-                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "gnu/sort": {
                         "branch": "master",
-                        "git_sha": "88f6e982fb8bd40488d837b3b08a65008e602840",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "merquryfk/merquryfk": {
                         "branch": "master",
-                        "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/merquryfk/merquryfk/merquryfk-merquryfk.diff"
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     },
                     "samtools/view": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/nf-core/agat/spstatistics/environment.yml b/modules/nf-core/agat/spstatistics/environment.yml
diff --git a/modules/nf-core/agat/spstatistics/meta.yml b/modules/nf-core/agat/spstatistics/meta.yml
diff --git a/modules/nf-core/agat/sqstatbasic/environment.yml b/modules/nf-core/agat/sqstatbasic/environment.yml
diff --git a/modules/nf-core/agat/sqstatbasic/meta.yml b/modules/nf-core/agat/sqstatbasic/meta.yml
diff --git a/modules/nf-core/busco/environment.yml → ...nf-core/bedtools/bamtobed/environment.yml b/modules/nf-core/busco/environment.yml → ...nf-core/bedtools/bamtobed/environment.yml
diff --git a/modules/nf-core/bedtools/bamtobed/main.nf b/modules/nf-core/bedtools/bamtobed/main.nf