Merge pull request #139 from sanger-tol/patch

Switch back to `scratch=false` for large genomes

CHANGELOG.md

@@ -3,7 +3,13 @@
 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).
 
-## [[1.2.1](https://github.com/sanger-tol/genomenote/releases/tag/1.2.1)] [2024-07-12]
+## [[1.2.2](https://github.com/sanger-tol/genomenote/releases/tag/1.2.2)] - Pyrenean Mountain Dog (patch 2) - [2024-09-10]
+
+### Enhancements & fixes
+
+- Bugfix: don't run Busco in scratch mode for large genomes as it takes too much space on /tmp
+
+## [[1.2.1](https://github.com/sanger-tol/genomenote/releases/tag/1.2.1)] - Pyrenean Mountain Dog (patch 1) - [2024-07-12]
 
 ### Enhancements & fixes
 
@@ -40,13 +46,13 @@ Note, since the pipeline is using Nextflow DSL2, each process will be run with i
 | ------------- | ------------- |
 |               | --cool_order  |
 
-## [[1.1.2](https://github.com/sanger-tol/genomenote/releases/tag/1.1.2)] [2024-04-29]
+## [[1.1.2](https://github.com/sanger-tol/genomenote/releases/tag/1.1.2)] - Golden Retriever (patch 2) - [2024-04-29]
 
 ### Enhancements & fixes
 
 - Bugfix: the BAM still needs to be filtered with `-F0x400`
 
-## [[1.1.1](https://github.com/sanger-tol/genomenote/releases/tag/1.1.1)] [2024-02-26]
+## [[1.1.1](https://github.com/sanger-tol/genomenote/releases/tag/1.1.1)] - Golden Retriever (patch 1) - [2024-02-26]
 
 ### Enhancements & fixes
 

CITATION.cff

@@ -2,16 +2,16 @@
 # Visit https://bit.ly/cffinit to generate yours today!
 
 cff-version: 1.2.0
-title: sanger-tol/genomenote v1.2.1
+title: sanger-tol/genomenote v1.2.2
 message: >-
     If you use this software, please cite it using the
     metadata from this file.
 type: software
 authors:
-    - given-names: Cibin
-      family-names: Sadasivan Baby
+    - given-names: Tyler
+      family-names: Chafin
       affiliation: Wellcome Sanger Institute
-      orcid: "https://orcid.org/0000-0002-8538-276X"
+      orcid: "https://orcid.org/0000-0001-8687-5905"
     - given-names: Matthieu
       family-names: Muffato
       affiliation: Wellcome Sanger Institute
@@ -20,12 +20,16 @@ authors:
       family-names: Qi
       affiliation: Wellcome Sanger Institute
       orcid: "https://orcid.org/0000-0003-1262-8973"
+    - given-names: Cibin
+      family-names: Sadasivan Baby
+      affiliation: Wellcome Sanger Institute
+      orcid: "https://orcid.org/0000-0002-8538-276X"
     - given-names: Priyanka
       family-names: Surana
       affiliation: Wellcome Sanger Institute
       orcid: "https://orcid.org/0000-0002-7167-0875"
-    - given-names: Yates
-      family-names: Bethan
+    - given-names: Bethan
+      family-names: Yates
       affiliation: Wellcome Sanger Institute
       orcid: "https://orcid.org/0000-0003-1658-1762"
 identifiers:
@@ -34,5 +38,5 @@ identifiers:
 repository-code: "https://github.com/sanger-tol/genomenote"
 license: MIT
 commit: TODO
-version: 1.2.1
+version: 1.2.2
 date-released: "2022-10-07"

conf/modules.config

@@ -50,7 +50,8 @@ process {
     }
 
     withName: BUSCO {
-        scratch = true
+        // Obey "use_work_dir_as_temp", except for large genomes
+        scratch = { !params.use_work_dir_as_temp || (meta.genome_size < 2000000000) }
         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

nextflow.config

@@ -222,7 +222,7 @@ manifest {
     description     = """Creating standarised genome assembly publications"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '1.2.1'
+    version         = '1.2.2'
     doi             = '10.5281/zenodo.7949384'
 }