Dev2Main - 1.4.2

CHANGELOG.md

@@ -3,6 +3,24 @@
 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).
 
+## [1.4.2] - Ancient Hippaforalkus (H2) - [2025-10-08]
+
+Our 9th release for sanger-tol/treeval, containing bug fixes.
+
+### Enhancements & Fixes
+
+- Bug fix preventing production of bin files.
+- Update handling of input params.
+
+## [1.4.1] - Ancient Hippaforalkus (H1) - [2025-08-26]
+
+Our 8th release for sanger-tol/treeval adding a new mode.
+
+### Enhancements & Fixes
+
+- Add FULL_COMBINED mode - running all subworkflows aside from gene_alignment and selfcomp - as not worth running on combined maps.
+- Update resource allocation based on usage.
+
 ## [1.4.0] - Ancient Hippaforalkus - [2025-06-05]
 
 Our 7th release for sanger-tol/treeval.

README.md

@@ -13,7 +13,7 @@
 
 ## Introduction
 
-**sanger-tol/treeval [1.2.0 - Ancient Destiny-]** is a bioinformatics best-practice analysis pipeline for the generation of data supplemental to the curation of reference quality genomes. This pipeline has been written to generate flat files compatible with [JBrowse2](https://jbrowse.org/jb2/) as well as HiC maps for use in Juicebox, PretextView and HiGlass.
+**sanger-tol/treeval [1.4.2 - Ancient Hippaforalkus-]** is a bioinformatics best-practice analysis pipeline for the generation of data supplemental to the curation of reference quality genomes. This pipeline has been written to generate flat files compatible with [JBrowse2](https://jbrowse.org/jb2/) as well as HiC maps for use in Juicebox, PretextView and HiGlass.
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!
 

assets/TreeValTinyFullSangerTest.yaml

@@ -33,5 +33,5 @@ telomere:
 synteny:
   - /nfs/treeoflife-01/resources/nextflow/test-data/resources/treeval/TreeValTinyData/synteny/fungi/LaetiporusSulphureus.fasta
 busco:
-  lineages_path: /nfs/treeoflife-01/resources/nextflow/test-data/resources/treeval/TreeValTinyData/busco/subset/
+  lineages_path: /data/tol/resources/busco/latest/
   lineage: fungi_odb10

main.nf

@@ -26,7 +26,10 @@ workflow {
 
     main:
 
-    params.mode    = params.mode ?: "FULL"
+    params.mode      = params.mode ?: "FULL"
+    params.binfile   = params.binfile ?: false
+    params.juicer    = params.juicer ?: false
+    params.run_hires = params.run_hires ?: true
 
     //
     // SUBWORKFLOW: Run initialisation tasks
@@ -38,7 +41,10 @@ workflow {
         args,
         params.outdir,
         params.input,
-        params.mode
+        params.mode,
+        params.binfile,
+        params.juicer,
+        params.run_hires
     )
 
     //
@@ -57,7 +63,11 @@ workflow {
         PIPELINE_INITIALISATION.out.intron_size,
         PIPELINE_INITIALISATION.out.teloseq,
         PIPELINE_INITIALISATION.out.lineageinfo,
-        PIPELINE_INITIALISATION.out.lineagespath
+        PIPELINE_INITIALISATION.out.lineagespath,
+        PIPELINE_INITIALISATION.out.binfile,
+        PIPELINE_INITIALISATION.out.juicer,
+        PIPELINE_INITIALISATION.out.mode,
+        PIPELINE_INITIALISATION.out.run_hires
     )
 
     //

nextflow.config

@@ -313,7 +313,7 @@ manifest {
     description     = """A pipeline to generate supplemental data for genome curation."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.04.4'
-    version         = '1.4.0'
+    version         = '1.4.2'
     doi             = '10.5281/zenodo.10047653'
 }
 

nextflow_schema.json

@@ -33,14 +33,12 @@
                     "type": "boolean",
                     "format": "boolean",
                     "description": "If false then turn off Juicer generation",
-                    "default": false,
                     "fa_icon": "fas fa-check"
                 },
                 "binfile": {
                     "type": "boolean",
                     "format": "boolean",
                     "description": "If false then turn off bin file generation",
-                    "default": false,
                     "fa_icon": "fas fa-check"
                 },
                 "steps": {