Update params and changelog

Author: weaglesBio

.github/workflows/nf-test.yml

@@ -50,6 +50,7 @@ jobs:
           NFT_VER: ${{ env.NFT_VER }}
         with:
           max_shards: 7
+          tag: "githubci"
 
       - name: debug
         run: |

CHANGELOG.md

@@ -3,7 +3,60 @@
 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).
 
-## [1.4.4] - Ancient Hippaforalkus (H1) - [2025-XX-XX]
+
+## [1.4.6] - Ancient Hippaforalkus (H5) - [2026-03-XX]
+
+Our 13th release for sanger-tol/treeval.
+
+### Enhancements & Fixes
+- Update to pretext map, adds option to generate Ultra HiRes map.
+- Changes to confirm with nf-core strict syntax.
+
+### Parameters
+| Old Parameter | New Parameter    |
+| ------------- | ---------------- |
+| -             | --run_ultra      |
+
+
+### Software dependencies
+| Module                                 | Old Version           | New Versions                       |
+| -------------------------------------- | --------------------- | ---------------------------------- |
+| GET_LARGEST_SCAFFOLD (coreutils)       | 9.1                   | REMOVED                            |
+| busco/busco                            | 5.7.1                 | 6.0.0                              |   
+| bwamem2/index (bwa-mem2)               | 2.2.1                 | 2.3+htslib=1.22.1+samtools=1.22.1  |   
+| cat/cat (pigz)                         | 2.3.4                 | 2.8                                |
+| cooler/cload (cooler)                  | 0.9.2                 | 0.10.4                             |
+| cooler/zoomify (cooler)                | 0.9.2                 | 0.10.4+numpy=1.26.4                |
+| custom/dumpsoftwareversions            | multiqc=1.20          | REMOVED                            |
+| custom/getchromsizes (htslib+samtools) | 1.21+1.22.1           | REMOVED                            |
+| fastk/fastk                            | 1.0.2                 | 1.2                                |
+| gnu/sort (coreutils)                   | 9.3                   | coreutils=9.5                      |
+| juicertools                            |                       | juicertools=2.20.00,openjdk=23.0.2 |
+| merquryfk/merquryfk                    | fastk=1.0.2           | 1.2                                |
+| minimap2/align (minimap2+samtools)     | 2.28+1.20+htslib=1.20 | 2.29+1.21                          |
+| minimap2/index (minimap2)              | 2.28                  | 2.29                               |
+| pretextmap (pretextmap+samtools)       | 0.1.9+1.17            | 0.2.4+1.23+htslib=1.23             |
+| pretextsnapshot                        | 0.0.4                 | 0.0.7                              |
+| samtools/faidx (htslib+samtools)       | 1.21+1.21             | 1.22.1+1.22.1                      |
+| samtools/index (htslib+samtools)       | 1.21+1.21             | REMOVED                            |
+| samtools/markdup (htslib+samtools)     | 1.21+1.21             | 1.22.1+1.22.1                      |
+| samtools/merge (htslib+samtools)       | 1.21+1.21             | 1.22.1+1.22.1                      |
+| samtools/sort (htslib+samtools)        | 1.21+1.21             | REMOVED                            |
+| samtools/view (htslib+samtools)        | 1.21+1.21             | REMOVED                            |
+| tabix/bgziptabix                       | 1.20+tabix=1.11       | 1.21                               |
+| windowmasker/mkcounts (blast)          | 2.15.0                | 2.17.0                             |
+| windowmasker/ustat (blast)             | 2.15.0                | 2.17.0                             |
+| yahs                                   | 1.2a.2                | 1.2.2
+
+## [1.4.5] - Ancient Hippaforalkus (H5) - [2025-11-24]
+
+Our 12th release for sanger-tol/treeval.
+
+### Enhancements & Fixes
+- Bug fix, pretext files weren't being output due to the use of a closure rather than a list in modules.config.
+- Updated to BEDTOOLS INTERSECT resources
+
+## [1.4.4] - Ancient Hippaforalkus (H4) - [2025-11-17]
 
 Our 11th release for sanger-tol/treeval.
 

conf/test.config

@@ -17,7 +17,7 @@
 process {
     resourceLimits = [
         cpus: 4,
-        memory: '40.GB', // required for pretext map ultra res test
+        memory: '10.GB', // required for pretext map ultra res test
         time: '1.h'
     ]
 }

conf/test_full.config

@@ -19,7 +19,7 @@ process {
     resourceLimits = [
         cpus: 4,
         memory: '40.GB', // required for pretext map ultra res test
-        time: '1.h'
+        time: '2.h'
     ]
 }
 

docs/output.md

@@ -22,7 +22,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [synteny](#synteny) - Generates syntenic alignments between the input and other high quality genomes.
 - [busco-analysis](#busco-analysis) - Uses BUSCO to identify ancestral elements. Also use to identify ancestral Lepidopteran genes (merian units).
 - [kmer](#kmer) - Counts k-mer and generates a copy number spectra plot.
-- [kmer coverage](#kmer-coverage) - Counts k-mer (or uses existing k-mer profile) and produces k-mer coverage.
 - [pretext-ingestion](#pretext-ingestion) - Ingests accessory files into the pretext file.
 
 - [pipeline-information](#pipeline-information) - Report metrics generated during the workflow execution
@@ -222,20 +221,6 @@ This subworkflow performs a k-mer count using [FASTK_FASTK](https://nf-co.re/mod
 
 ![Kmer Workflow](https://raw.githubusercontent.com/sanger-tol/treeval/main/docs/images/v1-1-0/treeval_1_1_0_kmer.png)
 
-## kmer coverage
-
-This subworkflow performs a k-mer count using [FASTK_FASTK](https://nf-co.re/modules/fastk_fastk) (or uses an already existing k-mer profile) then passes the results to FKUTILS_FKPROF to produces k-mer coverage track.
-
-<details markdown="1">
-<summary>Output files</summary>
-
-- `hic_files/`
-  - `*_{kmer_size}_.bw`: .png file of copy number k-mer spectra.
-
-</details>
-
-![Kmer coverage Workflow](https://raw.githubusercontent.com/sanger-tol/treeval/main/docs/images/v1-1-0/treeval_1_1_0_kmer_coverage.png)
-
 ## Full Workflow diagram
 
 The full pipeline diagram is very large, with the pipeline consisting of over 100 processes.

docs/usage.md

@@ -417,8 +417,6 @@ find v5/data -name "*.tar.gz" | parallel "cd {//}; tar -xzf {/}"
   - Uses BUSCO to identify ancestral elements. Also use to identify ancestral Lepidopteran genes (merian units).
 - `KMER`
   - Generating kmer graphs of the assembly.
-- `KMER_READ_COVERAGE`
-  - Generating read coverage using kmers.
 
 </details>
 

main.nf

@@ -65,10 +65,7 @@ workflow {
         PIPELINE_INITIALISATION.out.lineagespath,
         PIPELINE_INITIALISATION.out.binfile,
         PIPELINE_INITIALISATION.out.juicer,
-        PIPELINE_INITIALISATION.out.mode,
-        PIPELINE_INITIALISATION.out.split_telomere,
-        PIPELINE_INITIALISATION.out.run_hires,
-        PIPELINE_INITIALISATION.out.run_ultra
+        PIPELINE_INITIALISATION.out.mode
     )
 
     //

subworkflows/local/hic_mapping/main.nf

@@ -43,9 +43,6 @@ workflow HIC_MAPPING {
     workflow_setting    // string: Run mode (FULL, RAPID, RAPID_TOL, etc.)
     binfile             // boolean: Generate bin file using YAHS
     juicer              // boolean: Generate .hic file using Juicer
-    split_telomere      // boolean: Split telomere signal into 5p and 3p
-    run_hires           // boolean: Generate high resolution pretext maps
-    run_ultra           // boolean: Generate high resolution pretext maps
 
     main:
     ch_versions         = channel.empty()
@@ -208,11 +205,11 @@ workflow HIC_MAPPING {
         coverage_file.map{ _meta, covfile -> covfile },
         telo_file,
         repeat_density_file.map{ _meta, rdfile -> rdfile },
-        split_telomere
+        params.split_telomere
     )
     ch_versions         = ch_versions.mix( PRETEXT_INGEST_SNDRD.out.versions )
 
-    if (run_hires) {
+    if (params.run_hires) {
         //
         // MODULE: GENERATE PRETEXT MAP FROM MAPPED BAM FOR HIGH RES
         //
@@ -243,7 +240,7 @@ workflow HIC_MAPPING {
         hires_pretext       = channel.empty()
     }
 
-    if (run_ultra) {
+    if (params.run_ultra) {
         //
         // MODULE: GENERATE PRETEXT MAP FROM MAPPED BAM FOR HIGH RES
         //

subworkflows/local/utils_nfcore_treeval_pipeline/main.nf

@@ -37,9 +37,6 @@ workflow PIPELINE_INITIALISATION {
     mode              //  string: Run mode, default FULL, alternatives: JBROWSE, RAPID, RAPID_TOL, FULL_COMBINED
     binfile           // boolean: Generate bin file using YAHS
     juicer            // boolean: Generate .hic file using Juicer
-    split_telomere     // boolean: Split telomere scaffolds into 3p and 5p
-    run_hires         // boolean: Generate high resolution pretext maps
-    run_ultra         // boolean: Generate ultra high resolution pretext maps
     help              // boolean: Display help message and exit
     help_full         // boolean: Show the full help message
     show_hidden       // boolean: Show hidden parameters in the help message
@@ -110,9 +107,6 @@ workflow PIPELINE_INITIALISATION {
     binfile         = binfile
     juicer          = juicer
     mode            = mode
-    split_telomere  = split_telomere
-    run_hires       = run_hires
-    run_ultra       = run_ultra
     versions        = ch_versions
 }
 

tests/main.nf.test

@@ -0,0 +1,59 @@
+nextflow_pipeline {
+
+    name "Test TreeVal Full pipeline w/o hi res and ultra res pretext maps"
+    script "../main.nf"
+    tag "pipeline"
+    tag "full"
+    tag "githubci"
+
+    config '../conf/test.config'
+
+    test("Run w/o hi res and ultra res pretext maps") {
+
+        setup {
+            println "Downloading BUSCO test data..."
+            def busco_test_url = "https://tolit.cog.sanger.ac.uk/test-data/resources/treeval/TreeValTinyData/busco.tar.gz"
+            def busco_test_command = ['bash', '-c', "curl -L --retry 5 --retry-delay 10 ${busco_test_url} | tar xzf - -C ${launchDir}"]
+            def busco_test_proc = busco_test_command.execute()
+            busco_test_proc.waitFor()
+
+            if (busco_test_proc.exitValue() != 0) {
+                throw new RuntimeException("Error - failed to download busco data: ${busco_test_proc.err.text}")
+            }
+        }
+
+        when {
+            params {
+                outdir          = "$outputDir"
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}','hic_files/*.ktab*'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/treeval_software_versions.yml"),
+
+                    // All stable path name, with a relative path
+                    stable_name,
+
+                    // All files with stable contents
+                    stable_path
+
+                ).match() }
+            )
+        }
+        cleanup {
+            new File("${launchDir}/busco")
+        }
+    }
+}