Merge pull request #111 from sanger-tol/split_telo

Split telo

Author: weaglesBio

.github/workflows/ci.yml

@@ -67,11 +67,6 @@ jobs:
           mkdir -p $NXF_SINGULARITY_CACHEDIR
           mkdir -p $NXF_SINGULARITY_LIBRARYDIR
 
-      - name: Download test data
-        # Download A fungal test data set that is full enough to show some real output.
-        run: |
-          curl https://tolit.cog.sanger.ac.uk/test-data/resources/treeval/TreeValTinyData.tar.gz | tar xzf -
-
       - name: Install nf-test
         uses: nf-core/setup-nf-test@v1
 

.nf-core.yml

@@ -48,4 +48,4 @@ template:
     - seqera_platform
     - multiqc
     - rocrate
-  version: 1.4.2
+  version: 1.5.0

CHANGELOG.md

@@ -3,6 +3,51 @@
 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).
 
+## [[1.5.0](https://github.com/sanger-tol/curationpretext/releases/tag/1.5.0)] - UNSC Punic - [2025-08-04]
+
+### Added and Fixed
+
+- Template update to 3.3.3. <TODO in next PR>.
+- Addition of the `--split_telomere` boolean flag, this is false by default.
+  - When `true` the pipeline will split the telomere file into a 5 and 3 prime file.
+- Update `ACCESSORY_FILES` subworkflow:
+  - Remove `GET_LARGEST_SCAFFOLD` as we no longer need it, this was needed for TABIX so that the correct index file was used. This was used by the `TELO_FINDER` and `GAP_FINDER` subworkflows.
+- Update `TELO_FINDER` subworkflow:
+  - Remove `GAWK_MAP_TELO` as it is no longer needed.
+  - Remove `GAWK_CLEAN_TELOMERE` as it is no longer needed. The reason for its inclusion has been fixed.
+  - Update `EXTRACT_TELO` to `EXTRACT_TELOMERE` which also removed the use of the `cat {file} | awk` pattern, replacing it with just `awk`. This was supposed to happen in `1.4.0`, but was forgotten with the files lying dormant in the repo.
+  - Refactor of the `TELO_FINDER` subworkflow, introducing the `TELO_EXTRACTION` subworkflow which is run per telo file. With the introduction of `split_telomere` this can be 3 files.
+- Update `LONGREAD_COVERAGE` subworkflow:
+  - Remove `GRAPH_OVERALL_COVERAGE` as it is not in use.
+- Better formatting in some files.
+- Moved `GAWK_UPPER_SEQUENCE` from the `TELO_FINDER` subworkflow to the first step of the main `curationpretext` workflow, this simply makes more sense.
+- Removed no longer needed scripts from bin.
+- Added the module `GAWK_SPLIT_DIRECTIONS` module, a local copy of the nf-core `GAWK` module.
+- Added the `gawk_split_directions.awk` script for split telomere.
+- Addition of GUNZIP for the input reference genome.
+- Update tests.
+
+### Paramters
+
+| Old Version | New Versions     |
+| ----------- | ---------------- |
+| NA          | --split_telomere |
+
+### Software Dependencies
+
+Note, since the pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. 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.
+
+| Module                   | Old Version   | New Versions  |
+| ------------------------ | ------------- | ------------- |
+| `GRAPH_OVERALL_COVERAGE` | perl=5.26.2   | REMOVED       |
+| `EXTRACT_TELO`           | coreutils=9.1 | REMOVED       |
+| `EXTRACT_TELOMERE`       | NA            | coreutils=9.1 |
+| `GAWK_CLEAN_TELOMERE`    | 5.3.0         | REMOVED       |
+| `GAWK_MAP_TELO`          | 5.3.0         | REMOVED       |
+| `GET_LARGEST_SCAFF`      | coreutils=9.1 | REMOVED       |
+| `GUNZIP`                 | NA            | 1.13          |
+| `GAWK_SPLIT_DIRECTIONS`  | NA            | 5.3.0         |
+
 ## [[1.4.2](https://github.com/sanger-tol/curationpretext/releases/tag/1.4.2)] - UNSC Nereid (H2) - [2025-07-28]
 
 ### Added and Fixed

CITATION.cff

@@ -30,6 +30,6 @@ identifiers:
     value: 10.5281/zenodo.12773958
 repository-code: "https://github.com/sanger-tol/curationpretext"
 license: MIT
-version: 1.4.2
-date-released: "2025-07-28"
+version: 1.5.0
+date-released: "2025-08-04"
 url: "https://pipelines.tol.sanger.ac.uk/curationpretext"

bin/findHalfcoverage.py

@@ -0,0 +1,8 @@
+## Split telomere file based on column 4 contents
+## Date: 03/07/2025
+
+BEGIN {
+    FS="\t"; OFS="\t"
+} {
+    print > "direction."$3".telomere"
+}

bin/gawk_split_directions.awk

@@ -17,9 +17,18 @@ process {
     //
     withName: 'PRETEXT_INGEST_SNDRD|PRETEXT_INGEST_HIRES' {
         publishDir = [
-            path: { "${params.outdir}/pretext_maps_processed" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            [
+                path:       { "${params.outdir}/pretext_maps_processed" },
+                pattern:    "*normal.pretext",
+                mode:       params.publish_dir_mode,
+                saveAs:     { filename -> filename.equals('versions.yml') ? null : filename },
+            ],
+            [
+                path:       { "${params.outdir}/pretext_maps_processed" },
+                pattern:    "*hr.pretext",
+                mode:       params.publish_dir_mode,
+                saveAs:     { filename -> filename.equals('versions.yml') ? null : filename },
+            ],
         ]
     }
 
@@ -85,10 +94,9 @@ process {
         ext.suffix = 'fasta'
     }
 
-    withName: 'GAWK_CLEAN_TELOMERE' {
-        ext.args2 = "'/^>/'"
-        ext.prefix = { "${meta.id}_CLEAN" }
-        ext.suffix = 'telomere'
+    withName: 'GAWK_SPLIT_DIRECTIONS' {
+        ext.prefix  = { "${input}_telo" }
+        ext.suffix  = 'telomere'
     }
 
     //