Ultra Resolution Maps

.nf-core.yml

@@ -48,4 +48,4 @@ template:
     - seqera_platform
     - multiqc
     - rocrate
-  version: 1.6.0
+  version: 1.6.1

CHANGELOG.md

@@ -3,6 +3,26 @@
 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).
 
+## [[1.6.1](https://github.com/sanger-tol/curationpretext/releases/tag/1.6.1)] - UNSC Trafalgar (H1) - [2025-03-13]
+
+## Added and Fixed
+
+- Update to add `--run_ultra` parameter
+  - Enum of ["yes", "no", "force"]
+    - When run as 'yes', ultra resolution maps will be generated if the genome is > 4.Gb.
+    - When run as 'ultra', an ultra resolution map will be generated regardless of genome size.
+- Update to `pretextmap` to a version that supports `--ultraRes`
+- Update to config file to support the above.
+- Addition of example params file `assets/example_params_file.yaml`
+
+### 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 |
+| ------------ | ----------- | ------------ |
+| `PRETEXTMAP` | 0.1.9       | 0.2.4        |
+
 ## [[1.6.0](https://github.com/sanger-tol/curationpretext/releases/tag/1.6.0)] - UNSC Trafalgar - [2025-02-19]
 
 ## Added and Fixed

README.md

@@ -77,6 +77,12 @@ Currently, the pipeline uses the following flags:
 - `--cram_chunk_size`
   - The number of records in a cram file should be chunked into, defaults to 10000.
 
+- `--run_hires`
+  - A boolean to run the pipeline in hires mode, i.e., generate hires resolution maps. Default is `true`
+
+- `--run_ultra`
+  - A string argument to run the pipeline in ultra resolution mode, i.e., generate ultra resolution maps. Options are: `yes`, `force`, `no`. Default is `yes`, this runs ultra resolution maps is the genome file is > 4.Gb.
+
 Now, you can run the pipeline using:
 
 ```bash

assets/example_params_file.yaml

@@ -0,0 +1,14 @@
+sample: "CurationPretextTest_MIN"
+teloseq: "TTA"
+aligner: "bwamem2"
+all_output: false
+skip_tracks: "NONE"
+run_hires: false
+run_ultra: "force"
+split_telomere: true
+input: "https://tolit.cog.sanger.ac.uk/test-data/resources/treeval/TreeValTinyData/assembly/draft/grTriPseu1.fa"
+reads:
+  - "https://tolit.cog.sanger.ac.uk/test-data/resources/treeval/TreeValTinyData/genomic_data/pacbio/seqkitPacbio50000.fasta.gz"
+cram:
+  - "https://tolit.cog.sanger.ac.uk/test-data/resources/treeval/TreeValTinyData/genomic_data/hic-arima/SUBSET-1000.cram"
+  - "https://tolit.cog.sanger.ac.uk/test-data/resources/treeval/TreeValTinyData/genomic_data/hic-arima/SUBSET-2000.cram"

conf/base.config

@@ -69,14 +69,20 @@ process {
     }
 
     withName: ".*:CREATE_MAPS_STDRD:PRETEXTMAP" {
-        cpus    = { 8        * 1 }
+        cpus    = { 6        * 1 }
         memory  = { 3.GB     * task.attempt }
         time    = { 1.h      * ( ( fasta.size() < 4e9 ? 24 : 48 ) * task.attempt ) }
     }
 
     withName: ".*:CREATE_MAPS_HIRES:PRETEXTMAP" {
-        cpus    = {  8       * task.attempt }
-        memory  = {  20.GB   * Math.ceil( task.attempt * 2.6 ) }
+        cpus    = {  6       * task.attempt }
+        memory  = {  20.GB   * task.attempt }
+        time    = {  1.h     * ( ( fasta.size() < 4e9 ? 24 : 48 ) * Math.ceil( task.attempt * 1 ) ) }
+    }
+
+    withName: ".*:CREATE_MAPS_ULTRA:PRETEXTMAP" {
+        cpus    = {  6       * task.attempt }
+        memory  = {  40.GB   * task.attempt }
         time    = {  1.h     * ( ( fasta.size() < 4e9 ? 24 : 48 ) * Math.ceil( task.attempt * 1 ) ) }
     }
 

conf/modules.config

@@ -15,7 +15,7 @@ process {
     //
     // NOTE: GROUP THE PUBLISHDIR DIRECTIVES
     //
-    withName: 'PRETEXT_INGEST_SNDRD|PRETEXT_INGEST_HIRES' {
+    withName: 'PRETEXT_INGEST_SNDRD|PRETEXT_INGEST_HIRES|PRETEXT_INGEST_ULTRA' {
         publishDir = [
             [
                 path:       { "${params.outdir}/pretext_maps_processed" },
@@ -29,6 +29,12 @@ process {
                 mode:       params.publish_dir_mode,
                 saveAs:     { filename -> filename.equals('versions.yml') ? null : filename },
             ],
+            [
+                path:       { "${params.outdir}/pretext_maps_processed" },
+                pattern:    "*ultra.pretext",
+                mode:       params.publish_dir_mode,
+                saveAs:     { filename -> filename.equals('versions.yml') ? null : filename },
+            ],
         ]
     }
 
@@ -170,6 +176,11 @@ process {
         ext.prefix      = { "${meta.id}_hr" }
     }
 
+    withName: "PRETEXT_INGEST_ULTRA" {
+        ext.args        = { "--textureBuffer 1G" }
+        ext.prefix      = { "${meta.id}_ultra" }
+    }
+
     withName: "PRETEXTSNAPSHOT" {
         ext.args        = { "--sequences '=full' --resolution 1440 --memory ${task.memory}" }
         ext.prefix      = { "${meta.id}_normal" }
@@ -238,6 +249,11 @@ process {
         ext.prefix      = { "${meta.id}_hr_pi" }
     }
 
+    withName: ".*:CREATE_MAPS_ULTRA:PRETEXTMAP" {
+        ext.args        = { "${meta.map_order.equals("length") ? "--sortby length": "--sortby nosort" } --ultraRes --mapq ${params.multi_mapping}" }
+        ext.prefix      = { "${meta.id}_ultra_pi" }
+    }
+
     withName: ".*:ALIGN_CRAM:CRAMALIGN_BWAMEM2ALIGNHIC" {
         ext.args        = ""
         ext.args2       = "-F0xB00 -nt"

conf/test.config

@@ -32,5 +32,6 @@ params {
     all_output      = false
     skip_tracks     = "NONE"
     run_hires       = false
+    run_ultra       = "no"
     split_telomere  = true
 }

conf/test_full.config

@@ -29,6 +29,7 @@ params {
     all_output      = true
     skip_tracks     = "NONE"
     run_hires       = true
+    run_ultra       = "force"
     split_telomere  = true
 
 }

main.nf

@@ -39,6 +39,7 @@ workflow SANGER_TOL_CURATIONPRETEXT {
     aligner
     skip_tracks
     run_hires
+    run_ultra
     split_telomere
     cram_chunk_size
 
@@ -54,6 +55,7 @@ workflow SANGER_TOL_CURATIONPRETEXT {
         aligner,
         skip_tracks,
         run_hires,
+        run_ultra,
         split_telomere,
         cram_chunk_size
     )
@@ -98,6 +100,7 @@ workflow {
         params.aligner,
         params.skip_tracks,
         params.run_hires,
+        params.run_ultra,
         params.split_telomere,
         params.cram_chunk_size
     )

modules.json

@@ -77,9 +77,8 @@
                     },
                     "pretextmap": {
                         "branch": "master",
-                        "git_sha": "000647dd5c075642ac90213b17f67f76236a7346",
-                        "installed_by": ["modules", "pairs_create_contact_maps"],
-                        "patch": "modules/nf-core/pretextmap/pretextmap.diff"
+                        "git_sha": "b94e5739438038828eae63cdb55f8d8ac2d99bf6",
+                        "installed_by": ["modules", "pairs_create_contact_maps"]
                     },
                     "pretextsnapshot": {
                         "branch": "master",