Merge branch 'dev' into dp24_spelling

.github/workflows/linting.yml

@@ -19,7 +19,7 @@ jobs:
       - uses: actions/setup-node@v3
 
       - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
+        run: npm install -g editorconfig-checker@3.0.2
 
       - name: Run ECLint check
         run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|cff\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')

LICENSE

@@ -1,6 +1,8 @@
 MIT License
 
-Copyright (c) Damon-Lee B Pointon (@DLBPointon)
+Copyright (c) 2022-2024 Genome Research Ltd.
+except `bin/filter_five_end.pl`:
+Copyright (c) 2017 Arima Genomics, Inc.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -19,8 +21,3 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
-
-
-The filter_five_end.ph script has been taken from the Arima Mapping Pipeline, has not been modified and is subject to the below license:
-
-Copyright (c) 2017 Arima Genomics, Inc.

README.md

@@ -47,6 +47,10 @@ Currently, the pipeline uses the following flags:
 
   - The directory of the cram _and_ cram.crai files, e.g., `/path/to/cram/`
 
+- `--map_order`
+
+  - hic map scaffold order, input either `length` or `unsorted`
+
 - `--teloseq`
 
   - A telomeric sequence, e.g., `TTAGGG`
@@ -66,7 +70,8 @@ nextflow run sanger-tol/curationpretext \
   --longread { path/to/longread/fasta/ } \
   --longread_type { default is "hifi" }
   --sample { default is "pretext_rerun" } \
-  --teloseq { deafault is "TTAGGG" } \
+  --teloseq { default is "TTAGGG" } \
+  --map_order { default is "unsorted" } \
   --outdir { OUTDIR } \
   -profile <docker/singularity/{institute}>
 
@@ -81,7 +86,8 @@ nextflow run sanger-tol/curationpretext \
   --longread { path/to/longread/fasta/ } \
   --longread_type { default is "hifi" }
   --sample { default is "pretext_rerun" } \
-  --teloseq { deafault is "TTAGGG" } \
+  --teloseq { default is "TTAGGG" } \
+  --map_order { default is "unsorted" } \
   --outdir { OUTDIR } \
   -profile <docker/singularity/{institute}> \
   -entry MAPS_ONLY \

conf/modules.config

@@ -133,12 +133,12 @@ process {
     }
 
     withName: PRETEXTMAP_STANDRD {
-        ext.args        = { "--sortby length --mapq 0 --memory ${task.memory.giga}G" }
+        ext.args        = { "${meta.map_order.equals("length") ? "--sortby length": "--sortby nosort" } --mapq 0 --memory ${task.memory.giga}" }
         ext.prefix      = { "${meta.id}_normal_pi" }
     }
 
     withName: PRETEXTMAP_HIGHRES {
-        ext.args        = { "--sortby length --highRes --mapq 0 --memory ${task.memory.giga}G" }
+        ext.args        = { "${meta.map_order.equals("length") ? "--sortby length": "--sortby nosort" } --highRes --mapq 0" }
         ext.prefix      = { "${meta.id}_hr_pi" }
     }
 

modules/local/find_telomere_regions.nf

@@ -2,7 +2,7 @@ process FIND_TELOMERE_REGIONS {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'docker.io/library/gcc:7.1.0'
+    container 'quay.io/sanger-tol/telomere:0.0.1-c1'
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

nextflow.config

@@ -17,6 +17,7 @@ params {
     cram                       = null
     aligner                    = "bwamem2"
     longread_type              = "hifi"
+    map_order                  = "unsorted"
 
     // Boilerplate options
     outdir                     = "${params.outdir}/results"

nextflow_schema.json

@@ -10,7 +10,7 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": ["input", "cram", "sample", "outdir"],
+            "required": ["input", "cram", "sample", "outdir", "map_order"],
             "properties": {
                 "input": {
                     "type": "string",
@@ -46,6 +46,12 @@
                     "help_text": "Give me a telomeric motif",
                     "fa_icon": "fas fa-file-signature"
                 },
+                "map_order": {
+                    "type": "string",
+                    "description": "HiC map scaffold order. Default to unsorted",
+                    "help_text": "How you want to display your hic map, sorted by length?",
+                    "fa_icon": "fas fa-file-signature"
+                },
                 "aligner": {
                     "type": "string",
                     "description": "Aligner for use {minimap2, bwamem2} in generating map",

subworkflows/local/generate_maps.nf

@@ -20,6 +20,7 @@ workflow GENERATE_MAPS {
     reference_tuple     // Channel [ val(meta), path(file)      ]
     hic_reads_path      // Channel [ val(meta), path(directory) ]
 
+
     main:
     ch_versions         = Channel.empty()