Merge pull request #38 from sanger-tol/map_order

add map_order

.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')

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()