Merge branch 'min-coverage-param' into 'dev'

Adding min coverage parameter

See merge request epi2melabs/workflow-containers/wf-mpx!8

CHANGELOG.md

@@ -4,11 +4,15 @@ All notable changes to this project will be documented in this file.
 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).
 
+## [v0.0.4]
+### Added
+- Minimum coverage parameter
+
 ## [v0.0.3]
 ### Changed
 - Args parser for fastqingress
 - Set out_dir option type to ensure output is written to correct directory on Windows
-- 
+
 ## [v0.0.2]
 ### Changed
 - Tidied up docs

main.nf

@@ -81,7 +81,7 @@ process medakaVariants {
     medaka variant --gvcf ${reference} ${sample_id}.hdf ${sample_id}.vcf --verbose
     medaka tools annotate --debug --pad 25 ${sample_id}.vcf ${reference} ${sample_id}.bam ${sample_id}.annotate.vcf
 
-    bcftools filter -e "ALT='.'" ${sample_id}.annotate.vcf | bcftools filter -o ${sample_id}.annotate.filtered.vcf -O v -e "INFO/DP<20" -
+    bcftools filter -e "ALT='.'" ${sample_id}.annotate.vcf | bcftools filter -o ${sample_id}.annotate.filtered.vcf -O v -e "INFO/DP<${params.min_coverage}" -
 
     vcf-annotator ${sample_id}.annotate.filtered.vcf ${genbank} > ${sample_id}.vcf-annotator.vcf
     """
@@ -99,7 +99,7 @@ process makeConsensus {
         tuple val(sample_id), val(type), path("${sample_id}.draft.consensus.fasta")
     """
     reference_name=`basename ${reference} .fasta`
-    awk -v ref=\${reference_name} '{if (\$2<20) print ref"\t"\$1+1}' ${depth}  > mask.regions
+    awk -v ref=\${reference_name} '{if (\$2<${params.min_coverage}) print ref"\t"\$1+1}' ${depth}  > mask.regions
     bgzip ${sample_id}.annotate.filtered.vcf
     tabix ${sample_id}.annotate.filtered.vcf.gz
     bcftools consensus --mask mask.regions  --mark-del '-' --mark-ins lc --fasta-ref ${reference} -o ${sample_id}.draft.consensus.fasta ${sample_id}.annotate.filtered.vcf.gz

nextflow.config

@@ -17,10 +17,11 @@ params {
     sample = null
     sample_sheet = null
     sanitize_fastq = false
-    wfversion = "v0.0.3"
+    wfversion = "v0.0.4"
     threads = 4
     assembly = true
     medaka_options = null
+    min_coverage = 20
     aws_image_prefix = null
     aws_queue = null
     report_name = "report"

nextflow_schema.json

@@ -1,9 +1,9 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema",
     "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
-    "title": "epi2me-labs/wf-template",
-    "description": "Nextflow workflow template repository.",
-    "url": "https://github.com/epi2me-labs/wf-template",
+    "title": "epi2me-labs/wf-mpx",
+    "description": "A basic workflow for Monkeypox analysis.",
+    "url": "https://github.com/epi2me-labs/wf-mpx",
     "type": "object",
     "definitions": {
         "basic_input_output_options": {
@@ -15,7 +15,7 @@
                 "out_dir": {
                     "type": "string",
                     "default": "output",
-                    "format": "path",
+                    "format": "directory-path",
                     "description": "Directory for output of all user-facing files."
                 },
                 "fastq": {
@@ -42,6 +42,11 @@
                     "type": "string",
                     "description": "Pass through options to medaka."
                 },
+                "min_coverage": {
+                    "type": "number",
+                    "description": "Coverage threshold for masking in consensus step.",
+                    "default": 20
+                },
                 "reference": {
                     "type": "string",
                     "description": "The reference genome to use for mapping.",
@@ -129,7 +134,7 @@
         },
         "wfversion": {
             "type": "string",
-            "default": "v0.0.3",
+            "default": "v0.0.4",
             "hidden": true
         },
         "monochrome_logs": {