Merge pull request #197 from nf-cmgg/callable-regions

Exclude low coverage regions from variant calling
nf-cmgg · Sep 23, 2024 · 906cc8a · 906cc8a
2 parents 7fc0208 + df9ecc3
commit 906cc8a
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,11 +5,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v1.8.0dev
 
+## New features
+
+1. Added `watchpath` functionality to the pipeline. Add the `watch:` prefix to a file basename in the samplesheet and the pipeline will automatically wait for the file to be created in the `--watchdir` directory (the lookup happens recursively)
+
 ## Changes
 
 1. Bumped the minimal support nextflow version to `24.04.0`
 2. Bumped all modules to the newest versions
 3. The pipeline now also outputs `csi` indices
+4. Low coverage regions (regions with less than 5 reads) are no longer considered for variant calling
 
 ## Refactors
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -101,7 +101,7 @@ process {
 
     withName: "^.*CRAM_PREPARE_SAMTOOLS_BEDTOOLS:FILTER_BEDS\$" {
         ext.prefix = { "${meta.id}.filter"}
-        ext.args = "-vE \"NO_COVERAGE${params.keep_alt_contigs ? "" : "|alt|random|decoy|Un"}\""
+        ext.args = "-vE \"LOW_COVERAGE|NO_COVERAGE${params.keep_alt_contigs ? "" : "|alt|random|decoy|Un"}\""
         ext.args2 = "-d 150"
         publishDir  = [
             overwrite: true,

diff --git a/tests/subworkflows/local/cram_prepare_samtools_bedtools/main.nf.test.snap b/tests/subworkflows/local/cram_prepare_samtools_bedtools/main.nf.test.snap
@@ -60,7 +60,7 @@
                         "family_samples": "NA24143",
                         "duplicate_count": 1
                     },
-                    "NA24143.filter.bed:md5,9fc0cc2e4403678f18bc8b18646abd66"
+                    "NA24143.filter.bed:md5,85a5568a6976ed455caa712991b30ac2"
                 ]
             ],
             [
@@ -71,7 +71,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-06T14:32:19.290286542"
+        "timestamp": "2024-09-23T14:56:11.141634788"
     },
     "default - WES": {
         "content": [