upgrade clair3 version, make c3 variants less stringent

phac-nml · Nov 27, 2024 · d3c94eb · d3c94eb
1 parent 0ff60b6
commit d3c94eb
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Showing 6 changed files with 17 additions and 13 deletions.
diff --git a/bin/cs_vcf_filter.py b/bin/cs_vcf_filter.py
@@ -72,8 +72,12 @@ def check_filter(self, v):
         # These seem to not be being pulled out though so check if the qual is none to fail them
         if qual == None:
             return False
-        # Temp filter of qual 15, will need to re-evaluate with more data
-        if qual < 15:
+        # 2 is the default for clair3 so bump slightly up to 3
+        if qual < 3:
+            return False
+
+        # Allele fraction > 0.75 required
+        if len(v.samples) != 1 or v.samples[0].data.AF < 0.75:
             return False
 
         if self.no_frameshifts and not in_frame(v):

diff --git a/modules/local/nanopore_amplicon/env-clair3.yml b/modules/local/nanopore_amplicon/env-clair3.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::clair3=1.0.5
+  - bioconda::clair3=1.0.6
diff --git a/modules/local/nanopore_amplicon/main.nf b/modules/local/nanopore_amplicon/main.nf
@@ -135,8 +135,8 @@ process CLAIR3_VARIANTS {
 
     conda "${moduleDir}/env-clair3.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/clair3:1.0.5--py39hf5e1c6e_0' :
-        'biocontainers/clair3:1.0.5--py39hf5e1c6e_0' }"
+        'https://depot.galaxyproject.org/singularity/clair3:1.0.6--py39hf5e1c6e_0' :
+        'biocontainers/clair3:1.0.6--py39hf5e1c6e_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai), val(pool), path(pool_bed)
@@ -174,8 +174,8 @@ process CLAIR3_VARIANTS {
         --platform='ont' \\
         --model_path="\$MODEL_PATH" \\
         --output="${sampleName}-out" \\
-        --qual=15 \\
-        --min_coverage=10 \\
+        --qual=3 \\
+        --min_coverage=20 \\
         --haploid_precise \\
         --enable_long_indel \\
         --fast_mode \\

diff --git a/modules/local/nanopore_shotgun/env-clair3.yml b/modules/local/nanopore_shotgun/env-clair3.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::clair3=1.0.5
+  - bioconda::clair3=1.0.6
diff --git a/modules/local/nanopore_shotgun/main.nf b/modules/local/nanopore_shotgun/main.nf
@@ -133,8 +133,8 @@ process CLAIR3_VARIANTS {
 
     conda "${moduleDir}/env-clair3.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/clair3:1.0.5--py39hf5e1c6e_0' :
-        'biocontainers/clair3:1.0.5--py39hf5e1c6e_0' }"
+        'https://depot.galaxyproject.org/singularity/clair3:1.0.6--py39hf5e1c6e_0' :
+        'biocontainers/clair3:1.0.6--py39hf5e1c6e_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
@@ -171,8 +171,8 @@ process CLAIR3_VARIANTS {
         --platform='ont' \\
         --model_path="\$MODEL_PATH" \\
         --output="${sampleName}-out" \\
-        --qual=15 \\
-        --min_coverage=10 \\
+        --qual=2 \\
+        --min_coverage=20 \\
         --haploid_precise \\
         --enable_long_indel \\
         --fast_mode \\

diff --git a/nextflow.config b/nextflow.config
@@ -246,7 +246,7 @@ manifest {
     description     = """Assemble and QC viral reads"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.1.0'
+    version         = '1.1.1'
     doi             = ''
     defaultBranch   = 'main'
 }