adapt config files

genepi · Mar 6, 2024 · d3191d2 · d3191d2
1 parent 845a98f
commit d3191d2
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Showing 4 changed files with 27 additions and 10 deletions.
diff --git a/config/custom.config b/config/custom.config
@@ -21,13 +21,31 @@ params {
 
 	// adaptable parameters
 
-	output_format 				= "fastq"	
-	filter_strategy_clusters 	= "quality"
+    //READ FILTERING
+    min_read_length                       = 0
+    min_qscore                            = 10
 
-	call_variants 				= true
-	variant_caller 				= "freebayes"
+    // SUBSAMPLING
+    subsampling                           = false
+    subsampling_seed                      = 11
+    subsampling_readnumber                = 100000
+
+    // VARIANT_CALLING
+    call_variants                         = false    
+    variant_caller                        = "freebayes"
 
-	medaka_model 				= "r1041_e82_400bps_hac_g615"
+    // ADVANCED
+    min_reads_per_barcode                 = 1000
+    umi_errors                            = 2
+    max_dist_umi                          = 2
+    min_reads_per_cluster                 = 20
+    max_reads_per_cluster                 = 60
+	min_consensus_quality                 = 40
+	masking_strategy                      = "softmask"
+    filter_strategy_clusters              = "quality"
+    min_overlap                           = 0.95
+    balance_strands                       = true
+    medaka_model                          = "r1041_e82_400bps_hac_g615"
 }
 
 // NEXTFLOW REPORTING

diff --git a/env/Dockerfile b/env/Dockerfile
@@ -18,8 +18,6 @@ RUN conda update -y conda && \
     conda clean --all
 
 WORKDIR "/opt"
-RUN wget https://github.com/seppinho/mutserve/releases/download/v2.0.0-rc15/mutserve.zip && \
-    unzip mutserve.zip
-ENV PATH="/opt/mutserve:${PATH}"
+RUN wget https://github.com/seppinho/mutserve/releases/download/v2.0.0-rc13.lpa/mutserve_LPA_adapted.jar
 
 
diff --git a/lib/processes/variant_calling/mutserve.nf b/lib/processes/variant_calling/mutserve.nf
@@ -14,7 +14,7 @@ process MUTSERVE {
 
     script:
     """
-      mutserve call  \
+      java -jar /opt/mutserve_LPA_adapted.jar call  \
       --output ${type}.vcf \
       --write-raw \
       --reference ${reference} \

diff --git a/nextflow.config b/nextflow.config
@@ -39,7 +39,8 @@ params {
 
     // ADVANCED
     min_reads_per_barcode                 = 1000
-    umi_errors                            = 3
+    umi_errors                            = 2
+    max_dist_umi                          = 2
     min_reads_per_cluster                 = 20
     max_reads_per_cluster                 = 60
 	min_consensus_quality                 = 40