Created delly container

AndersenLab · Sep 20, 2024 · 8abba5e · 8abba5e
1 parent b0ab7c4
commit 8abba5e
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Showing 3 changed files with 14 additions and 3 deletions.
diff --git a/env/Dockerfile b/env/Dockerfile
@@ -0,0 +1,10 @@
+FROM mambaorg/micromamba:1.5.0
+
+RUN micromamba install -n base bcftools delly -c bioconda -y \
+	&& micromamba clean -a -y
+
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+
+USER $MAMBA_USER
+ENV PATH="/opt/conda/bin:$PATH"
+ENTRYPOINT source /usr/local/bin/_entrypoint.sh
diff --git a/main.nf b/main.nf
@@ -170,8 +170,9 @@ process delly_call_indel {
     """
     echo -e "${control}\tcontrol\n${sample}\ttumor" > samples.tsv
     delly call -q 20 -g ${genome} ${bam} ${ref_bam} > sample.vcf
-    bcftools index sample.vcf
-    delly filter -f somatic -o ${sample}.bcf -a 0.75 -p -m 50 -n 1000 -s samples.tsv sample.vcf
+    bcftools sort sample.vcf -Oz -o sample.vcf.gz
+    bcftools index -t sample.vcf.gz
+    delly filter -f somatic -o ${sample}.bcf -a 0.75 -p -m 50 -n 1000 -s samples.tsv sample.vcf.gz
     """
 
 }

diff --git a/nextflow.config b/nextflow.config
@@ -38,5 +38,5 @@ timeline {
 }
 
 process {
-    container = "dellytools/delly:v1.2.6"
+    container = "andersenlab/delly:v1.2.8"
 }