Merge branch 'main' of https://github.com/CCBR/LOGAN

CHANGELOG.md

@@ -3,4 +3,5 @@
 - Changed over to Nextflow CCBR template and pip packaging
     - Processes moved to `modules/local` directory
     - Workflows under the `subworkflows/local` directory
-    - Processes fall under low/med/high, but adding a somaticvariant caller process
+    - Processes fall under low/med/high, but added a somaticvariant caller process
+    - Built AnnotSV/ClassifyCNV container (#40)

conf/containers.config

@@ -1,10 +1,11 @@
 // containers accessed in process definitions with $params.containers.NAME
 params {
     containers {
-        base = 'nciccbr/ccbr_ubuntu_base_20.04:v6.1'
+        base = 'docker://nciccbr/ccbr_ubuntu_base_20.04:v6.1'
         logan = 'docker://dnousome/ccbr_logan_base:v0.3.4'
         vcf2maf = 'docker://dnousome/ccbr_vcf2maf:v102.0.0'
         lofreq = 'docker://dnousome/ccbr_lofreq:v0.0.1'
         octopus = 'docker://dancooke/octopus:latest'
+        annotcnvsv = 'docker://dnousome/ccbr_annotate_cnvsv:latest:v0.0.1'
     }
 }

docker/annotate_cnvsv/Dockerfile

@@ -16,17 +16,26 @@ WORKDIR /opt2
 
 ###Create AnnotSV 
 RUN wget https://github.com/lgmgeo/AnnotSV/archive/refs/tags/v3.3.6.tar.gz \
-    && tar -xvjf /opt2/v3.3.6.tar.gz \
+    && tar -xvzf /opt2/v3.3.6.tar.gz \
     && rm /opt2/v3.3.6.tar.gz
 ENV PATH="/opt2/AnnotSV-3.3.6/bin:$PATH"
 
 ##ClassifyCNV
 ##Update the resources for ClassifyCNV
 RUN wget https://github.com/Genotek/ClassifyCNV/archive/refs/tags/v1.1.1.tar.gz \
-    && tar -xvjf /opt2/v1.1.1.tar.gz \
-    && rm /opt2/v1.1.1.tar.gz
-ENV PATH="/opt2/ClassifyCNV-1.1.1:$PATH"
-RUN update_clingen.sh
+    && tar -xvzf /opt2/v1.1.1.tar.gz \
+    && rm /opt2/v1.1.1.tar.gz 
+    #&& chmod a+rx /opt2/ClassifyCNV-1.1.1/update_clingen.sh 
+ENV PATH="/opt2/ClassifyCNV-1.1.1/:$PATH"
+#RUN update_clingen.sh
+
+##Survivor 
+RUN wget https://github.com/fritzsedlazeck/SURVIVOR/archive/refs/tags/v1.0.6.tar.gz \
+    && tar -xvzf /opt2/v1.0.6.tar.gz \
+    && rm /opt2/v1.0.6.tar.gz \
+    && cd /opt2/SURVIVOR-1.0.6/Debug \
+    && make
+ENV PATH="/opt2/SURVIVOR-1.0.6/:$PATH"
 
 
 COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}

docker/annotate_cnvsv/build.sh

@@ -0,0 +1,10 @@
+##BUILD cnv/sv
+docker build --platform linux/amd64 --tag ccbr_annotate_cnvsv:v0.0.1 -f Dockerfile . 
+
+docker tag ccbr_annotate_cnvsv:v0.0.1 dnousome/ccbr_annotate_cnvsv:v0.0.1
+docker tag ccbr_annotate_cnvsv:v0.0.1 dnousome/ccbr_annotate_cnvsv
+
+docker push dnousome/ccbr_annotate_cnvsv:v0.0.1
+docker push dnousome/ccbr_annotate_cnvsv:latest
+
+

modules/local/structural_variant.nf

@@ -103,8 +103,8 @@ process manta_somatic {
 process annotsv_tn {
      //AnnotSV for Manta/Svaba works with either vcf.gz or .vcf files
      //Requires bedtools,bcftools
-    module = ['annotsv/3.3.1']
-
+    container = "${params.containers.annotcnvsv}"
+    process
     input:
         tuple val(tumorname), path(somaticvcf), val(sv)
 
@@ -245,7 +245,7 @@ process gunzip {
 
 
 process survivor_sv {
-    module = ['survivor']
+    container = "${params.containers.annotcnvsv}"
 
     input:
         tuple val(tumorname),
@@ -277,7 +277,7 @@ process survivor_sv {
 process annotsv_tonly {
      //AnnotSV for Manta/Svaba works with either vcf.gz or .vcf files
      //Requires bedtools,bcftools
-    module = ['annotsv/3.3.1']
+    container = "${params.containers.annotcnvsv}"
 
     input:
         tuple val(tumorname), path(somaticvcf), val(sv)