bumps version

docker/Dockerfile

@@ -4,6 +4,6 @@ RUN apt-get update && apt-get install -y procps
 RUN conda create -n env -c conda-forge python=3.7 numpy>=1.16.2 jinja2>=2.10.1
 RUN echo "source activate env" > ~/.bashrc
 ENV PATH /opt/conda/envs/env/bin:$PATH
-RUN /opt/conda/envs/env/bin/pip install --no-cache-dir covviz==1.3.2
+RUN /opt/conda/envs/env/bin/pip install --no-cache-dir covviz==1.3.3
 RUN wget -qO /usr/bin/goleft https://github.com/brentp/goleft/releases/download/v0.2.3/goleft_linux64
 RUN chmod +x /usr/bin/goleft

main.nf

@@ -150,9 +150,10 @@ process build_report {
 
     script:
     gff_opt = params.gff ? "--gff ${gff}" : ""
+    gff_attr = params.gffattr ? "--gff-attr ${gffattr}" : ""
     """
     covviz --min-samples ${params.minsamples} --sex-chroms ${params.sexchroms} --exclude '${params.exclude}' \
         --z-threshold ${params.zthreshold} --distance-threshold ${params.distancethreshold} \
-        --slop ${params.slop} --ped ${ped} ${gff_opt} --skip-norm ${bed}
+        --slop ${params.slop} --ped ${ped} ${gff_opt} ${gff_attr} --skip-norm ${bed}
     """
 }

nextflow.config

@@ -19,13 +19,14 @@ params {
     ped = false
     // column of sample IDs in your custom ped file
     samplecol = 'sample_id'
+    gffattr = false
 }
 
 process {
     errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'terminate' }
     maxRetries = 3
     maxErrors = '-1'
-    container = 'brwnj/covviz:v1.3.2'
+    container = 'brwnj/covviz:v1.3.3'
     withLabel: 'indexcov' {
         memory = { 8.GB * task.attempt }
         cache = 'deep'
@@ -62,7 +63,7 @@ manifest {
     name = 'brwnj/covviz'
     author = 'Joe Brown'
     description = "find large, coverage-based variations on chromosomes"
-    version = '1.3.2'
+    version = '1.3.3'
     nextflowVersion = '>=0.32.0'
     homePage = 'https://github.com/brwnj/covviz'
     mainScript = 'main.nf'

setup.py

@@ -18,7 +18,7 @@
 EMAIL = "[email protected]"
 AUTHOR = "Joe Brown"
 REQUIRES_PYTHON = ">=3.6.0"
-VERSION = "1.3.2"
+VERSION = "1.3.3"
 
 # What packages are required for this module to be executed?
 REQUIRED = ["Jinja2", "numpy", "pandas"]