diff --git a/docker/Dockerfile b/docker/Dockerfile index c03777e..fe291d2 100644 --- a/docker/Dockerfile +++ b/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 diff --git a/main.nf b/main.nf index 16e6da9..4bfe2f9 100644 --- a/main.nf +++ b/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} """ } diff --git a/nextflow.config b/nextflow.config index 346a4e2..156d90a 100644 --- a/nextflow.config +++ b/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' diff --git a/setup.py b/setup.py index 9b0c7a1..a0583ba 100644 --- a/setup.py +++ b/setup.py @@ -18,7 +18,7 @@ EMAIL = "brwnjm@gmail.com" 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"]