externalized container download

Snakefile

@@ -31,30 +31,11 @@ rule clean:
 
 # download the required singularity container from zenodo.org
 rule download_container:
-    output:
-        "container_unchecked.sif"
-    shell:
-        """
-        wget https://zenodo.org/record/{config[zenodo_record_id]}/files/container.sif -O container_unchecked.sif
-        """
-
-# check md5
-rule check_container:
-    input:
-        "container_unchecked.sif"
     output:
         "container.sif"
-    singularity:
-        "container_unchecked.sif"
     shell:
         """
-        set -e
-        checksum=($(md5sum container_unchecked.sif))
-        if [ $checksum != {config[container_mdf5]} ]; then
-            echo md5 mismatch for container, download corrupted!
-            exit 1
-        fi
-        mv container_unchecked.sif container.sif
+        bash scripts/download_container.sh
         """
 
 # extract dosages in custom PrediXcan format from vcf file

config.yml

@@ -23,6 +23,3 @@ brain_regions:
     - 'Putamen_basal_ganglia'
     - 'Spinal_cord_cervical_c-1'
     - 'Substantia_nigra'
-
-zenodo_record_id: '3376504'
-container_mdf5: '1f5aada82c1aeb8e00b0328421ed009b'

scripts/download_container.sh

+wget https://zenodo.org/record/3376504/files/container.sif -O container.sif