Add description, URL and MD5 checksum

run_default_VIPERA.sh

@@ -1,35 +1,51 @@
 #!/usr/bin/env bash
 
+# run_default_VIPERA.sh
+# 
+# This script is used to download and analyze intra-patient SARS-CoV-2 data
+# using VIPERA, a tool for the automated detection of serially sampled infections
+# and the identification of evolutionary patterns within the same viral infection.
+# 
+# Access the full data record via DOI: 10.20350/digitalCSIC/15648
+
 set -e
 
 logthis () {
     echo $(date) "|" $@
 }
 
 NCPU=1
-ZENODO_URL=""
+DATA_URL="https://digital.csic.es/bitstream/10261/337461/1/data.zip"
+MD5_SUM="07447bdae794a6c82adbf79423b79c30"
 
 tmpdir=$(mktemp -d)
 
-logthis "Downloading compressed data"
-curl -O ${tmpdir}/zenodo.zip ${ZENODO_URL}
+logthis "Downloading compressed data from '$DATA_URL'"
+curl -o ${tmpdir}/data.zip ${DATA_URL}
+
+logthis "Validating file"
+md5_sum_dwld="$(md5sum ${tmpdir}/data.zip | cut -d' ' -f1)"
+if [ "$md5_sum_dwld" != "$MD5_SUM" ]; then
+    logthis "ERROR: MD5 checksum does not match"
+    exit 1
+fi
 
-logthis "Creating directories"
+logthis "Creating data directories"
 mkdir -p data/bam data/fasta
 
 logthis "Decompressing"
-unzip -d ${tmpdir} ${tmpdir}/zenodo.zip
-rm ${tmpdir}/zenodo.zip
+unzip -d ${tmpdir} ${tmpdir}/data.zip
+rm ${tmpdir}/data.zip
 
 logthis "Organizing files"
-mv ${tmpdir}/*.bam data/bam
-mv ${tmpdir}/*.fa data/fasta
-mv ${tmpdir}/*.csv data
+mv ${tmpdir}/**/*.bam data/bam
+mv ${tmpdir}/**/*.fa data/fasta
+mv ${tmpdir}/**/*.csv data
 
 logthis "Running VIPERA"
 snakemake --use-conda -c ${NCPU}
 
 logthis "Cleaning up"
-rmdir ${tmpdir}
+rm -r ${tmpdir}
 
 logthis "Done!"