Minor cosmetic fixes

apps/generate_bs_indices.sh

@@ -44,7 +44,7 @@ N_proc=`expr $( grep -c processor /proc/cpuinfo ) / 2`
 
 # 1) Obtain GRCh38 human genome from ENCODE
 echo "1/8 - Downloading GRCh38 reference..."
-wget -o wget.log --show-progress -O ${grch38_fasta}.gz ${GRCH38_url}
+wget --show-progress -O ${grch38_fasta}.gz ${GRCH38_url}
 echo "      Decompressing GRCh38 reference..."
 gunzip -f ${grch38_fasta}.gz
 
@@ -52,7 +52,7 @@ gunzip -f ${grch38_fasta}.gz
 
 # 2) Obtain Lambda genome
 echo "2/8 - Downloading Lambda genome..."
-wget -a wget.log --show-progress -O ${lambda_fasta}.gz ${LAMBDA_url}
+wget --show-progress -O ${lambda_fasta}.gz ${LAMBDA_url}
 echo "      Decompressing Lambda reference..."
 gunzip -f ${lambda_fasta}.gz
 

wgbs-pipeline.sh

@@ -40,8 +40,8 @@ set -e
 
 # Ensure reference files/indices are there, download and index otherwise
 if [[ ! -s ${b38_ref}/Bisulfite_Genome/GA_conversion/genome_mfa.GA_conversion.fa ]]; then
-    echo "Reference files not found. Downloading and indexing..."
-    bash ${generate_bs_indices} ${ref_dir}
+    echo "Reference files not found. Downloading and indexing... (THIS SHOULD TAKE A WHILE)"
+    bash ${generate_bs_indices} ${ref_dir} > ${ref_dir}.stdout.log 2> ${ref_dir}.stderr.log
 fi