create migrate rename script

workflow/scripts/migrate_rename.sh

@@ -0,0 +1,70 @@
+#!/bin/bash
+
+# Example
+# bash workflow/scripts/migrate_rename.sh \
+#   ../plague-phylogeography-projects/test/metadata/all/metadata.tsv \
+#   "Ancient" \
+#   results/data/ \
+#   test/data \
+#   test/sym
+
+METADATA=$1
+FILTER=$2
+INDIR=$3
+OUTDIR=$4
+SYMDIR=$5
+
+# Exit if the metadata file was not supplied
+if [[ ! $METADATA ]] || [[ ! $INDIR ]] || [[ ! $OUTDIR ]]; then
+    exit
+fi;
+
+tail -n+2 $METADATA | grep -v "Reference" | grep $FILTER | cut -f 1 | while read sample;
+do
+  in_dir=`ls -d $INDIR**/$sample`;
+  origin=`echo ${in_dir} | rev | cut -d "/" -f 2 | rev`;
+  if [[ $origin != "sra" ]]; then continue; fi
+
+  out_dir="$OUTDIR/$origin/$sample";
+
+  # Create new sample directory and migrate fastq
+  if [[ ! -d $out_dir ]]; then
+    echo "Migrating ${in_dir} to ${out_dir}"
+    mkdir -p $out_dir;
+    cp -r $in_dir/* $out_dir;
+  fi;
+
+  # Make sym link directory
+  if [[ $SYMDIR ]]; then
+    sym_dir="$SYMDIR/Sample_$sample";
+    mkdir -p $sym_dir;
+
+    # Rename to illumina format
+    lane=1;
+    for r1_file in `ls ${out_dir}/*_1.fastq.gz`;
+    do
+    r2_file=`echo $r1_file | sed 's/_1.fastq.gz/_2.fastq.gz/g'`;
+    filename=`basename $r1_file`;
+    run=`echo $filename | cut -d "_" -f 1`;
+    r1_illumina="${sample}_${run}_L00${lane}_R1_001.fastq.gz"
+    r2_illumina=`echo $r1_illumina | sed 's/R1/R2/g'`;
+
+    # Symlink rename to the R1 file
+    if [[ ! -L $sym_dir/$r1_illumina ]]; then
+        echo "Symlinking $r1_file to $sym_dir/$r1_illumina";
+        ln -s $r1_file $sym_dir/$r1_illumina;
+    fi;
+
+    # Symlink rename to the R2 file
+    if [[ -f $r2_file ]]; then
+        if [[ ! -L $sym_dir/$r2_illumina ]]; then
+            echo "Symlinking $r2_file to $sym_dir/$r2_illumina";
+            ln -s $r2_file $sym_dir/$r2_illumina;
+        fi;
+    fi;
+
+    lane=`expr $lane + 1`
+
+    done;
+  fi;
+done;