added missing script

Author: olabiyi

Amplicon/Illumina/Workflow_Documentation/NF_AmpIllumina/workflow_code/bin/clean-paths.sh

@@ -0,0 +1,24 @@
+#!/usr/bin/env bash
+set -e
+
+# only built for use on N288 cluster
+
+# example usage: bash clean-paths.sh <input-file> <workflow-dir>
+
+# making sure by chance we are not overwriting a wanted file called 't'
+
+if [ -s t ]; then
+    printf "\n    This simple program temporarily writes to a file called 't'\n"
+    printf "    Since that exists already here, we are not going to continue.\n\n"
+    exit
+fi
+
+
+ROOT_DIR=$(echo $2 | awk '{N=split($0,a,"/"); for(i=0; i < N-1; i++) printf "%s/", a[i]}' | sed 's|//|/|')
+
+ 
+sed -E 's|.*/GLDS_Datasets/(.+)|\1|g'  ${1} \
+    | sed -E 's|.+/miniconda.+/envs/[^/]*/||g' \
+    | sed -E 's|/[^ ]*/GLDS-|GLDS-|g' \
+    | sed -E 's|/[a-z]{6}/[^ ]*|<path-removed-for-security-purposes>|g' \
+    | sed -E "s|${ROOT_DIR}||g" > t && mv t ${1}