Added scripts/README.txt

phages/scripts/README.txt

+## Contents of scripts folder
+
+The scripts are numbered in the order they are run.
+If in doubt use the scripts which are executable.
+
+The description of the files is here below
+
+Files:
+
+* 00_create_py_env.sh
+* 01_quality_check.sh*
+* 02_trimm_and_clean.sh*
+* 03_mapping.sh*
+* 04_snpcalling.sh*
+* 05b_convert_protospacer_dico2fasta.py*
+* 06b_blast_protospaces.sh*
+* 07_2_run_vcf_parser_all_files.py
+* 07_2_test.py
+* 07_run_vcf_parser_all_files.py*
+
+* procedure.sh
+* README.txt
+* requirements_py-env.txt
+
+* vcf_parser3.py
+
+Folders:
+
+
+Files to ignore for a while ^_^
+
+### 
\ No newline at end of file

phages/scripts/procedure.sh

+/bin/bash