Remove obsolete scripts - backup runfolder now in automated_scripts, …

…findfastqs.sh not needed

.gitignore

@@ -1,4 +1,2 @@
 *.pyc
 wscleaner/wscleaner/config.json
-wscleaner/test/test_dir*.txt
-wscleaner/test/data

README.md

@@ -2,49 +2,6 @@
 
 Scripts to manage data on the NGS workstation
 
----
-
-## backup_runfolder.py
-
-Uploads an Illumina runfolder to DNANexus.
-
-### Usage
-
-```bash
-backup_runfolder.py [-h] -i RUNFOLDER [-a AUTH_TOKEN] [--ignore IGNORE] [-p PROJECT] [--logpath LOGPATH]
-```
-
-### What are the dependencies for this script?
-
-This tool requires the DNAnexus utilities `ua` (upload agent) and `dx` (DNAnexus toolkit) to be available in the system PATH. Python3 is required, and this tool uses packages from the standard library.
-
-### How does this tool work?
-
-* The script parses the input parameters, asserting that the given runfolder exists.
-* If the `-p` option is given, the script attempts to find a matching DNAnexus project. Otherwise, it looks for a single project matching the runfolder name. If more or less than 1 project matches, the script logs an error and exits.
-* The runfolder is traversed and a list of files in each folder is obtained. If any comma-separated strings passed to the `--ignore` argument are present within the filepath, or filename the file is excluded.
-
-* The DNAnexus `ua` utility is used to upload files in batches of 100 at a time. The number of upload tries is set to 100 with the `--tries` flag.
-* Orthogonal tests are performed to:
-    * A count of files that should be uploaded (using the ignore terms if provided)
-    * A count of files in the DNA Nexus project
-    * (If relevant) A count of files in the DNA Nexus project containing a pattern to be ignored. NB this may not be accurate if the ignore term is found in the result of dx find data (eg present in project name)
-* Logs from this and the script are written to a logfile, named "runfolder_backup_runfolder.log". A destination for this file can be passed to the `--logpath` flag.
-
----
-
-## findfastqs.sh
-
-Report the number of gzipped fastq files in an Illumina runfolder.
-
-### Usage
-
-```bash
-$ findfastqs.sh RUNFOLDER
->>> RUNFOLDER has 156 demultiplexed fastq files with 2 undetermined. Total: 158
-```
-
----
 
 ## Workstation Cleaner (wscleaner)