Merge pull request #2 from moka-guys/development

Add script to report number of fastqs in runfolder

README.md

@@ -1,6 +1,8 @@
 # Workstation Housekeeping
 Scripts to manage data on the NGS workstation
 
+---
+
 ## backup_runfolder.py v1.0
 Uploads an Illumina runfolder to DNANexus.
 
@@ -19,3 +21,16 @@ This tool requires the DNAnexus utilities `ua` (upload agent) and `dx` (DNAnexus
 * From a list of files in the runfolder, files matching any of the comma-separated strings passed to `--ignore` are removed. The default is '/L00', which ignores BCL files in directories with this prefix. To upload all files in a runfolder, pass the argument `--ignore ""`.
 * Finally, each remaining file is passed to the DNAnexus `ua` utility. This will attempt an upload if the files are not found in the expected location in the DNAnexus project. The number of upload tries is set to 100 with the `--tries` flag.
 * Logs from this and the script are written to STDERR and a logfile, named after the runfolder. 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
+```
+$ findfastqs.sh RUNFOLDER
+>>> RUNFOLDER has 156 demultiplexed fastq files with 2 undetermined. Total: 158
+```
+
+---

findfastqs.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+# Commands to help with runfolder managemenet (Nana)
+findfastqs(){ 
+    input_directory=$1
+    # Find all fastqs in the input directory.
+    # Grep -v filters out undetermined fastqs from this list, which are not typically uploaded to DNAnexus
+    numfqs=$(find $input_directory -iname "*.fastq.gz" | grep -v "Undetermined" |  wc -l);
+    # Count the number of undetermined fastqs in input directory
+    undetermined=$(find $1 -iname "Undetermined*.fastq.gz" | wc -l);
+    total=$((numfqs + undetermined))
+    echo "$input_directory has $numfqs demultiplexed fastq files with $undetermined undetermined. Total: $total";
+    }
+
+findfastqs $1