rusty_samplesheet

Very simple Illumina SampleSheet validation

Help, my SampleSheet is a bit rusty, and by that I mean crap.

A windows/linux program written in Rust

• parse an Illumina SampleSheet.csv in the directory
• complain about format problems in a (hopefully) biologist friendly fashion
• link to examples showing properly formatted SampleSheets (internal MHH network only at present)

Installation

Just clone or download the repository. The binary executables (eg exe for Windows) are directly in the repository.

git clone https://github.com/colindaven/rusty_samplesheet

We anticipate most users will run the tool under Windows.

Run it!

Windows:

1. Call your SampleSheet SampleSheet.csv (Windows, set this in the validate_samplesheet.bat if you like).
2. Double click the validate_samplesheet.bat
3. Results will be printed in output.txt, open this with Wordpad or Notepad++ or another competent text editor (NOT notepad!).

Linux:

chmod a+x validate_samplesheet
./validate_samplesheet -f your_SampleSheet.csv

Checks performed

• No "." in sample IDs and names, allowed on lines containing Date
• German Umlaut äüö etc disallowed
• Incorrect headers, eg Sample_ID present more than once
• Incorrect adapters lines with more than three """ (should be something like "Index Adapters,""TruSeq DNA CD Indexes (96 Indexes)""" )
• Semicolons ; used instead of commas , as delimiters
• [Data] section - duplicate Sample_Name strings, Sample_ID strings, duplicate indices.
• Should check for " in lines, but this is difficult since parsing fails.

What output is given if everything is ok ? Very little, i.e. no specific lines are mentioned.

INFO: Welcome to Rusty Samplesheet version 0.27 by Colin Davenport
Usage: Call your SampleSheet SampleSheet.csv in the same directory. Double click the .bat file to start.
Remember to use Wordpad or Notepad++ to read the output.txt file
If this file appears empty, the tools didn't find any errors - good job!
Checking data section of SampleSheet. IDs, Names, Indices must be unique!

What output is produced if faulty lines are present ?

One line shows a single duplicated text string is present, eg this index is duplicated by mistake.

The second error shows an illegal semicolon was found

INFO: Welcome to Rusty Samplesheet version 0.27 by Colin Davenport
Usage: Call your SampleSheet SampleSheet.csv in the same directory. Double click the .bat file to start.
Remember to use Wordpad or Notepad++ to read the output.txt file
If this file appears empty, the tools didn't find any errors - good job!
Checking data section of SampleSheet. IDs, Names, Indices must be unique!
Duplicate string found!: CGTATTCG 

ERROR: Semicolon ; illegal found, Only commas ',' should be used! Exiting. Field: ;
Line containing error: "leer 4leer41D01S709TTTACGGTCTS575GCAATGGA;"

Compile for Windows (done on hpc03 internally)

# first setup Ubuntu
sudo apt update && sudo apt install mingw-w64

# now setup rust
rustup target add x86_64-pc-windows-gnu
rustup target add i686-pc-windows-gnu
rustup toolchain install stable-x86_64-pc-windows-gnu
rustup toolchain install i686-pc-windows-gnu

# now add this to rust cargo.toml in your project directory:

[target.x86_64-pc-windows-gnu]
linker = "/usr/bin/x86_64-w64-mingw32-gcc"

[target.i686-pc-windows-gnu]
linker = "/usr/bin/i686-w64-mingw32-gcc"
rustflags = "-C panic=abort"

# build 
# Scripted in copy_built_release.sh for Linux and Windows
bash copy_built_release.sh
#cargo rustc --target=i686-pc-windows-gnu --release -- -C link-args=-mwindows
#cargo rustc --target=stable-i686-pc-windows-gnu --release -- -C link-args=-mwindows
#You can build your crate easily with
cargo build --target x86_64-pc-windows-gnu

Compile for Linux

cargo build --target release