v0.2

Full Changelog

New features

• Added --no_indel option (#56)
• Added --out_folder option
• The software is now called needlestack (#31)
• Added program usage when launched with --help (#40)
• Added information about the pipeline in the log (#41)
• We now verify the user inputs are correct (#42)

Improvements

• Added a zoomed regression plot (#21)
• Added contigs in VCF header (#25 and #34)
• Moved to IARCbioinfo organisation repo (#22)
• Corrected typos in readme, help and log (#53)

Changes

• Option all_sites is now a flag called all_SNVs and no longer needs to be set to TRUE or FALSE (#33)
• Option do_plots is now a flag called --no_plots and no longer needs to be set to TRUE or FALSE
• Option sample_namesis now a flag called --use_file_name and no longer needs to be set to BAM or FILE

Bug fixes

• QVAL was wrongly called GQ for indels (#36)
• The pipeline no longer crashes if PDF files are not copied correctly (#49)

Testing/deployment bug fixes (don't affect users)

• CircleCI deploy.sh now triggers correctly Docker Hub (#26)
• Dockerfile now adds scripts from the correct branch (#27)