IARCbioinfo/needlestack: v1.1

Full Changelog

Implemented enhancements:

• add needlestack logo in log.info #182
• add INFO field containing allelic frequency #174
• Add an option to only plot somatic mutations #149
• Make the main 3 processes pipe-friendly to avoid intermediate outputs #147
• Re-write pileup2baseindel.pl in C++ #146
• Flag possible cross-sample contamination of normal DNA in tumor samples #138
• Put ./. genotype when there is no power to identify a variant #137
• Implement Tumor-Normal pair somatic variant calling #133
• Add alignment plot in the PDF #73
• Make a script that would run needlestack without nextflow #72

Fixed bugs:

• max_dp default value in readme is wrong #176
• --help should exit 0 #161
• Manage bed specification for both bed and region #157
• Using renamed symlinks as input BAM files doesn't work with --use_file_name option #152

Closed issues:

• How to identify each sample? #166
• Github readme != Docker readme #159