added function to common-py to check availability of the tools I am going to run
major changes in the pipeline
major changes in the pipeline
bug fix in run_MP_analys.py causing failure in report generation without alignment
run_QC_analysis and plot_kmer_cov added for automated analysis
working version -- tested up to QC
bug fix
added option --afterQC to scilifelab_util run_assemblies so that assemblies can be run using QCcontrol output
clean up code in run_assemblies
added sciLifeLab_utils/run_validation.py
bug fix in assemble.py and implementation of run_validation to automate validation of assemblies
bug finxing on evalaute and progree on report generation for assembly evaluation
added automatic project name retriaval when starting de novo from QC folder
automated de novo assembly completed
updated config file for amanita
tested run_valiadation, fixed a bug in dir creation
Assembly report implemented
working version
fixed bug in alignment report: now all analysis are run in the correct folder
MP.py deleted