Version 1.1.1

• Added a script to calculate mean rho and rho/theta (get_mean_rho_rps_by_tps.py)

Version 1.1.0

• Switched to semantic versioning.
• collect_results.py output is now more informative.
• align_reads.nf can now be run using a list of input files in the form of a csv. This version is called aligned_reads_input_list.nf
• Ground work for calculating substitution probability, which can be used to derive r/m.
• Updated dependencies (docker file and conda environment.yaml).
• Outlier SNP entries (based on top n% of depth) can now be removed in rho_est and theta_est and related input_list nextflow files.
• align_all_est.nf and all_esf.nf updated to reflected latest changes.

Version 1.0.8

• Re-enabled the reporting of pileup_mean_depth and corresponding theta

Version 1.0.7

• Final aligned, filtered bams from aligned_reads.nf are now saved in Align_Reads_Output folder.

Version 1.0.6

• align_all_est.nf and all_est.nf updated to work with vcf file filtering steps in rho_est.nf and theta_est.nf

Version 1.0.5

• Important bug fix for counting variant sites in theta_est.py

• Added vcf file filtering steps to rho_est and theta_est scripts

• rho_est and theta_est scripts can now be run using list of input files in the form of a csv. rho_est_input_list.nf and theta_est_input_list.nf should be used respectively

Version 1.0.4

• Optimisations for bulk runs.
• Theta estimate and results plot code separated. Plotting can be disabled if necessary.
• rho_est.nf now reports additional parameters.
• Optimisation and clean up of theta estimate scripts.

Version 1.0.3

• Added align_reads.nf. This pipeline can be used to align reads to references.
• Added combined_align_est.nf. This pipeline can be used to align reads and run theta_est.nf and rho_est.nf on them in one go. It can process multiple fastqs and fa simultaneously and process them in parallel.
• Added combined_est.nf. Similar to above pipeline but it instead uses bams and fa as input. It can process multiple bas and fa simultaneously and process them in parallel.
• Added collect_results.py. Used to collect and tabulate results generated by combined_align_est.nf pipeline.
• Various other minor improvements to pipelines and scripts.

Version 1.0.2

• Support added for bams aligned to multi-entry reference in theta_est.nf.
• Output files for all nextflow scripts are now better organised.
• Subsample bam process now consumes less memory in rho_est.nf.

Version 1.0.0

First release 🎉