Release v2.0.0 · ShujiaHuang/ilus

[release v2.0.0] - 2023-12-05

Enable raw fastq data filtering by using SOAPnuke.
Enable to create pipeline for WES or other kinds of capture sequencing data.
Add Sentieon mudules. Enable to create WGS/capseq analysis pipeline by using Sentieon
Rewrite the format of the configuration file.

Rewrite the format of configuration file, isolated the resources option from gatk section as a new section to facilitate shared use by Sentieon and GATK.
Added sentieon module and constructed WGS/WES analysis workflows based on sentieon.
Removed the --max-gaussians option from the vqsr_options in the configuration file and replaced it with separate settings for SNP (vqsr_snp_max_gaussians) and Indel (vqsr_indel_max_gaussians).
Moved the calculation of alignment statistics and data contamination section out from BQSR section to bwamem section. Changed the suffix from .recal.table to .BQSR.recal.table.
Added the --dbsnp parameter for genotypeGVCFs to annotate known sites.
Added fastq data filtering module based on SOAPnuke.
Encapsulated the gatk module as a GATK class.
Added the --interval parameter for WGS as the variant-calling-interval.
Added a parameter to the workflow to automatically remove unnecessary sub-vcfs for WGS/WES.
Rewrote the genotype-joint-calling module, allowing the first column of the input parameter gvcf.list to contain arbitrary interval information, including chromosome ID, chr:start-end, or a .bed file.