diff --git a/README.md b/README.md index af42fd8..938427d 100644 --- a/README.md +++ b/README.md @@ -49,6 +49,8 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool > **Clean read data undergo assembly and influenza typing and subtyping. Based on the subtype information, Nextclade variables are gathered.** * Assembly of influenza gene segments with (`IRMA`) using the built-in FLU module. Also, influenza typing and H/N subtype classifications are made. +* Calculate the reference length, sequence length, and percent_coverage for segments assembled by IRMA with (`IRMA_SEGMENT_COVERAGE`) +* Calculate the number of mapped reads and mean depth for segments assembled by IRMA with (`SAMTOOLS_MAPPED_READS`) * QC of consensus assembly (`IRMA_Consensus_QC`). * Generate IRMA consensus QC report (`IRMA_Consensus_QC_Reportsheet`) * Annotation of IRMA consensus sequences with (`VADR`) @@ -69,6 +71,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool > **Compiles report sheets from modules and outputs a pipeline summary report tsv file.** * The (`Summary_Report`) consolidates and merges multiple report sheets into a single comprehensive summary report. +* The (`merged_bam_coverage_results`) merges the gene segment report sheets detailing mapped reads, mean depth, reference length, sequence length, and percent_coverage. ## Quick Start