fix website deploy and update readme

.github/workflows/website.yml

@@ -44,6 +44,9 @@ jobs:
         uses: actions/configure-pages@v3
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v1
+        with:
+          # Upload dist repository
+          path: './dist'
       - name: Deploy to GitHub Pages
         id: deployment
         uses: actions/deploy-pages@v1

README.md

@@ -1,55 +1,3 @@
-# ViralConsensus
-ViralConsensus is a fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data. ViralConsensus is orders of magnitude faster and more memory-efficient than existing methods. Further, unlike existing methods, ViralConsensus can pipe data directly from a read mapper via standard input and performs viral consensus calling on-the-fly, making it an ideal tool for viral sequencing pipelines.
+## ViralWasm-Consensus 
 
-# Installation
-ViralConsensus is written in C++ and depends on htslib. You can simply download the latest release tarball (or clone the repo) and compile with `make`:
-
-```bash
-# install dependencies
-sudo apt-get install libbz2-dev libcurl4-openssl-dev liblzma-dev
-
-# install ViralConsensus
-git clone https://github.com/niemasd/ViralConsensus.git
-cd ViralConsensus
-make
-sudo mv viral_consensus /usr/local/bin/ # optional; install NGG executables globally
-```
-
-You can also find a Docker container of ViralConsensus on DockerHub: [niemasd/viral_consensus](https://hub.docker.com/r/niemasd/viral_consensus)
-
-# Usage
-```
-viral_consensus -i IN_READS -r REF_GENOME -o OUT_CONSENSUS [-op OUT_POS_COUNTS] [-oi OUT_INS_COUNTS] [-q MIN_QUAL] [-d MIN_DEPTH] [-f MIN_FREQ] [-a AMBIG] [-p PRIMER_BED] [-po PRIMER_OFFSET]
-  -i/--in_reads IN_READS                Input reads file (CRAM/BAM/SAM), or '-' for standard input
-  -r/--ref_genome REF_GENOME            Input reference genome (FASTA)
-  -o/--out_consensus OUT_CONSENSUS      Output consensus genome (FASTA), or '-' for standard output
-  -op/--out_pos_counts OUT_POS_COUNTS   Output position counts (TSV), or '-' for standard output (default: don't output)
-  -oi/--out_ins_counts OUT_INS_COUNTS   Output insertion counts (JSON), or '-' for standard output (default: don't output)
-  -q/--min_qual MIN_QUAL                Minimum base quality to count base in counts (default: 20)
-  -d/--min_depth MIN_DEPTH              Minimum depth to call base/insertion in consensus (default: 10)
-  -f/--min_freq MIN_FREQ                Minimum frequency to call base/insertion in consensus (default: 0.5)
-  -a/--ambig AMBIG                      Ambiguous symbol (default: N)
-  -p/--primer_bed PRIMER_BED            Primer file (BED)
-  -po/--primer_offset PRIMER_OFFSET     Number of bases after primer to also trim (default: 0)
-  -v/--version                          Print version number
-  -h/--help                             Print this usage message
-```
-
-## Piping from Read Mapper
-Because ViralConsensus does not require reads to be sorted, data can be piped directly from the read mapper to ViralConsensus to avoid unnecessary disk I/O (and thus improve speed):
-
-```bash
-# ViralConsensus is single-threaded, so if running many samples, best to run mapper single-threaded as well and parallelize across samples
-minimap2 -t 1 -a -x sr reference.fas reads.fastq.gz | viral_consensus -i - -r reference.fas -o consensus.fas
-```
-
-Users will likely want to keep the output of the read mapper (e.g. as a compressed BAM file) for other downstream analyses, but rather than writing the output SAM/BAM/CRAM to disk and *then* having ViralConsensus read from that file, `tee` should be used instead to send the stream down two (or more) paths:
-
-```bash
-minimap2 -t 1 -a -x sr reference.fas reads.fastq.gz | tee >(viral_consensus -i - -r reference.fas -o consensus.fas) | samtools view -b -@ 1 > reads.bam
-```
-
-# Citing ViralConsensus
-If you use ViralConsensus in your work, please cite:
-
-> Moshiri N (2023). "ViralConsensus: A fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data." *Bioinformatics*. btad317. [doi:10.1093/bioinformatics/btad317](https://doi.org/10.1093/bioinformatics/btad317)
+A client-side WebAssembly pipeline for viral consensus sequence calling. For an offline version of this site, please see the offline-mode branch: https://github.com/Niema-Lab/ViralWasm-Consensus/tree/offline-mode