Update README.md

README.md

@@ -19,53 +19,54 @@
 
 ## Introduction
 
-**nf-core/pacvar** is a bioinformatics pipeline that ...
+**nf-core/pacvar** is a bioinformatics pipeline that processes long read pacbio data. Specifically the pipeline contains two workflows, one to process whole genome sequence data and other to process reads from the PureTarget expansion panel Pacbio offers - this repeat workflow characterizes tandem repeats. The workflow, is designed for pacbio reads and thus uses Pacbio's released tools.  
 
-<!-- TODO nf-core:
-   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
-   major pipeline sections and the types of output it produces. You're giving an overview to someone new
-   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction
--->
+![nf-core/rnaseq metro map](docs/images/metro_update.svg)
 
-<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
-     workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
-<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
+1. Demultiplex reads  ([`lima`](https://lima.how))
+2. Align reads ([`lima`](https://github.com/PacificBiosciences/pbmm2))
+3. Sort and Index alignments  ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))
 
-1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+wgs workflow
+1. Choice of SNP calling routes:
+   a. ([`deepvariant`](https://github.com/google/deepvariant))
+   b. ([`HaplotypeCaller`](https://gatk.broadinstitute.org/hc/en-us/articles/360037225632-HaplotypeCaller))
+2. Call SVs ([`pbsv`](https://github.com/PacificBiosciences/pbsv))
+3. Index VCF files ([`bcftools`](https://samtools.github.io/bcftools/bcftools.html))
+4. Phase SNPS, SVs and BAM files ([`hiphase`](https://github.com/PacificBiosciences/HiPhase))
 
-## Usage
-
-> [!NOTE]
-> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
+repeat workflow
+1. Genotype tandem repeats - produce spanning bams and vcf ([`TRGT`](https://github.com/PacificBiosciences/trgt))
+2. Index and Sort tandem tepeat spanning bam ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))
+3. Plot repeat motif plots ([`TRGT`](https://github.com/PacificBiosciences/trgt))
+4. Sort spanning VCF ([`bcftools`](https://samtools.github.io/bcftools/bcftools.html))
 
-<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
-     Explain what rows and columns represent. For instance (please edit as appropriate):
+## Usage
 
 First, prepare a samplesheet with your input data that looks as follows:
 
 `samplesheet.csv`:
 
 ```csv
-sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
+sample,bam,bai
+CONTROL,AEG588A1_S1_L002_R1_001.bam,AEG588A1_S1_L002_R1_001.bai
 ```
 
-Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
+Each row represents an unaligned bam file and their associated index.
 
--->
 
 Now, you can run the pipeline using:
 
-<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
-
 ```bash
 nextflow run nf-core/pacvar \
    -profile <docker/singularity/.../institute> \
    --input samplesheet.csv \
-   --outdir <OUTDIR>
+   --outdir <OUTDIR> \ 
+   --workflow <wgs/repeat> \
+   --barcodes barcode.fasta \
+   --intervals intervals.bed
 ```
-
+optional paramaters include: --skip_demultiplexing, --skip_snp --skip_sv  --skip_phase
 > [!WARNING]
 > Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
 > see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
@@ -84,8 +85,6 @@ nf-core/pacvar was originally written by Tanya Sarkin Jain.
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
-<!-- TODO nf-core: If applicable, make list of people who have also contributed -->
-
 ## Contributions and Support
 
 If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
@@ -97,8 +96,6 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 <!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
 <!-- If you use nf-core/pacvar for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
 
-<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
-
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
 You can cite the `nf-core` publication as follows: