Merge pull request #38 from CDCgov/update_docs_kao

Update documentation ufp0

README.md

@@ -25,7 +25,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 **Reference-free analyses**
 1. De novo assembly. ([`Unicycler`](https://github.com/rrwick/Unicycler))
 1. Calculate assembly quality metrics. ([`QUAST`](http://quast.sourceforge.net/))
-1. Assembly graph resolution. ([`mpxv-AssemblyGraph_gfaPy.py`](/bin/mpxv-AssemblyGraph_gfaPy.py))
+1. Assembly graph resolution. ([`AssemblyGraph_gfaPy.py`](/bin/AssemblyGraph_gfaPy.py))
 1. Align reads to assembled genome. ([`BWA`](http://bio-bwa.sourceforge.net/))
 1. Correct assembly errors and ambiguities. ([`iVar`](https://andersen-lab.github.io/ivar/html/manualpage.html))
 1. Quantify assembly corrections. ([`MUMmer`](https://github.com/mummer4/mummer#dnadiff))
@@ -34,82 +34,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 1. Visualize reads metrics and summary of software versions. ([`MultiQC`](http://multiqc.info/))
 1. Compile various QC metrics. ([`summarize_qc.py`](/bin/summarize_qc.py))
 
-```mermaid
-graph TD
-  subgraph filter_reads["Filter Reads"]
-    kraken2["Kraken2<br>classify opxv reads"]
-    seqtk["Seqtk<br>subsample opxv reads"]
-    fastp["Fastp:<br>quality trim + filter"]
-    kraken2 -- read_assignments --> seqtk
-    seqtk -- subsampled_reads --> fastp
-  end
-
-subgraph ref_based["Reference-based assembly"]
-  direction LR
-  bwa["Bwa mem<br>map to reference"];
-  samtools["Samtools<br>calculate mapping stats"];
-  ivar_cons["Ivar consensus<br>generate consensus fasta"];
-  ivar_var["Ivar variants<br>call variants"]
-  var_filt[Filtered variants];
-  bwa -- bam --> samtools
-  bwa -- bam --> ivar_cons
-  bwa -- bam --> ivar_var
-  ivar_var-."if filter=true".->var_filt
-  ref_fasta([Consensus fasta]);
-  vcf([VCF]);
-
-  ivar_cons --> ref_fasta
-  ivar_var --> vcf
-end
-
-  subgraph denovo[Denovo assembly]
-    %% Assign the processes (nodes)
-    unicycler["Unicycler<br>Denovo assembly"]
-    graph_recon["graph_reconstruct.py<br>Reconstruct assembly path"]
-    bwa_denovo["Bwa mem<br>map to assembly"]
-    samtools_denovo["Samtools<br>calculate mapping stats"]
-    ivar_polish["Ivar consensus<br>generate consensus fasta"]
-    summarize_asmb["Mummer and Quast<br>Summarize assembly"]
-
-    %% Assign output files
-    assembly_fasta(["Final assembly"])
-    assembly_contigs(["Assembly contigs"])
-
-    %% Assign the arrows
-    %%fastp -- cleaned_reads --> unicycler
-    unicycler -- assembly_graph --> graph_recon
-    graph_recon -- fasta assembly --> bwa_denovo
-    graph_recon -."if unable to reconstruct graph".->  assembly_contigs
-    %%fastp -- cleaned_reads --> bwa_denovo
-    bwa_denovo -- bam --> samtools_denovo
-    bwa_denovo -- bam --> ivar_polish
-    ivar_polish --> assembly_fasta
-    graph_recon --> summarize_asmb
-    assembly_fasta --> summarize_asmb
-    end 
-
-  subgraph summarize[Summarize and QC]
-    direction LR
-    %% Assign the processes (nodes)
-    multiqc["MultiQC<br>Gather and summarize"]
-    summarizeqc["Summarize_qc.py<br>Summarize all processes"]
-
-    %% Assign output files
-    sample_summary(["sample_summary.tsv<br>Summary table of all processes"])
-
-    %% Assign the arrows
-    %%assembly_fasta --> multiqc
-    %%ref_fasta --> multiqc
-    multiqc --> summarizeqc
-    summarizeqc --> sample_summary
-  end
-  
-  %% Connect the subworkflows
-  filter_reads -- cleaned reads --> denovo
-  filter_reads -- cleaned reads --> ref_based
-  denovo --> summarize
-  ref_based --> summarize
-```
+![workflow diagram](/docs/images/polkapox_workflow.png)
 
 ## Quick Start
 
@@ -139,7 +64,7 @@ CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
    nextflow run polkapox/main.nf --input {SAMPLESHEET.csv OR input_directory} --outdir {OUTDIR} --fasta {REF.fa} -profile sge,singularity --kraken_db {PATH/TO/DB} --gff {ANNOTATION.gff} --workflow {WORKFLOW} --filter {true/false}
    ```
 
-   **note**: If you do not provide `--fasta`, `--gff`, or `--kraken_db`, they will default to the reference and gff in the `assets` folder of this repo, and a kraken db hosted on the SciComp file system, respectively. If you do not specify `--filter` then it will default to `true`. See `nextflow.config` for details.  Add `--file_levels {top (default)/nested}` if passing a directory as input. See [usage](/docs/usage.md) for details.
+   **note**: If you do not provide `--fasta`, `--gff`, or `--kraken_db`, they will default to a Clade II reference and gff in the `assets` folder of this repo, and a kraken db will be downloaded from `s3://io-pe1-prod-ncezid-oamd-nextstrain/polkapox/orthopox_kdb/`. If you do not specify `--filter` then it will default to `true`. See `nextflow.config` for details.  Add `--file_levels {top (default)/nested}` if passing a directory as input. See [usage](/docs/usage.md) for details.
 
 ## Pipeline configuration
 
@@ -175,6 +100,7 @@ Pipeline outputs are organized into sub-directories for each step in the selecte
 ```
 ${outdir}/
   ├── bwa
+  ├── bandage
   ├── fastp
   ├── final_assembly
   ├── graph_recon
@@ -198,9 +124,9 @@ The **PolkaPox** pipeline includes de novo assembly optimized for the linear gen
 ## Credits
 
 Contributors:\
-Lynsey Kovar | Hunter Seabolt | Shatavia Morrison | Kristen Knipe\
-Kyle O'Connell | Ethan Hetrick | Michael Weigand | Crystal Gigante\
-Dhwani Batra | Ankush  Gupta | Jessica Rowell | Daisy McGrath\
+Kyle O'Connell | Michael Weigand | Jessica Rowell | Shatavia Morrison\
+Kristen Knipe | Ethan Hetrick | Crystal Gigante | Lynsey Kovar\
+Hunter Seabolt | Dhwani Batra | Daisy McGrath\
 Yesh Kulasekarapandian | Jason Caravas
 
 ## Contributions and Support