Quick update of README to replace ncov2019 with mpxv (#2)

BCCDC-PHL · Aug 2, 2022 · 7d9715e · 7d9715e
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diff --git a/README.md b/README.md
@@ -1,58 +1,32 @@
-# ncov2019-artic-nf
-A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
+# mpxv-artic-nf
+A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on monkeypox virus (mpxv).
 
-![push master](https://github.com/BCCDC-PHL/ncov2019-artic-nf/actions/workflows/push_master.yml/badge.svg)
+![push master](https://github.com/BCCDC-PHL/mpxv-artic-nf/actions/workflows/push_master.yml/badge.svg)
 
 #### Introduction
 
 ------------
-
-This Nextflow pipeline automates the ARTIC network [nCoV-2019 novel coronavirus bioinformatics protocol](https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html "nCoV-2019 novel coronavirus bioinformatics protocol"). The upstream repository ([connor-lab/ncov2019-artic-nf](https://github.com/connor-lab/ncov2019-artic-nf)) was created to aid the harmonisation of the analysis of sequencing data generated by the [COG-UK](https://github.com/COG-UK) project. This fork ([BCCDC-PHL/ncov2019-artic-nf](https://github.com/BCCDC-PHL/ncov2019-artic-nf)) has a few modifications designed to support the SARS-CoV-2 sequencing efforts at the BC Centre for Disease Control Public Health Laboratory, and to conform to standardization efforts in the context of the [CanGOGeN](https://www.genomecanada.ca/en/cancogen) project. It will turn SARS-COV2 sequencing data (Illumina or Nanopore) into consensus sequences and provide other helpful outputs to assist the project's sequencing centres with submitting data.
+This pipeline is based on the [BCCDC-PHL/ncov2019-artic-nf](https://github.com/BCCDC-PHL/ncov2019-artic-nf) pipeline, which is a fork of the [connor-lab/ncov2019-artic-nf](https://github.com/connor-lab/ncov2019-artic-nf) pipeline. It has been modified to support analysis of monkeypox virus.
 
 
 #### Quick-start
 ##### Illumina
 
 ```
-nextflow run BCCDC-PHL/ncov2019-artic-nf [-profile conda,singularity,docker,slurm,lsf] \
+nextflow run BCCDC-PHL/mpxv-artic-nf -profile conda \
   --illumina --prefix "output_file_prefix" \
+  --bed /path/to/primers.bed \
+  --ref /path/to/ref.fa \
   --primer_pairs_tsv /path/to/primer_pairs_tsv \
-  --composite_ref /path/to/human_and_sars-cov-2_composite_ref \
-  --directory /path/to/reads 
+  --composite_ref /path/to/human_and_mpxv_composite_ref \
+  --directory /path/to/reads \
+  --outdir /path/to/outputs
 ```
-You can also use cram file input by passing the --cram flag.
-You can also specify cram file output by passing the --outCram flag.
-
-For production use at large scale, where you will run the workflow many times, you can avoid cloning the scheme repository, creating an ivar bed file and indexing the reference every time by supplying both `--bed /path/to/ivar-compatible.bed` and `--ref /path/to/bwa-indexed/ref.fa`.
-
-Alternatively you can avoid just the cloning of the scheme repository to remain on a fixed revision of it over time by passing --schemeRepoURL /path/to/own/clone/of/github.com/artic-network/artic-ncov2019. This removes any internet access from the workflow except for the optional upload steps.
 
-##### Nanopore
-###### Nanopolish
-
-```
-nextflow run BCCDC-PHL/ncov2019-artic-nf [-profile conda,singularity,docker,slurm,lsf] \
-  --nanopolish --prefix "output_file_prefix" \
-  --basecalled_fastq /path/to/directory \
-  --fast5_pass /path/to/directory \
-  --sequencing_summary /path/to/sequencing_summary.txt
-```
-
-###### Medaka
-
-```
- nextflow run connor-lab/ncov2019-artic-nf [-profile conda,singularity,docker,slurm,lsf] \
-   --medaka --prefix "output_file_prefix" \
-   --basecalled_fastq /path/to/directory \
-   --fast5_pass /path/to/directory \
-   --sequencing_summary /path/to/sequencing_summary.txt
-```
 
 #### Installation
 An up-to-date version of Nextflow is required because the pipeline is written in DSL2. Following the instructions at https://www.nextflow.io/ to download and install Nextflow should get you a recent-enough version. 
 
-#### Containers
-This repo contains both [Singularity]("https://sylabs.io/guides/3.0/user-guide/index.html") and Dockerfiles. You can build the Singularity containers locally by running `scripts/build_singularity_containers.sh` and use them with `-profile singularity` The containers will be available from Docker/Singularityhub shortly.
 
 #### Conda
 The repo contains a environment.yml files which automatically build the correct conda env if `-profile conda` is specifed in the command. Although you'll need `conda` installed, this is probably the easiest way to run this pipeline.
@@ -66,23 +40,7 @@ By default, the pipeline just runs on the local machine. You can specify `-profi
 You can use multiple profiles at once, separating them with a comma. This is described in the Nextflow [documentation](https://www.nextflow.io/docs/latest/config.html#config-profiles) 
 
 #### Config
-Common configuration options are set in `conf/base.config`. Workflow specific configuration options are set in `conf/nanopore.config` and `conf/illumina.config` They are described and set to sensible defaults (as suggested in the [nCoV-2019 novel coronavirus bioinformatics protocol](https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html "nCoV-2019 novel coronavirus bioinformatics protocol"))
-
-##### Options
-- `--outdir` sets the output directory.
-- `--bwa` to swap to bwa for mapping (nanopore only).
-
-##### Workflows
-
-###### Nanopore
-Use `--nanopolish` or `--medaka` to run these workflows. `--basecalled_fastq` should point to a directory created by `guppy_basecaller` (if you ran with no barcodes), or `guppy_barcoder` (if you ran with barcodes). It is imperative that the following `guppy_barcoder` command be used for demultiplexing:
-
-```
-guppy_barcoder --require_barcodes_both_ends -i run_name -s output_directory --arrangements_files "barcode_arrs_nb12.cfg barcode_arrs_nb24.cfg"
-```
-
-###### Illumina
-The Illumina workflow leans heavily on the excellent [ivar](https://github.com/andersen-lab/ivar) for primer trimming and consensus making. This workflow will be updated to follow ivar, as its also in very active development! Use `--illumina` to run the Illumina workflow. Use `--directory` to point to an Illumina output directory usually coded something like: `<date>_<machine_id>_<run_no>_<some_zeros>_<flowcell>`. The workflow will recursively grab all fastq files under this directory, so be sure that what you want is in there, and what you don't, isn't! 
+Common configuration options are set in `conf/base.config`. Workflow specific configuration options are set in `conf/illumina.config` They are described and set to sensible defaults (as suggested in the [nCoV-2019 novel coronavirus bioinformatics protocol](https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html "nCoV-2019 novel coronavirus bioinformatics protocol"))
 
 Important config options are:
 
@@ -94,7 +52,7 @@ Important config options are:
 | `mpileupDepth`                   | `100000` | Mpileup depth for ivar                                                                                              |
 | `varFreqThreshold`               | `0.75`   | ivar/freebayes frequency threshold for consensus variant                                                            |
 | `varMinFreqThreshold             | `0.25`   | ivar/freebayes frequency threshold for ambiguous variant                                                            |
-| `varMinDepth`                    | `10`     | Minimum coverage depth to call variant                                                                    |
+| `varMinDepth`                    | `10`     | Minimum coverage depth to call variant                                                                              |
 | `ivarMinVariantQuality`          | `20`     | ivear minimum mapping quality to call variant                                                                       |
 | `downsampleMappingQuality`       | `20`     | Exclude reads below this mapping quality while downsampling                                                         |
 | `downsampleAmpliconSubdivisions` | `3`      | Number of times amplicons are subdivided to determine locations of checkpoints to test for depth while downsampling |

diff --git a/environments/illumina/Dockerfile b/environments/illumina/Dockerfile
@@ -1,10 +1,10 @@
 FROM continuumio/miniconda3:latest
 LABEL authors="Matt Bull" \
-      description="Docker image containing all requirements for an Illumina ncov2019 pipeline"
+      description="Docker image containing all requirements for an Illumina mpxv pipeline"
 
 COPY environments/extras.yml /extras.yml
 COPY environments/illumina/environment.yml /environment.yml
 RUN apt-get update && apt-get install -y curl g++ git make procps && apt-get clean -y
 RUN /opt/conda/bin/conda env create -f /environment.yml 
-RUN /opt/conda/bin/conda env update -f /extras.yml -n artic-ncov2019-illumina && /opt/conda/bin/conda clean -a
-ENV PATH=/opt/conda/envs/artic-ncov2019-illumina/bin:$PATH
+RUN /opt/conda/bin/conda env update -f /extras.yml -n artic-mpxv-illumina && /opt/conda/bin/conda clean -a
+ENV PATH=/opt/conda/envs/artic-mpxv-illumina/bin:$PATH
diff --git a/environments/illumina/Singularity b/environments/illumina/Singularity
@@ -5,13 +5,13 @@ environments/illumina/environment.yml /environment.yml
 environments/extras.yml /extras.yml
 %labels
 authors="Matt Bull" 
-description="Docker image containing all requirements for the ARTIC project's ncov2019 pipeline"
+description="Docker image containing all requirements for the ARTIC project's mpxv pipeline"
 %post
 
 apt-get update && apt-get install -y g++ git make procps rsync && apt-get clean -y
 /opt/conda/bin/conda env create -f /environment.yml
-/opt/conda/bin/conda env update -f /extras.yml -n artic-ncov2019-illumina
-PATH=/opt/conda/envs/artic-ncov2019-illumina/bin:$PATH
+/opt/conda/bin/conda env update -f /extras.yml -n artic-mpxv-illumina
+PATH=/opt/conda/envs/artic-mpxv-illumina/bin:$PATH
 
 %environment
-export PATH=/opt/conda/envs/artic-ncov2019-illumina/bin:$PATH
+export PATH=/opt/conda/envs/artic-mpxv-illumina/bin:$PATH
diff --git a/environments/illumina/environment.yml b/environments/illumina/environment.yml
@@ -1,4 +1,4 @@
-name: artic-ncov2019-illumina
+name: artic-mpxv-illumina
 channels:
   - conda-forge
   - bioconda