Merge pull request #194 from cidgoh/development

Merge dev to master

.github/workflows/nextflow_CI.yml

@@ -0,0 +1,49 @@
+name: Nextflow CI
+
+on:
+  push:
+    branches:
+      - development
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  test_sarscov2_user:
+    name: Run pipeline test (user)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Run pipeline test (user)
+        run: |
+          nextflow run main.nf -profile docker --prefix "covidmvp-user-$(date +%Y-%m-%d)" -params-file covidmvp_user.yaml
+
+  test_sarscov2_reference:
+    name: Run pipeline test (reference)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Run pipeline test (reference)
+        run: |
+          nextflow run main.nf -profile docker --prefix "covidmvp-$(date +%Y-%m-%d)" --end_date $(date +%Y-%m-%d) -params-file covidmvp_clinical_params.yaml
+
+  check_success:
+    name: Check if all tests passed
+    needs: [test_sarscov2_user, test_sarscov2_reference]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check job status
+        if: ${{ failure() }}
+        run: exit 1

.gitignore

@@ -1,23 +1,18 @@
 .nextflow*
-work/*
 results/*
 .idea/*
-.github/data/metadata
-.github/data/sequence
 .DS_store
-testing/*
 *.ipynb
 weekly*
 *.error
 *.out
 bin/__*
 *.sh
 latest*
-data/*
 *.fa.xz
 *.gz
 hMPXV_*
 bin/web.log
 assets/config.ini
-*-params.yaml
-*.xz
+*.xz
+*.log

.vscode/extensions.json

@@ -0,0 +1,3 @@
+{
+  "recommendations": ["nextflow.nextflow"]
+}

.vscode/settings.json

@@ -0,0 +1,6 @@
+{
+  "cSpell.words": ["bioinformatics", "cpus"],
+  "nextflow.debug": true,
+  "nextflow.formatting.harshilAlignment": true,
+  "nextflow.java.home": "/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/17.0.2/"
+}

README.md

@@ -7,19 +7,37 @@
 
 ## Introduction
 
-**nf-ncov-voc** is a bioinformatics analysis workflow used for
-performing variant calling on SARS-CoV-2 genomes to identify and
-profile mutations in Variants of Concern (VOCs), Variants of
-Interest (VOIs) and Variants under Monitoring (VUMs). This workflow has
-four main stages - **Preprocessing**, **Genomic Analysis (Variant
-Calling)** , **Functional Annotation** and **Surveillance**.
+**nf-ncov-voc** is a bioinformatics workflow developed to process viral genomes and integrate the contextual data.
+The workflow was intially designed for processing SARS-CoV-2 for COVID-19 pandemic response and has been later adapted for more priority viruses e.g., Mpox and Influenza. The workflow is developed in a modular structure with several modules and sub-workflows leveraged from [nf-core](https://nf-co.re). These modules and sub-workflows are assembled in a plug-n-play manner based on the data and viral charatceristics. Each virus supported by the workflow has its own workflow file that directs the assembly of sub-workflows and modules.
+
+The workflow is built using [Nextflow](https://www.nextflow.io)- [DSL2](https://www.nextflow.io/docs/latest/dsl2.html), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It can use `conda`/`Docker`/`Singularity` containers making installation trivial and results highly reproducible.
+
 **nf-ncov-voc** workflow can be used in combination with an interactive
-visualization tool [COVID-MVP](https://github.com/cidgoh/COVID-MVP)
-or as a stand-alone high-throughput analysis tool to produce
-mutation profiles and surveillance reports.
+visualization tool [VIRUS-MVP](https://github.com/cidgoh/VIRUS-MVP) or as a stand-alone high-throughput analysis tool to produce mutation profiles and surveillance reports.
+
+A detailed structure and each module of the workflow is presented
+below in the dataflow diagram
+
+### nf-ncov-voc Dataflow
+
+![DataFlow](figs/COVIDMVP.drawio.png)
+
+### Functional Annotation
+
+**nf-ncov-voc** offers a unique opportunity to integrate the contextual data with genomics data. Variant Called File (VCF) generated for each group or sample is then converted to a Genome Variant File (GVF) to integrate the functions associated to different mutations. For more information of how the functions are curated and structured see the dedicated repository [_Pokay_](https://github.com/nodrogluap/pokay)
+
+**nf-ncov-voc** with the help of functional data in _Pokay_, produces surveillance reports that are developed in collaboration with the Public Health partners and offers a high-level yet comprehensive report on each mutation its associated functions in literature.
+
+### Input data
+
+As an input, **nf-ncov-voc** can accept different formats, Whole Genome Sequences (WGS) in `FASTA` format with a Metadata file in `TSV` format; paired-end short read sequences in `FASTQ` format with a Metadata file in `TSV` format. Additionally, the input can also be `VCF` file that contains variants called.
+
+### Grouping data
+
+### Quality control
+
+### Variant Calling
 
-As an input, **nf-ncov-voc** workflow requires SARS-CoV-2 consensus
-sequences in `FASTA` format and Metadata file in `TSV` format.
 Sequences in pre-processing stage are filtered using Metadata
 variables, quality filtered and assigned lineages. Sequences
 assigned as VOCs, VOIs and VUMs are then mapped to SARS-CoV-2 genome,
@@ -35,19 +53,6 @@ summarized using functional indicators to highlight key functions
 and mutations responsible for them for e.g. **P618H** role in
 _convalescent plasma escape_.
 
-The workflow is built using [Nextflow](https://www.nextflow.io)-
-[DSL2](https://www.nextflow.io/docs/latest/dsl2.html), a workflow
-tool to run tasks across multiple compute infrastructures in a very
-portable manner. It can use `conda`/`Docker`/`Singularity`
-containers making installation trivial and results highly reproducible.
-
-A detailed structure and each module of the workflow is presented
-below in the dataflow diagram
-
-### nf-ncov-voc Dataflow
-
-![DataFlow](figs/COVIDMVP.drawio.png)
-
 ### Pre-Processing
 
 This module offers two ways to get lineage information for each
@@ -121,6 +126,8 @@ See the
 [parameters](https://github.com/cidgoh/nf-ncov-voc/blob/master/docs/PARAMETERS.md)
 docs for all available options when running the workflow.
 
+** Further developments will continue to adapt nf-ncov-voc to other viruses in near furture. **
+
 ## Usage
 
 1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.04.0`)