Updated to v2

.github/workflows/github-actions-demo.yml

@@ -0,0 +1,17 @@
+name: test CBP nextflow pipeline
+run-name: ${{ github.actor }} is testing the Canafian Biogenome Project pipeline
+on: [push]
+jobs:
+  Explore-GitHub-Actions:
+    runs-on: ubuntu-latest
+    steps:
+      - run: echo "🎉 The job was automatically triggered by a ${{ github.event_name }} event."
+      - run: echo "🐧 This job is now running on a ${{ runner.os }} server hosted by GitHub!"
+      - run: echo "🔎 The name of your branch is ${{ github.ref }} and your repository is ${{ github.repository }}."
+      - name: List files in the repository
+        run: |
+          ls ${{ github.workspace }}
+      - uses: actions/checkout@v3
+      - uses: nf-core/setup-nextflow@v1
+      - run: nextflow run bcgsc/Canadian_Biogenome_Project -latest -r V2 -profile conda -c nextflow_github_test.config
+      - run: echo "🍏 This job's status is ${{ job.status }}."

.gitignore

@@ -0,0 +1,18 @@
+/work/*
+/work
+/assembly/*
+/assembly
+/blobtools/*
+/blobtools
+/hic_scaffolding/*
+/hic_scaffolding
+/preprocessing/*
+/preprocessing
+/purge_dups/*
+/purge_dups
+/QC/*
+/QC
+.n*
+.git/
+/V2
+/V2/*

README.md

@@ -7,12 +7,21 @@ In short, each step of the pipeline is included in a module. Most of the modules
 
 A lot of the modules available in this pipeline were developed by members of the nf-core/genomeassembler group, if you want to participate, feel free to join the community.
 
+## **Table of Contents**
+* **[Input data](#input-data)**
+* **[Output data](#output-files)**
+* **[Process](#process)**
+  * [Running the pipeline with test data](#running-the-pipeline-with-test-data-(will-work-once-the-repo-is-public))
+  * [Running the pipeline with your own data](#running-the-pipeline-with-your-own-data)
+* **[Credits](#credits)**
+* **[Details on the test dataset](#details-on-the-test-dataset)**
+
 
 
 ## Input data 
-The pipeline was developped to take as input PacBio ccs files (bam) and Hi-C files (fastq.gz). The pipeline also support the inclusion of nanopore data and short-reads for polishing.
+The pipeline was developped to take as input PacBio files (bam, from Sequel II or Revio machines) and Hi-C files (fastq.gz). The pipeline also support the inclusion of nanopore data and short-reads for polishing.
 
-The pipeline also require information related to the specie of interest such as genome size or ploidy. This information can be found on GoaT (https://goat.genomehubs.org).
+The pipeline also require the specie NCBI Taxonomy ID, which can be found on GoaT (https://goat.genomehubs.org) or on NCBI.
 
 
 
@@ -22,40 +31,39 @@ The pipeline generates many files and intermediate files, most are self explanat
 
 
 ## Process
-An overview of the pipeline is visible on the following subway map. Some parts of the pipeline may have been commented out in this version as they relied on locaaly installed software. The code is still available in case you also want to locally install the software and try it out.
+An overview of the pipeline is visible on the following subway map. Some parts of the pipeline may have been commented out in this version as they relied on localy installed software. The code is still available in case you also want to locally install the software and try it out.
 
 By default, the pipeline will use hifiasm with PacBio data for the assembly, and if Hi-C data is available, YAHS is used for the scaffolding.
 Other assembler and scaffolder are available within the pipeline, to change, you need to edit the nextflow.config file.
 
 Software used that would require local installation:
 
-- LongQC
-
-- MitoHifi
+- [LongQC](https://github.com/yfukasawa/LongQC)
+- [MitoHifi](https://github.com/marcelauliano/MitoHiFi)
+- [Juicer](https://github.com/aidenlab/juicer)
 
-- Juicer
 
 Software that relies on locally downloaded files / databases :
 
-- Busco
-
-- Kraken
+- [Busco](https://busco.ezlab.org/busco_userguide.html#download-and-automated-update)
+- [Kraken](http://ccb.jhu.edu/software/kraken/)
 
 <p align="center">
-    <img title="The Canadian Biogenome Project Workflow" src="https://github.com/bcgsc/Canadian_Biogenome_Project/CBP_workflow.png" width=50%>
+    <img title="The Canadian Biogenome Project Workflow" src="res/CBP_workflow.png" width=50%>
 </p>
 <p align="center">
 Figure : Overview of the Canadian Biogenome project assembly pipeline
 </p>
 
 
-## Running the pipeline with test data (will work once the repo is public)
-To run this pipeline, you need nextflow, conda and singularity installed on your system.
+
+## Running the pipeline with test data
+To run this pipeline, you need nextflow and conda or singularity installed on your system.
 
 A set of test data are available in this repo to allow you to test the pipeline with just one command line:
 
 ```
-nextflow run bcgsc/Canadian_Biogenome_Project -latest -r dev
+nextflow run bcgsc/Canadian_Biogenome_Project -latest -r V2 -profile conda
 ```
 
 The outputs are organized in several subfolder that are self-explenatory.
@@ -87,16 +95,18 @@ nextflow run main.nf -profile singularity
 
 ## Credits
 
-The pipeline was originnally written by @scorreard with the help and input from :
+The pipeline was originnally written by [@scorreard](https://github.com/scorreard) with the help and input from :
 
 - Members of the Jones lab (Canada's Michael Smith Genome Sciences Centre, Vancouver, Canada).
 
-- Members of the Earth Biogenome Project and other affiliated projects.
+	- Special thanks to [@Glenn Chang](https://github.com/Glenn032787) for reviewing that repo.
 
+- Members of the Earth Biogenome Project and other affiliated projects.
 - Members of the nf-core / nextflow community.
 
 
 
+
 ## Details on the test dataset
 
 The PacBio data is a subset of covid ssequences obtained with this command lines :