Merge pull request #62 from nf-core/dev

Dev > Master for first release!

Author: drpatelh

.github/workflows/ci.yml

@@ -21,7 +21,8 @@ jobs:
           sudo mv nextflow /usr/local/bin/
       - name: Pull docker image
         run: |
-          docker pull nfcore/nanoseq:dev && docker tag nfcore/nanoseq:dev nfcore/nanoseq:dev
+          docker pull nfcore/nanoseq:dev
+          docker tag nfcore/nanoseq:dev nfcore/nanoseq:1.0.0
       - name: Basecall and demultiplex (minimap2)
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner minimap2

.github/workflows/linting.yml

@@ -1,26 +1,39 @@
 name: nf-core linting
 # This workflow is triggered on pushes and PRs to the repository.
 # It runs the `nf-core lint` and markdown lint tests to ensure that the code meets the nf-core guidelines
-on: [push, pull_request]  
+on:
+  push:
+  pull_request:
+  release:
+    types: [published]
 
 jobs:
   Markdown:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v2
       - uses: actions/setup-node@v1
         with:
           node-version: '10'
       - name: Install markdownlint
-        run: |
-          npm install -g markdownlint-cli
+        run: npm install -g markdownlint-cli
       - name: Run Markdownlint
-        run: |
-          markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
-  nf-core:
+        run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
+  YAML:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v1
+      - uses: actions/setup-node@v1
+        with:
+          node-version: '10'
+      - name: Install yaml-lint
+        run: npm install -g yaml-lint
+      - name: Run yaml-lint
+        run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml")
+  nf-core:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
       - name: Install Nextflow
         run: |
           wget -qO- get.nextflow.io | bash
@@ -29,13 +42,9 @@ jobs:
         with:
           python-version: '3.6'
           architecture: 'x64'
-      - name: Install pip
-        run: |
-          sudo apt install python3-pip
-          pip install --upgrade pip
-      - name: Install nf-core tools
+      - name: Install dependencies
         run: |
+          python -m pip install --upgrade pip
           pip install nf-core
       - name: Run nf-core lint
-        run: |
-          nf-core lint ${GITHUB_WORKSPACE}
+        run: nf-core lint ${GITHUB_WORKSPACE}

.gitignore

@@ -3,5 +3,6 @@ work/
 data/
 results/
 .DS_Store
-test*
+tests/
+testing/
 *.pyc

CHANGELOG.md

@@ -3,14 +3,6 @@
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-## v1.0dev - [date]
+## [1.0.0] - 2020-03-05
 
 Initial release of nf-core/nanoseq, created with the [nf-core](http://nf-co.re/) template.
-
-### `Added`
-
-### `Fixed`
-
-### `Dependencies`
-
-### `Deprecated`

Dockerfile

@@ -1,4 +1,4 @@
-FROM nfcore/base:1.8
+FROM nfcore/base:1.9
 LABEL authors="Chelsea Sawyer" \
       description="Docker image containing all software requirements for the nf-core/nanoseq pipeline"
 
@@ -7,7 +7,7 @@ COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-nanoseq-1.0dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-nanoseq-1.0.0/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-nanoseq-1.0dev > nf-core-nanoseq-1.0dev.yml
+RUN conda env export --name nf-core-nanoseq-1.0.0 > nf-core-nanoseq-1.0.0.yml

README.md

@@ -1,7 +1,5 @@
 # ![nfcore/nanoseq](docs/images/nf-core-nanoseq_logo.png)
 
-**A pipeline to demultiplex, QC and map Nanopore data**.
-
 [![GitHub Actions CI Status](https://github.com/nf-core/nanoseq/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/nanoseq/actions)
 [![GitHub Actions Linting Status](https://github.com/nf-core/nanoseq/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/nanoseq/actions)
 [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A519.10.0-brightgreen.svg)](https://www.nextflow.io/)
@@ -10,7 +8,7 @@
 
 ## Introduction
 
-**nfcore/nanoseq** is a bioinformatics analysis pipeline that can be used to perform basecalling, demultiplexing, mapping and QC of Nanopore data.
+**nfcore/nanoseq** is a bioinformatics analysis pipeline that can be used to perform basecalling, demultiplexing, mapping and QC of Nanopore DNA/RNA sequencing data.
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.
 
@@ -20,6 +18,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 2. Sequencing QC ([`pycoQC`](https://github.com/a-slide/pycoQC), [`NanoPlot`](https://github.com/wdecoster/NanoPlot))
 3. Raw read QC ([`NanoPlot`](https://github.com/wdecoster/NanoPlot), [`FastQC`](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
 4. Alignment ([`GraphMap2`](https://github.com/lbcb-sci/graphmap2) or [`minimap2`](https://github.com/lh3/minimap2))
+    * Both aligners are capable of performing unspliced and spliced alignment. Sensible defaults will be applied automatically based on a combination of the input data and user-specified parameters
     * Each sample can be mapped to its own reference genome if multiplexed in this way
     * Convert SAM to co-ordinate sorted BAM and obtain mapping metrics ([`SAMtools`](http://www.htslib.org/doc/samtools.html))
 5. Create bigWig ([`BEDTools`](https://github.com/arq5x/bedtools2/), [`bedGraphToBigWig`](http://hgdownload.soe.ucsc.edu/admin/exe/)) and bigBed ([`BEDTools`](https://github.com/arq5x/bedtools2/), [`bedToBigBed`](http://hgdownload.soe.ucsc.edu/admin/exe/)) coverage tracks for visualisation
@@ -37,7 +36,7 @@ iii. Download the pipeline and test it on a minimal dataset with a single comman
 nextflow run nf-core/nanoseq -profile test,<docker/singularity/institute>
 ```
 
-> Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile institute` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
+> Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
 
 iv. Start running your own analysis!
 
@@ -52,7 +51,7 @@ nextflow run nf-core/nanoseq \
     -profile <docker/singularity/institute>
 ```
 
-See [usage docs](docs/usage.md) for all of the available options when running the pipeline.
+See [usage docs](docs/usage.md) for all of the available options when running the pipeline. An example input samplesheet for performing both basecalling and demultiplexing can be found [here](assets/samplesheet.csv).
 
 ## Documentation
 
@@ -69,7 +68,7 @@ The nf-core/nanoseq pipeline comes with documentation about the pipeline, found
 
 ## Credits
 
-nf-core/nanoseq was originally written by [Chelsea Sawyer](https://github.com/csawye01) and [Harshil Patel](https://github.com/drpatelh) from [The Bioinformatics & Biostatistics Group](https://www.crick.ac.uk/research/science-technology-platforms/bioinformatics-and-biostatistics/) for use at [The Francis Crick Institute](https://www.crick.ac.uk/), London. [Laura Wratten](https://github.com/lwratten) from the [Genome Institute of Singapore](https://www.a-star.edu.sg/gis) is one of the primary contributors along with [Johannes Alneberg](https://github.com/alneberg) and [Franziska Bonath](https://github.com/FranBonath) from [SciLifeLab](https://www.scilifelab.se/), Sweden.
+nf-core/nanoseq was originally written by [Chelsea Sawyer](https://github.com/csawye01) and [Harshil Patel](https://github.com/drpatelh) from [The Bioinformatics & Biostatistics Group](https://www.crick.ac.uk/research/science-technology-platforms/bioinformatics-and-biostatistics/) for use at [The Francis Crick Institute](https://www.crick.ac.uk/), London. Other primary contributors include [Laura Wratten](https://github.com/lwratten), [Chen Ying](https://github.com/cying111) and [Jonathan Goeke](https://github.com/jonathangoeke) from the [Genome Institute of Singapore](https://www.a-star.edu.sg/gis), [Johannes Alneberg](https://github.com/alneberg) and [Franziska Bonath](https://github.com/FranBonath) from [SciLifeLab](https://www.scilifelab.se/), Sweden.
 
 Many thanks to others who have helped out along the way too, including (but not limited to): [@crickbabs](https://github.com/crickbabs), [@AnnaSyme](https://github.com/AnnaSyme).
 
@@ -82,7 +81,13 @@ For further information or help, don't hesitate to get in touch on [Slack](https
 ## Citation
 
 <!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi. -->
-<!-- If you use nf-core/nanoseq for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+<!-- If you use  nf-core/nanoseq for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+
+You can cite the `nf-core` publication as follows:
 
-You can cite the `nf-core` pre-print as follows:
-> Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v1).
+> **The nf-core framework for community-curated bioinformatics pipelines.**
+>
+> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
+>
+> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).  
+> ReadCube: [Full Access Link](https://rdcu.be/b1GjZ)

assets/samplesheet.csv

@@ -0,0 +1,7 @@
+sample,fastq,barcode,genome,transcriptome
+Sample1,,1,mm10,
+Sample2,,2,hg19,
+Sample3,,3,/path/to/local/genome.fa,
+Sample4,,4,,/path/to/local/transcriptome.fa
+Sample5,,5,/path/to/local/genome.fa,/path/to/local/transcriptome.gtf
+Sample6,,6,,