diff --git a/CHANGELOG.md b/CHANGELOG.md index 5a5c32db..85e02ffa 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,14 +3,33 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.0.0 - [date] +## [1.0.0] - 2021-11-05 Initial release of nf-core/cutandrun, created with the [nf-core](https://nf-co.re/) template. -### `Added` +This pipeline is a best-practice bioinformatic analysis pipeline for CUT&Run and CUT&Tag experimental protocols that where developed to study protein-DNA interactions and epigenomic profiling. -### `Fixed` +nf-core/cutandrun was originally written by Chris Cheshire ([@chris-cheshire](https://github.com/chris-cheshire)) and Charlotte West ([@charlotte-west](https://github.com/charlotte-west)) from [Luscombe Lab](https://www.crick.ac.uk/research/labs/nicholas-luscombe) at [The Francis Crick Institute](https://www.crick.ac.uk/), London, UK. -### `Dependencies` +The pipeline structure and parts of the downstream analysis were adapted from the original CUT&Tag analysis [protocol](https://yezhengstat.github.io/CUTTag_tutorial/) from the [Henikoff Lab](https://research.fredhutch.org/henikoff/en.html). -### `Deprecated` +We thank Harshil Patel ([@drpatelh](https://github.com/drpatelh)) and everyone in the Luscombe Lab ([@luslab](https://github.com/luslab)) for their extensive assistance in the development of this pipeline. + +### Pipeline summary + +1. Check input files +2. Merge re-sequenced FastQ files ([`cat`](http://www.linfo.org/cat.html)) +3. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) +4. Adapter and quality trimming ([`Trim Galore!`](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)) +5. Alignment to both target and spike-in genomes ([`Bowtie 2`](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)) +6. Filter on quality, sort and index alignments ([`samtools`](https://sourceforge.net/projects/samtools/files/samtools/)) +7. Duplicate read marking ([`picard`](https://broadinstitute.github.io/picard/)) +8. Create bedGraph files ([`bedtools`](https://github.com/arq5x/bedtools2/) +9. Create bigWig coverage files ([`bedGraphToBigWig`](http://hgdownload.soe.ucsc.edu/admin/exe/)) +10. Peak calling specifically tailored for low background noise experiments ([`SEACR`](https://github.com/FredHutch/SEACR)) +11. Consensus peak merging and reporting ([`bedtools`](https://github.com/arq5x/bedtools2/)) +12. Quality control and analysis: + 1. Alignment, fragment length and peak analysis and replicate reproducibility ([`python`](https://www.python.org/)) + 2. Heatmap peak analysis ([`deepTools`](https://github.com/deeptools/deepTools/)) +13. Genome browser session ([`IGV`](https://software.broadinstitute.org/software/igv/)) +14. Present QC for raw read, alignment and duplicate reads ([`MultiQC`](http://multiqc.info/)) diff --git a/nextflow.config b/nextflow.config index 6bb5ee3a..2e50983c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -226,7 +226,7 @@ manifest { description = "Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes sequencing QC, spike-in normalisation, IgG control normalisation, peak calling and downstream peak analysis." mainScript = "main.nf" nextflowVersion = '!>=21.04.0' - version = '1.0.0dev' + version = '1.0.0' } // Function to ensure that resource requirements don't go beyond