-
Notifications
You must be signed in to change notification settings - Fork 133
/
README.md
113 lines (80 loc) · 8.54 KB
/
README.md
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
#  
[](https://github.com/nf-core/methylseq/actions?query=workflow%3A%22nf-core+CI%22)
[](https://github.com/nf-core/methylseq/actions?query=workflow%3A%22nf-core+linting%22)[](https://nf-co.re/methylseq/results)[](https://doi.org/10.5281/zenodo.1343417)
[](https://www.nextflow.io/)
[](https://docs.conda.io/en/latest/)
[](https://www.docker.com/)
[](https://sylabs.io/docs/)
[](https://tower.nf/launch?pipeline=https://github.com/nf-core/methylseq)
[](https://github.com/askimed/nf-test)
[](https://nfcore.slack.com/channels/methylseq)[](https://twitter.com/nf_core)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)
## Introduction
**nf-core/methylseq** is a bioinformatics analysis pipeline used for Methylation (Bisulfite) sequencing data. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.
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 uses Docker / Singularity containers making installation trivial and results highly reproducible.
On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/methylseq/results).
## Pipeline Summary
The pipeline allows you to choose between running either [Bismark](https://github.com/FelixKrueger/Bismark) or [bwa-meth](https://github.com/brentp/bwa-meth) / [MethylDackel](https://github.com/dpryan79/methyldackel).
Choose between workflows by using `--aligner bismark` (default, uses bowtie2 for alignment), `--aligner bismark_hisat` or `--aligner bwameth`.
| Step | Bismark workflow | bwa-meth workflow |
| -------------------------------------------- | ---------------- | --------------------- |
| Generate Reference Genome Index _(optional)_ | Bismark | bwa-meth |
| Merge re-sequenced FastQ files | cat | cat |
| Raw data QC | FastQC | FastQC |
| Adapter sequence trimming | Trim Galore! | Trim Galore! |
| Align Reads | Bismark | bwa-meth |
| Deduplicate Alignments | Bismark | Picard MarkDuplicates |
| Extract methylation calls | Bismark | MethylDackel |
| Sample report | Bismark | - |
| Summary Report | Bismark | - |
| Alignment QC | Qualimap | Qualimap |
| Sample complexity | Preseq | Preseq |
| Project Report | MultiQC | MultiQC |
## Usage
> [!NOTE]
> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
First, prepare a samplesheet with your input data that looks as follows:
`samplesheet.csv`:
```csv
sample,fastq_1,fastq_2
SRR389222_sub1,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz
SRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz
SRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz
Ecoli_10K_methylated,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz
```
Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
Now, you can run the pipeline using:
```bash
nextflow run nf-core/methylseq --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
```
> [!WARNING]
> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/methylseq/usage) and the [parameter documentation](https://nf-co.re/methylseq/parameters).
## Pipeline output
To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/methylseq/results) tab on the nf-core website pipeline page.
For more details about the output files and reports, please refer to the
[output documentation](https://nf-co.re/methylseq/output).
## Credits
These scripts were originally written for use at the [National Genomics Infrastructure](https://portal.scilifelab.se/genomics/) at [SciLifeLab](http://www.scilifelab.se/) in Stockholm, Sweden.
- Main author:
- Phil Ewels ([@ewels](https://github.com/ewels/))
- Maintainers:
- Felix Krueger ([@FelixKrueger](https://github.com/FelixKrueger))
- Sateesh Peri ([@Sateesh_Peri](https://github.com/sateeshperi))
- Edmund Miller ([@EMiller88](https://github.com/emiller88))
- Contributors:
- Rickard Hammarén ([@Hammarn](https://github.com/Hammarn/))
- Alexander Peltzer ([@apeltzer](https://github.com/apeltzer/))
- Patrick Hüther ([@phue](https://github.com/phue/))
## Contributions and Support
If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
For further information or help, don't hesitate to get in touch on the [Slack `#methylseq` channel](https://nfcore.slack.com/channels/methylseq) (you can join with [this invite](https://nf-co.re/join/slack)).
## Citations
If you use nf-core/methylseq for your analysis, please cite it using the following doi: [10.5281/zenodo.1343417](https://doi.org/10.5281/zenodo.1343417)
An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
You can cite the `nf-core` publication as follows:
> **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).