-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Wrote documentation. Improved bismark output organisation.
Added --saveAlignedIntermediates and --saveTrimmed (don't save trimmed FastQ and undeduplicated BAM by default) Made output saved in subdirectories
- Loading branch information
Showing
6 changed files
with
574 additions
and
160 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,164 +1,31 @@ | ||
| #  | ||
|
|
||
| > # UNDER DEVELOPMENT | ||
| > This pipeline is currently under active development and has very little in the way of testing. You may well have problems running it. Any help debugging is very welcome! Please fork, make changes and submit a pull request. | ||
| [](https://travis-ci.org/SciLifeLab/NGI-MethylSeq) | ||
| [](https://www.nextflow.io/) | ||
|
|
||
| **NGI-MethylSeq** is a bioinformatics best-practice analysis pipeline used for Methylation (BS-Seq) data analysis at the [National Genomics Infastructure](https://ngisweden.scilifelab.se/) at [SciLifeLab Stockholm](https://www.scilifelab.se/platforms/ngi/), Sweden. | ||
| ### Introduction | ||
|
|
||
| NGI-MethylSeq is a bioinformatics best-practice analysis pipeline used for Methylation (BS-Seq) data analysis at the [National Genomics Infastructure](https://ngisweden.scilifelab.se/) at [SciLifeLab Stockholm](https://www.scilifelab.se/platforms/ngi/), Sweden. | ||
|
|
||
| The pipeline uses [Nextflow](https://www.nextflow.io), a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results. | ||
|
|
||
| This pipeline is primarily used with a SLURM cluster on the Swedish [UPPMAX systems](https://www.uppmax.uu.se). However, the pipeline should be able to run on any system that Nextflow supports. We have done some limited testing using Docker and AWS, and the pipeline comes with some configuration for these systems. See the [installation docs](docs/installation.md) for more information. | ||
|
|
||
| ## Pipeline Results | ||
| See the [pipeline documentation](docs/README.md) for explanations of | ||
| the results files. | ||
|
|
||
| ## Installation | ||
| ### NextFlow installation | ||
| See https://github.com/SciLifeLab/NGI-NextflowDocs for instructions on how to install and configure | ||
| Nextflow. | ||
|
|
||
| ### Pipeline installation | ||
| This pipeline itself needs no installation - NextFlow will automatically fetch it from GitHub when run if | ||
| `SciLifeLab/NGI-MethylSeq` is specified as the pipeline name. | ||
|
|
||
| If you prefer, you can download the files yourself from GitHub and run them directly: | ||
| ``` | ||
| git clone https://github.com/SciLifeLab/NGI-MethylSeq.git | ||
| nextflow NGI-MethylSeq/main.nf | ||
| ``` | ||
|
|
||
| ## Configuration | ||
| By default, the pipeline is configured to run on the Swedish UPPMAX cluster (milou / irma). | ||
|
|
||
| You will need to specify your UPPMAX project ID when running a pipeline. To do this, use | ||
| the command line flag `--project <project_ID>`. | ||
|
|
||
| To avoid having to specify this every time you run Nextflow, you can add it to your | ||
| personal Nextflow config file instead. Add this line to `~/.nextflow/config`: | ||
|
|
||
| ```groovy | ||
| params.project = 'project_ID' | ||
| ``` | ||
|
|
||
| The pipeline will exit with an error message if you try to run it pipeline with the default | ||
| UPPMAX config profile and don't set project. | ||
|
|
||
|
|
||
| ### Running on other clusters | ||
| It is entirely possible to run this pipeline on other clusters, though you will need to set up | ||
| your own config file so that the script knows where to find your reference files and how your | ||
| cluster works. | ||
|
|
||
| Copy the contents of [`conf/uppmax.config`](conf/uppmax.config) to your own config file somewhere | ||
| and then reference it with `-c` when running the pipeline. | ||
|
|
||
| If you think that there are other people using the pipeline who would benefit from your configuration | ||
| (eg. other common cluster setups), please let us know. It should be easy to create a new config file | ||
| in `conf` and reference this as a named profile in [`nextflow.config`](nextflow.config). Then these | ||
| configuration options can be used by specifying `-profile <name>` when running the pipeline. | ||
|
|
||
|
|
||
| ## Running the pipeline | ||
| The typical command for running the pipeline is as follows: | ||
| ``` | ||
| nextflow SciLifeLab/NGI-MethylSeq --reads '*_R{1,2}.fastq.gz' --genome GRCh37 | ||
| ``` | ||
|
|
||
| Note that the pipeline will create files in your working directory: | ||
| ```bash | ||
| work # Directory containing the nextflow working files | ||
| results # Finished results (configurable, see below) | ||
| .nextflow_log # Log file from Nextflow | ||
| # Other nextflow hidden files, eg. history of pipeline runs and old logs. | ||
| ``` | ||
|
|
||
| ### `--reads` | ||
| Location of the input FastQ files: | ||
| ``` | ||
| --reads 'path/to/data/sample_*_{1,2}.fastq' | ||
| ``` | ||
|
|
||
| **NB: Must be enclosed in quotes!** | ||
|
|
||
| Note that the `{1,2}` parentheses are required to specify paired end data. Running `--reads '*.fastq'` will treat | ||
| all files as single end. Also, note that the file path should be in quotation marks to prevent shell glob expansion. | ||
|
|
||
| If left unspecified, the pipeline will assume that the data is in a directory called `data` in the working directory. | ||
|
|
||
| ### `--genome` | ||
| The reference genome to use of the analysis, needs to be one of the genome specified in the config file. | ||
|
|
||
| See [`conf/uppmax.config`](conf/uppmax.config) for a list of the supported reference genomes | ||
| and their keys. Common genomes that are supported are: | ||
|
|
||
| * Human | ||
| * `--genome GRCh37` | ||
| * Mouse | ||
| * `--genome GRCm38` | ||
| * Drosophila | ||
| * `--genome BDGP6` | ||
| * _S. cerevisiae_ | ||
| * `--genome 'R64-1-1'` | ||
|
|
||
| > There are numerous others - check the config file for more. | ||
| If you usually want to work with a single species, you can set a default in your user config file. | ||
| For example, add this line to `~/.nextflow/config`: | ||
| ``` | ||
| params.genome = 'GRCh37' | ||
| ``` | ||
|
|
||
| ### Trimming Parameters | ||
| The pipeline accepts a number of parameters to change how the trimming is done, according to your data type. | ||
| The following settings are set for these command line flags: | ||
|
|
||
| | Parameter | 5' R1 Trim | 5' R2 Trim | 3' R1 Trim | 3' R2 Trim | | ||
| |-----------------|------------|------------|------------|------------| | ||
| | `--pbat` | 6 | 9 | 6 | 9 | | ||
| | `--single_cell` | 6 | 6 | 6 | 6 | | ||
| | `--epignome` | 8 | 8 | 8 | 8 | | ||
| | `--accel` | 10 | 15 | 10 | 10 | | ||
| | `--zymo` | 10 | 15 | 10 | 10 | | ||
| | `--cegx` | 6 | 6 | 2 | 2 | | ||
|
|
||
| You can specify custom trimming parameters as follows: | ||
|
|
||
| * `--clip_r1 <NUMBER>` | ||
| * `--clip_r2 <NUMBER>` | ||
| * `--three_prime_clip_r1 <NUMBER>` | ||
| * `--three_prime_clip_r2 <NUMBER>` | ||
|
|
||
| Finally, specifying `--rrbs` will pass on the `--rrbs` parameter to TrimGalore! | ||
|
|
||
| ### Bismark Parameters | ||
| Using the `--pbat` parameter will affect the trimming (see above) and also set the `--pbat` flag when | ||
| aligning with Bismark. | ||
|
|
||
| Using the `--single_cell` or `--zymo` parameters will set the `--non_directional` flag when aligning with Bismark. | ||
| This can also be set with `--non_directional` (doesn't affect trimming). | ||
|
|
||
| Use the `--unmapped` flag to set the `--unmapped` flag with Bismark align and save the unmapped reads. | ||
| ### Documentation | ||
| The NGI-MethylSeq pipeline comes with documentation about the pipeline, found in the `docs/` directory: | ||
|
|
||
| ### Deduplication | ||
| By default, the pipeline includes a deduplication step after alignment. This is skipped if `--rrbs` or `--nodedup` are specified on the command line. | ||
| 1. [Installation and configuration](docs/installation.md) | ||
| 2. [Running the pipeline](docs/usage.md) | ||
| 3. [Output and how to interpret the results](docs/output.md) | ||
|
|
||
| ### `--bismark_index` | ||
| If you prefer, you can specify the full path to your reference genome when you run the pipeline: | ||
| ``` | ||
| --bismark_index [path to Bismark index] | ||
| ``` | ||
| If you're interested in running the pipeline in the cloud, please read the docs about using our pipeline with Amazon Web Services on the [NGI-RNAseq pipeline](https://github.com/SciLifeLab/NGI-RNAseq/blob/master/docs/amazon_web_services.md) (the instructions should work with this pipeline as well). | ||
|
|
||
| ### `--outdir` | ||
| The output directory where the results will be saved. | ||
| ### Credits | ||
| These scripts were written for use at the [National Genomics Infrastructure](https://portal.scilifelab.se/genomics/) at [SciLifeLab](http://www.scilifelab.se/) in Stockholm, Sweden. Written by Phil Ewels (@ewels) and Rickard Hammarén (@Hammarn). | ||
|
|
||
| ### `-c` | ||
| Specify the path to a specific config file (this is a core NextFlow command). Useful if using different UPPMAX | ||
| projects or different sets of reference genomes. | ||
| --- | ||
|
|
||
| ## Credits | ||
| These scripts were written for use at the [National Genomics Infrastructure](https://portal.scilifelab.se/genomics/) | ||
| at [SciLifeLab](http://www.scilifelab.se/) in Stockholm, Sweden. | ||
| Written by Phil Ewels (@ewels) and Rickard Hammarén (@Hammarn). | ||
| [](http://www.scilifelab.se/) | ||
| [](https://ngisweden.scilifelab.se/) | ||
|
|
||
| <p align="center"><a href="stand_alone/http://www.scilifelab.se/" target="_blank"><img src="docs/images/SciLifeLab_logo.png" title="SciLifeLab"></a></p> | ||
| --- |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Oops, something went wrong.