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Commit b6950062 authored by Phil Ewels's avatar Phil Ewels
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Readme: Fix example commands

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...@@ -15,7 +15,7 @@ ...@@ -15,7 +15,7 @@
This pipeline is based on the This pipeline is based on the
[HiC-Pro workflow](https://github.com/nservant/HiC-Pro). [HiC-Pro workflow](https://github.com/nservant/HiC-Pro).
It was designed to process Hi-C data from raw fastq files (paired-end Illumina It was designed to process Hi-C data from raw FastQ files (paired-end Illumina
data) to normalized contact maps. data) to normalized contact maps.
The current version supports most protocols, including digestion protocols as The current version supports most protocols, including digestion protocols as
well as protocols that do not require restriction enzymes such as DNase Hi-C. well as protocols that do not require restriction enzymes such as DNase Hi-C.
...@@ -50,13 +50,13 @@ ii. Install one of [`docker`](https://docs.docker.com/engine/installation/), ...@@ -50,13 +50,13 @@ ii. Install one of [`docker`](https://docs.docker.com/engine/installation/),
iii. Download the pipeline and test it on a minimal dataset with a single command iii. Download the pipeline and test it on a minimal dataset with a single command
```bash ```bash
nextflow run hic -profile test,<docker/singularity/conda> nextflow run nf-core/hic -profile test,<docker/singularity/conda/institute>
``` ```
iv. Start running your own analysis! iv. Start running your own analysis!
```bash ```bash
nextflow run hic -profile <docker/singularity/conda> --reads '*_R{1,2}.fastq.gz' --genome GRCh37 nextflow run nf-core/hic -profile <docker/singularity/conda/institute> --reads '*_R{1,2}.fastq.gz' --genome GRCh37
``` ```
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.
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