{% if is_nfcore -%}
{% else -%}
{% endif -%}
{% if github_badges -%}
{% if codespaces %}[
{% endif -%}
{%- if is_nfcore -%}[](https://nfcore.slack.com/channels/{{ short_name }}){% endif -%}
{%- if is_nfcore -%}
{% endif -%}
{{ name }} is a bioinformatics pipeline that ...
{%- if fastqc %}1. Read QC (FastQC){% endif %}
{%- if multiqc %}2. Present QC for raw reads (MultiQC){% endif %}
Note
If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. {% if test_config %}Make sure to test your setup with -profile test before running the workflow on actual data.{% endif %}
Now, you can run the pipeline using:
nextflow run {{ name }} \
-profile <docker/singularity/.../institute> \
--input samplesheet.csv \
--outdir <OUTDIR>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.
{% if is_nfcore -%}
For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/{{ short_name }}/usage) and the [parameter documentation](https://nf-co.re/{{ short_name }}/parameters).
To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/{{ short_name }}/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/{{ short_name }}/output).
{% endif -%}
{{ name }} was originally written by {{ author }}.
We thank the following people for their extensive assistance in the development of this pipeline:
If you would like to contribute to this pipeline, please see the contributing guidelines.
{% if is_nfcore -%}
For further information or help, don't hesitate to get in touch on the [Slack #{{ short_name }} channel](https://nfcore.slack.com/channels/{{ short_name }}) (you can join with this invite).
{% endif -%}
{% if citations %}
An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.
{%- endif %}
{% if is_nfcore -%}
You can cite the nf-core publication as follows:
{% else -%} This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.
{% endif -%}
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.