/nf-core-practice

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nf-core/practice nf-core/practice

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Nextflow run with conda run with docker run with singularity Launch on Nextflow Tower

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Introduction

nf-core/practice is a way for my to get used to utilizing NF-CORE's create function

I have no figure to add ere.

With this tutoria I would ultimately like to:

  • write a readme for practice
  • link to the repository in github
  • write a readme for SYLENS

Usage

:::note If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data. :::

Thiswill be helpful when I work on sylen' nextflow/nf-core. This will help determine if queries are single or paired files.

Now, you can run the pipeline using:

We will be using sylens through a docker image

nextflow run nf-core/practice \
   -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. :::

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

Credits

nf-core/practice was originally written by eva gunawan.

Kelsey and CJ because I'm not great at coding yet!

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on the Slack #practice channel (you can join with this invite).

Citations

perhaps one day, but not for this practice session!

An extensive list of references for the tools used by the pipeline can be found in the 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.