Introduction

nf-core/fspassemblypipeline is a bioinformatics pipeline that ...

1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))

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.

Required inputs

Pre-dowloaded BUSCO lineages

To run BUSCO using a lineage closely related to each of the samples, we need to input a list of available busco lineages, and to download them beforehand. This can be achieved as follows:

cd to/where/you/want/to/store/busco/databases

conda activate busco

busco --list > busco_lineages.txt

gawk '/fungi_odb12/{flag=1; indent=length($0)-length(ltrim($0)); print "fungi_odb12"; next}
     flag && /- [a-z_]*_odb12/ {
         current_indent=length($0)-length(ltrim($0))
         if(current_indent <= indent) flag=0
         else print gensub(/.*- ([a-z_]*_odb12).*/, "\\1", "g")
     }
     function ltrim(s) { sub(/^[ \t\r\n]+/, "", s); return s }' busco_lineages.txt > fungi_busco_lineages.txt

In the example above we are extracting the names of all the BUSCO lineages that belong to the fungi kingdom. The target group can be different and its taxonomic level doesn't matter. The user can for example target eukaryota or something more specific like basidiomycota using the same code. Note that odb12 extension refers to a specific version of BUSCO lineages, and it can be changed when newer versions will be available.

fungi_busco_lineages.txt and the extension must to be provided through the nextflow.config:

    busco_db_extension         = 'odb12'
    lineages_list_file         = 'path/to/fungi_busco_lineages.txt'

Using the list of lineages of interest we can then easily download all of them in one go:

for i in $(cat fungi_busco_lineages.txt); do
  echo "downloading $i database"
  busco --download_path . --download $i
done

This speeds up the pipeline as it will not have to download busco lineages on the fly, and will avoid connection problems during the run.

We also need to provide the path to where busco lineages are downloaded in nextflow.config:

    busco_lineages_path        = 'path/to/lineages/parent/directory'

Note that BUSCO automatically downloads lineages in a directory called lineages. In nextflow.config we need to provide the path to the parent directory of lineages. This needs to be the full absolute path.

Run the pipeline

Now, you can run the pipeline using:

nextflow run nf-core/fspassemblypipeline \
   -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/fspassemblypipeline was originally written by Lia Obinu, Niall Garvey, Wu Huang, Chris Wyatt, Fernando Duarte Frutos.

We thank the following people for their extensive assistance in the development of this pipeline:

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 #fspassemblypipeline channel (you can join with this invite).

Citations

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.