pATLASflow

A pipeline to run mapping, mash screen and assembly methods for pATLAS.

TOC

• Brief description
• Requirements
  • Conda recipe for nextflow
• Usage
• Example run
• TL;DR

TL;DR

1. Read files must be placed in <current working dir>/reads/ folder

2. Fasta files must be placed in <current working dir>/fasta/ folder

3. Run the pipeline nextflow run tiagofilipe12/pATLASflow with the options you require:

   • Assembly: nextflow run tiagofilipe12/pATLASflow --assembly
   • Mapping: nextflow run tiagofilipe12/pATLASflow --mapping
   • Mash screen: nextflow run tiagofilipe12/pATLASflow --mash_screen

   Note: you can even run all approaches by doing: nextflow run tiagofilipe12/pATLASflow --assembly --mapping --mash_screen

Brief description

This Nextflow script is an implementation of mash-wrapper for mash screen module. It will output a JSON file that can be imported into pATLAS.

Requirements

First of all, pATLASflow is a Nextflow pipeline and thus does not require the installation of third party programs since they are provided through docker container that can be used both with singularity and docker.

• Java 8 or higher.
• Docker or Singularity.
• Nextflow - follow the two installation steps (there is no need to read anything else).

Conda recipe for nextflow

If you prefer you can use this conda recipe for nextflow:

conda install nextflow

Usage

Usage: nextflow run tiagofilipe12/pATLASflow [options] or nextflow run main.nf [options] or ./main.nf [options]

  Nextflow magic options:
       -profile    Forces nextflow to run with docker or singularity.   Default: standard     Choices: standard, singularity, slurm
   Main options:
       --help  Opens this help. It will open only when --help is provided. So, yes, this line is pretty useless since you already know that if you reached here.
       --version   Prints the version of the pipeline script.
       --mash_screen   Enables mash screen run.
       --assembly  Enables mash dist run to use fasta file against plasmid db
       --mapping   Enables mapping pipeline.
   Mash options:
       --kMer  the length of the kmer to be used by mash.   Default: 21
       --pValue    The p-value cutoff. Default: 0.05
   Mash screen exclusive options:
       --identity  The minimum identity value between two sequences. Default: 0.9
       --noWinner  This option allows to disable the -w option of mash screen  Default: false
   Mash dist exclusive options:
       --mash_distance     Provide the maximum distance between two plasmids to be reported.   Default: 0.1
   Reads options:
       --reads The path to the read files. Here users may provide many samples in the same directory. However be assured that glob pattern is unique (e.g. 'path/to/*_{1,2}.fastq').
       --singleEnd Provide this option if you have single-end reads. By default the pipeline will assume that you provide paired-end reads.    Default: false
   Fasta options:
       --fasta     Provide fasta file pattern to be searched by nextflow.  Default: 'fasta/*.fas'
   Bowtie2 options:
       --trim5     Provide parameter -5 to bowtie2 allowing to trim 5' end.    Default: 0
       --cov_cutoff    Provide a cutoff value to filter results for coverage results.  Default: 0.60

Example run

nextflow run tiagofilipe12/pATLASflow --assembly

Slurm profile

One can run this pipeline using the slurm profile, which enalbes to use it with shifter and slurm.

IMM-lobo users

In order to avoid the usage of compute-1 you need to uncomment line 62 in nextflow.config file.

Results

Results will be placed in a folder named results within the current working directory.