A pipeline to run mash screen for pATLAS.
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.
- Java 8 or higher.
- Docker or Singularity.
- Nextflow - follow the two installation steps (there is no need to read anything else).
If you prefer you can use this conda recipe for nextflow:
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: docker Choices: standard, singularity
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.
--threads Number of threads that the pipeline will have to run. Default: 1
--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:
--max_k Provide the maximum number of alignments allowed per read. Default: 10949 (the number of plasmids present in pATLAS)
--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
nextflow run tiagofilipe12/pATLASflow --assembly
-
Read files must be placed in
<current working dir>/reads/folder -
Fasta files must be placed in
<current working dir>/fasta/folder -
Run the pipeline
nextflow run tiagofilipe12/pATLASflowwith 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 - Assembly: