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.
Usage:
nextflow run tiagofilipe12/pATLAS_mash_screen.nf
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 mash screen 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
nextflow run tiagofilipe12/pATLAS_auxiliary_scripts --assembly