The method pipeline is designed to run with a minimum of three supplied parameters:
* path in which report folder is to be created (-o)
* path to reference target database (-r)
* path to mounted MiSeq folder (-m)
* name of MiSeq run to process (-f)
method.py -o /output/path -r /reference/target/path -m /path/to/miseq -f run name
usage: method.py [-h] -o OUTPUTPATH -r REFERENCEFILEPATH -m MISEQPATH -f
MISEQFOLDER [-n NUMTHREADS] [-d DESTINATIONFASTQ]
[-r1 READLENGTHFORWARD] [-r2 READLENGTHREVERSE]
[-c CUSTOMSAMPLESHEET] [-P PROJECTNAME] [-C]
Perform FASTQ creation and typing
optional arguments:
-h, --help
show this help message and exit
-o, --outputpath OUTPUTPATH
Path to directory in which report folder is to be created
-r, --referencefilepath REFERENCEFILEPATH
Provide the location of the folder containing the target files
-m, --miseqpath MISEQPATH
Path of the folder containing MiSeq run data folder
-f, --miseqfolder MISEQFOLDER
Name of the folder containing MiSeq run data
-n, --numthreads NUMTHREADS
Number of threads. Default is the number of cores in the system
-d, --destinationfastq DESTINATIONFASTQ
Optional folder path to store .fastq files created using the
fastqCreation module. Defaults to outputpath/miseqfolder
-r1, --readlengthforward READLENGTHFORWARD
Length of forward reads to use. Can specify "full" to
take the full length of forward reads specified on the
SampleSheet. Default value is "full"
-r2, --readlengthreverse READLENGTHREVERSE
Length of reverse reads to use. Can specify "full" to
take the full length of reverse reads specified on the
SampleSheet. Default value is "full"
-c, --customsamplesheet CUSTOMSAMPLESHEET
Path of folder containing a custom sample sheet (still
must be named "SampleSheet.csv")
-P, --projectName PROJECTNAME
A name for the analyses. If nothing is provided, then
the "Sample_Project" field in the provided sample
sheet will be used. Please note that bcl2fastq creates
subfolders using the project name, so if multiple
names are provided, the results will be split as into
multiple projects
-C, --copy
Normally, the program will create symbolic links of
the files into the sequence path, however, the are
occasions when it is necessary to copy the files
instead