CLI arguments explained
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--input*
PATH
Beta CSV file or directory containing raw IDAT files and metadata. The pipeline mode (complete or trees-only) will be chosen automatically based on the input.
--output*
PATH
Output identifier. Affects some output file names only.
--patientinfo*
PATH
Path to patient metadata in CSV format. It must be sample-wise, and should indicate the id, and the patient id it belongs to. We recommend to add the sample age, age at diagnosis of the patient and sample type (tumor or normal). The sample sheet could be passed since it matches these requirements.
--luca-mode
TEXT
Should LUCA be fixed to birth or free (recommended when no normals available). PHYFUM selects an option automatically according to the type of samples in the metadata
--patient-col
TEXT
Column name for the patients in the metadata.
--sample-col
TEXT
Column name for the samples in the metadata.
--age-col
TEXT
Column name for the sample age in the metadata.
--age-diagnosis-col
TEXT
Column name for the age at diagnosis in the metadata.
--sample-type-col
TEXT
Column name for the patient id column in the sample sheet.
--fcpgs
TEXT
Set of fCpGs (one per row) to use in the inference step. Skips fCpG calling step. The file should contain a list of CpG sites with their official name (cgXXXXXXXX).
--blacklist
TEXT
Set of fcpgs (one per row) to blacklist. They will be merged with the crossreactive probe set shared here
--cnv
--no-cnv
FLAG
Whether to activate or not CNV calling. Requires both tumor and normal samples. Only available in the complete mode.
--genome-plot
--no-genome-plot
FLAG
Whether to generate CNV genome plots.
--manifest
TEXT
Path to Illumina EPIC manifest CSV file. Default is Infinium MethylationEPIC v1.0 B4 Manifest File
--percent
INTEGER
Float specifying the top percentage of most heterogeneous CpG loci to include when calling fCpGs.
--stemcells
TEXT
Range of stem cells to run Phyfum in the format 'start:end:step'. For example, 3:8:1 will make the inference considering: 3,4,5,6,7,8 stem cells.
--delta
TEXT
Prior for the delta parameter.
--eta
TEXT
Prior for the eta parameter.
--kappa
INTEGER
Prior for the kappa parameter.
--mu
TEXT
Prior for the mu parameter.
--gamma
TEXT
Prior for the gamma parameter.
--lam
TEXT
Prior for the lambda parameter.
--iterations
INTEGER
Number of MCMC iterations.
--precision
INTEGER
Number of significant digits to consider when digitizing the values. Recommended >2 at least.
--sampling
INTEGER
Frequency of sampling in the log file.
--screensampling
INTEGER
Frequency of sampling to print on the screen.
--striprownames
--no-striprownames
FLAG
Activate the flag if the first column are rownames. Necessary if the full workflow is run.
--mle-ps
--no-mle-ps
FLAG
Activates/deactivates the analysis of the MLE samples to estimate the MLE using Path Sampling.
--mle-ss
--no-mle-ss
FLAG
Activates/deactivates the analysis of the MLE samples to estimate the MLE using Stepping Stone.
--hme
--no-hme
FLAG
Activates/deactivates the estimation of the MLE using the Harmonic Mean Estimate.
--mle-steps
INTEGER
Number of power posteriors to use for MLE.
--mle-iterations
INTEGER
Number of MCMC iterations to run in each step. Defaults to MCMC --iterations / --mle-steps.
--mle-sampling
INTEGER
Sampling period for the power-posterior MCMC samplers. Defaults to --iterations / 1000.
--nchains
INTEGER
Number of independent runs to perform with BEAST (recommended 3). The program automatically checks and merges the chains.
--seed
INTEGER
Set a seed for BEAST. Make it negative to inactivate this parameter. If nchain>1, we draw random seeds for each independent run, but using the user seed to keep control of them.
--workdir
PATH
Path to the output directory.
--force/-f
FLAG
Force the execution of the pipeline regardless of already created output.
--dry/-n
FLAG
Do not execute anything, and display what would be done.
--cores/-c
INTEGER
Set the number of cores to use. If None will use all cores.
*Required argument
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