Parameters¶
All the parameters of the pipeline, generated from the parameter schema (nextflow_schema.json) used to validate them when the pipeline starts. See the usage page for how the parameters work together, e.g. which reference each deconvolution tool uses.
The parameters can be given on the command line (e.g. --meth_atlas) or in a parameters file (-params-file params.yaml). Parameters hidden in the help message (--help) are not listed.
Input/output options¶
Define where the pipeline should find input data and save output data.
| Parameter | Description | Type | Default | Required |
|---|---|---|---|---|
--input |
Path to comma-separated file containing information about the reference samples. You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. |
string |
||
--ref_matrix |
The path of the reference matrix that you want to use for ref-based deconvolution. | string |
||
--celfie_ref_matrix |
The path of the reference matrix of read counts used by CelFiE instead of the reference samples. Tab-separated file with the columns chr, start and end, followed by a '<cell type>_meth' and a '<cell type>_depth' column (methylated and total read counts) per cell type. |
string |
||
--metdecode_ref_matrix |
The path of the reference matrix of read counts used by MetDecode instead of the reference samples. Tab-separated file with the columns chr, start and end, followed by a '<cell type>_meth' and a '<cell type>_depth' column (methylated and total read counts) per cell type. |
string |
||
--outdir |
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. | string |
yes | |
--storedir |
The store directory where the results are saved. You have to use absolute paths to storage on Cloud infrastructure. | string |
||
--bulk_samples |
Path to comma-separated file containing information about the samples to deconvolve. You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. |
string |
yes | |
--ground_truth |
Path to comma-separated file with the expected cell type proportions of the bulk samples, to evaluate the reference-based tools. Optional. One row per bulk sample: a 'sample' column with the names used in the bulk samplesheet, followed by one column per cell type of the reference with the expected proportions (between 0 and 1). If provided, the report includes the MSE, RMSE and Spearman correlation of each reference-based tool. |
string |
Intermediate files options¶
Less common options for the pipeline, typically set in a config file.
| Parameter | Description | Type | Default | Required |
|---|---|---|---|---|
--save_intermeds |
Save intermediate files. | boolean |
false |
Deconvolution tools¶
| Parameter | Description | Type | Default | Required |
|---|---|---|---|---|
--benchmark |
If True, it runs all the tools present in the pipeline | boolean |
||
--epidish |
Run the corresponding tool | boolean |
||
--houseman_eq |
Run the corresponding tool | boolean |
||
--houseman_ineq |
Run the corresponding tool | boolean |
||
--methyl_resolver |
Run the corresponding tool | boolean |
||
--episcore |
Run the corresponding tool | boolean |
||
--prmeth |
Run the corresponding tool | boolean |
||
--ref_freecell_mix |
Run the corresponding tool | boolean |
||
--medecom |
Run the corresponding tool | boolean |
||
--celfie |
Run the corresponding tool | boolean |
||
--meth_atlas |
Run the corresponding tool | boolean |
||
--cibersort |
Run the corresponding tool | boolean |
||
--metdecode |
Run the corresponding tool | boolean |
Options for the preprocessing of the reference samples¶
| Parameter | Description | Type | Default | Required |
|---|---|---|---|---|
--min_counts |
Minimum number of counts to keep a CpG position | integer |
10 |
|
--min_cpgs |
Minimum number of CpGs per region | integer |
3 |
Options for the preprocessing for bulk samples.¶
| Parameter | Description | Type | Default | Required |
|---|---|---|---|---|
--bulk_min_cpgs |
Minimum number of counts to keep a CpG position for the bulk samples. | integer |
0 |
|
--bulk_min_counts |
Minimum number of CpGs per region for the bulk samples. | integer |
0 |
DMR analysis general options¶
| Parameter | Description | Type | Default | Required |
|---|---|---|---|---|
--adjp |
Adjusted p-value threshold | number |
0.001 |
|
--min_delta_beta |
Minimum absolute delta beta of a DMR. Difference in mean methylation between a cell type and the other cell types, from 0 to 1. DMRs passing the adjusted p-value threshold (--adjp) but with a smaller difference are removed. 0 disables the filter. Minimum: 0. |
number |
0 |
|
--collapse_method |
Method to collapse the sample values for each region Allowed values: mean, median |
string |
mean |
|
--direction |
Direction of methylation. Allowed values: hypo, hyper, both, random |
string |
both |
|
--top |
Take the top x number of DMRs per cell state. Default is "None". It can be used only if "direction" flag is specified. Minimum: 1. |
integer |
Limma options¶
| Parameter | Description | Type | Default | Required |
|---|---|---|---|---|
--regions |
Path to the region file used for limma DMR selection and reference-free deconvolution. | string |
||
--cgi_genome |
Genome whose CpG islands are used as regions when no regions file (--regions) is provided. The CpG islands are downloaded from UCSC (cpgIslandExt table of the given assembly), converted to the 1-based coordinates used by the pipeline and restricted to the primary chromosomes. Ignored if --regions is given. Allowed values: hg19, hg38, mm10, mm39 |
string |
||
--adj_method |
Multiple testing correction method among the ones available in limma R package Allowed values: holm, hochberg, hommel, bonferroni, BH, BY, fdr, none |
string |
BH |
|
--include_na |
When merging samples for limma DMR analysis, include the regions even if some samples have missing values | boolean |
false |
Reference-free deconvolution options.¶
| Parameter | Description | Type | Default | Required |
|---|---|---|---|---|
--clusters |
Number of cell types expected (necessary for ref-free modality) Minimum: 2. |
integer |
2 |
MeDeCom parameters¶
| Parameter | Description | Type | Default | Required |
|---|---|---|---|---|
--ninit |
Number of random initializations | integer |
10 |
|
--nfold |
Number of folds for CV | integer |
10 |
|
--itermax |
Max number of iterations | integer |
300 |
EpiSCORE parameters¶
| Parameter | Description | Type | Default | Required |
|---|---|---|---|---|
--weight |
Weight parameter used for deconvolution (can go from 0.05 to 0.9) | number |
0.4 |
MethylResolver parameters¶
| Parameter | Description | Type | Default | Required |
|---|---|---|---|---|
--alpha |
Alpha parameter used by the model (can go from 0.5 to 0.9) | number |
0.5 |
PRMeth parameters¶
| Parameter | Description | Type | Default | Required |
|---|---|---|---|---|
--prmeth_mod |
PRMeth deconv modality QP is reference-based, NMF is partially reference-based. Allowed values: QP, NMF |
string |
QP |
|
--prmeth_NMF_entities |
PRMeth number of entities when using NMF | integer |
3 |
CelFiE parameters¶
| Parameter | Description | Type | Default | Required |
|---|---|---|---|---|
--celfie_maxiter |
How long the EM should iterate before stopping, unless convergence criteria is met | integer |
1000 |
|
--unknown |
Number of unknown categories to be estimated along with the reference data | integer |
0 |
|
--parall_job |
Replicate number in a simulation experiment | integer |
1 |
|
--converg |
Convergence criteria for EM | number |
0.0001 |
|
--celfie_randrest |
CelFiE will perform several random restarts and select the one with the highest log-likelihood | integer |
10 |
MetDecode parameters¶
| Parameter | Description | Type | Default | Required |
|---|---|---|---|---|
--unknown_tissues |
Number of unknown entities. | integer |
||
--sum1 |
If specified, it makes the sum of the proportions to 1. | boolean |
||
--no_coverage |
Disable CpG coverage factor. | boolean |
||
--supervised |
Disable the unsupervised refinment of the proportions. | boolean |
Generic options¶
Less common options for the pipeline, typically set in a config file.
| Parameter | Description | Type | Default | Required |
|---|---|---|---|---|
--help |
Display the help message. | ['boolean', 'string'] |
||
--help_full |
Display the full detailed help message. | boolean |
||
--show_hidden |
Display hidden parameters in the help message (only works when --help or --help_full are provided). | boolean |