nf-core/tfactivity
Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.
Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about the samples in the experiment.
string
^\S+\.csv$
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. See usage docs.
Path to comma-separated file containing information about the BAM files in the experiment.
string
^\S+\.csv$
You will need to create a design file with information about the BAM files in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 4 columns, and a header row. See usage docs.
Path to comma-separated file containing the counts for the samples in the experiment. Can also be a file containing just gene identifiers. In this case, count values need to be referenced in the counts_design file.
string
^\S+\.(csv|txt)$
You will need to create a counts file with the counts for 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 a header row. See usage docs.
Path to comma-separated file containing information about the counts file.
string
^\S+\.csv$
You will need to create a counts design file with information about the counts file 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. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Email address for completion summary.
string
^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$
Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config
) then you don't need to specify this on the command line for every run.
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
string
Options for the pipeline itself.
Merge samples with the same condition and assay.
boolean
If you have multiple samples with the same condition and assay, you can set this parameter to true
to merge them into a single sample. This is useful if you have technical replicates and want to combine them into a single sample for analysis.
Minimum number of samples that a peak has to occur in to keep it while merging.
integer
1
If you have multiple samples with the same condition and assay and use the --merge_samples
parameter, you can set this parameter to the minimum number of samples that a peak has to occur in to keep it while merging.
Size of the window to search for binding sites.
integer
50000
Size of the window to search for binding sites. The default value is 50000.
Use decay in STARE
boolean
true
Use decay in STARE. The default value is true
.
Method to aggregate expression values.
string
mean
Method to aggregate expression values. The default value is mean
.
Method to aggregate affinity values.
string
max
Method to aggregate affinity values. The default value is max
.
Number of ChromHMM states.
integer
10
Number of ChromHMM states. The default value is 10.
Threshold for ChromHMM enhancer detection.
number
0.75
Threshold for ChromHMM enhancer detection. The default value is 0.9.
Comma-separated ChromHMM enhancer marks.
string
H3K27ac,H3K4me1
ChromHMM enhancer marks. The default value is H3K27ac
.
Comma-separated ChromHMM promoter marks.
string
H3K4me3
ChromHMM promoter marks. The default value is H3K4me3
.
TSS window in base pairs
integer
2500
ROSE window size around transcription start sites
Stichting window in base pairs
integer
12500
ROSE window size for stitching two regions together
Minimum number of total counts to keep a gene in the analysis.
integer
50
Minimum number of total counts to keep a gene in the analysis. The default value is 50.
Minimum TPM to keep a gene in the analysis.
number
1
Minimum TPM to keep a gene in the analysis. The default value is 1.
Minimum number of total counts to keep a transcription factor in the analysis.
integer
50
Minimum number of total counts to keep a transcription factor in the analysis. The default value is 50.
Minimum TPM to keep a transcription factor in the analysis.
number
1
Minimum TPM to keep a transcription factor in the analysis. The default value is 1.
Number of outer folds for dynamite.
integer
3
Number of outer folds for dynamite. The default value is 3.
Number of inner folds for dynamite.
integer
6
Number of inner folds for dynamite. The default value is 6.
Alpha value for dynamite.
number
0.1
Alpha value for dynamite. The default value is 0.1.
Randomize the data for dynamite.
boolean
false
Randomize the data for dynamite. The default value is false
.
Minimum regression value for dynamite.
number
0.1
Minimum regression value for dynamite. The default value is 0.1.
Alpha value for the Mann-Whitney U test.
number
0.05
Alpha value for the Mann-Whitney U test. The default value is 0.05.
Reference genome related files and options required for the workflow.
Name of iGenomes reference.
string
If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38
.
See the nf-core website docs for more details.
Path to FASTA genome file.
string
^\S+\.fn?a(sta)?(\.gz)?$
This parameter is mandatory if --genome
is not specified.
Path to GTF gene annotation file.
string
^\S+\.gtf(\.gz)?$
This parameter is mandatory if --genome
is not specified.
Path to blacklist regions file.
string
^\S+\.bed(\.gz)?$
This parameter is mandatory if --genome
is not specified.
Path to transcription factor motifs file.
string
^\S+\.(cisbp|homer|jaspar|meme|transfac|uniprobe)?$
This parameter is mandatory if --genome
is not specified. Alternatively, you can use the --taxon_id
parameter to fetch the motifs from the JASPAR database.
NCBI Taxonomy ID.
integer
This parameter is mandatory if --genome
and --motifs
are not specified. Use this parameter to fetch the motifs from the JASPAR database.
Do not load the iGenomes reference config.
boolean
Do not load igenomes.config
when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config
.
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer
16
Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string
128.GB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
Maximum amount of time that can be requested for any single job.
string
240.h
^(\d+\.?\s*(s|m|h|d|day)\s*)+$
Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Less common options for the pipeline, typically set in a config file.
Display help text.
boolean
Display version and exit.
boolean
Method used to save pipeline results to output directory.
string
The Nextflow publishDir
option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string
^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$
An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
string
Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Show all params when using --help
boolean
By default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help
. Specifying this option will tell the pipeline to show all parameters.
Validation of parameters fails when an unrecognised parameter is found.
boolean
By default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
boolean
Allows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.
Base URL or local path to location of pipeline test dataset files
string
https://raw.githubusercontent.com/nf-core/test-datasets/