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.
stringEmail 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.
Options for gene expression analysis.
Method to aggregate expression values.
stringmeanMethod to aggregate expression values. The default value is mean.
Minimum number of total counts to keep a gene in the analysis.
integer50Minimum 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.
number1Minimum 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.
integer50Minimum 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.
number1Minimum TPM to keep a transcription factor in the analysis. The default value is 1.
Options for merging peaks across samples.
Merge samples with the same condition and assay.
booleanIf 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.
integer1If 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.
Options for ranking analysis.
Alpha value for the Mann-Whitney U test.
number0.05Alpha value for the Mann-Whitney U test. The default value is 0.05.
Options for STARE (Significance Tool for Accessible Regulatory Elements) analysis.
Size of the window to search for binding sites.
integer50000Size of the window to search for binding sites. The default value is 50000.
Use decay in STARE
booleantrueUse decay in STARE. The default value is true.
Method to aggregate affinity values.
stringmaxMethod to aggregate affinity values. The default value is max.
Options for ROSE (Rank Ordering of Super-Enhancers) analysis.
TSS window in base pairs
integer2500ROSE window size around transcription start sites
Stichting window in base pairs
integer12500ROSE window size for stitching two regions together
Options for SNEEP (SNP Effect on Expression Prediction) analysis.
Path to SNEEP scale file.
stringPath to the scale file used by SNEEP for SNP effect prediction.
Path to SNEEP motif file.
stringPath to the motif file used by SNEEP for SNP effect prediction.
Options to skip specific pipeline steps.
Skip chromhmm. This also skips rose automatically since rose requires chromhmm input.
booleanSkip rose.
booleanSkip fimo. This also skips sneep automatically since sneep requires fimo input.
booleanSkip sneep.
booleanOptions for DYNAMITE analysis.
Number of outer folds for dynamite.
integer3Number of outer folds for dynamite. The default value is 3.
Number of inner folds for dynamite.
integer6Number of inner folds for dynamite. The default value is 6.
Alpha value for dynamite.
number0.1Alpha value for dynamite. The default value is 0.1.
Randomize the data for dynamite.
booleanfalseRandomize the data for dynamite. The default value is false.
Minimum regression value for dynamite.
number0.1Minimum regression value for dynamite. The default value is 0.1.
Options for ChromHMM analysis.
Number of ChromHMM states.
integer10Number of ChromHMM states. The default value is 10.
Threshold for ChromHMM enhancer detection.
number0.75Threshold for ChromHMM enhancer detection. The default value is 0.9.
Comma-separated ChromHMM enhancer marks.
stringH3K27ac,H3K4me1ChromHMM enhancer marks. The default value is H3K27ac.
Comma-separated ChromHMM promoter marks.
stringH3K4me3ChromHMM promoter marks. The default value is H3K4me3.
Reference genome related files and options required for the workflow.
Name of iGenomes reference.
stringIf 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)?$This parameter is mandatory if --genome is not specified. Alternatively, you can use the --taxon_id parameter to fetch the motifs from the JASPAR database.
File containing SNPs for organism.
string^\S+\.(bed.gz)?$This parameter is mandatory if --genome is not specified and --skip_sneep is false.
NCBI Taxonomy ID.
integerThis 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.
booleanDo 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.
The base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf 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.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe 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.
booleanDo not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Boolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string