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$Path to comma-separated file containing information about the BAM files in the experiment.
string^\S+\.csv$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)$Path to comma-separated file containing information about the counts file.
string^\S+\.csv$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})$Options for gene expression analysis.
Method to aggregate expression values.
stringmeanMinimum number of total counts to keep a gene in the analysis.
integer50Minimum TPM to keep a gene in the analysis.
number1Minimum number of total counts to keep a transcription factor in the analysis.
integer50Minimum TPM to keep a transcription factor in the analysis.
number1Options for motif workflow
Specifies how to handle duplicate motifs. Available options are remove (only keep first occurrence of motif), merge (average motifs with same symbol), and keep (keep all motifs and adjust background during statistical testing).
stringOptions for merging peaks across samples.
Merge samples with the same condition and assay.
booleanMinimum number of samples that a peak has to occur in to keep it while merging.
integer1Options for ranking analysis.
Alpha value for the Mann-Whitney U test.
number0.05Options for STARE (Significance Tool for Accessible Regulatory Elements) analysis.
Size of the window to search for binding sites.
integer50000Use decay in STARE
booleantrueMethod to aggregate affinity values.
stringOptions for ROSE (Rank Ordering of Super-Enhancers) analysis.
TSS window in base pairs
integer2500Stichting window in base pairs
integer12500Options for SNEEP (SNP Effect on Expression Prediction) analysis.
Path to SNEEP scale file.
stringPath to SNEEP motif file.
stringOptions 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 inner folds for dynamite.
integer6Alpha value for dynamite.
number0.1Randomize the data for dynamite.
booleanfalseMinimum regression value for dynamite.
number0.1Options for ChromHMM analysis.
Number of ChromHMM states.
integer10Threshold for ChromHMM enhancer detection.
number0.75Comma-separated ChromHMM enhancer marks.
stringH3K27ac,H3K4me1Comma-separated ChromHMM promoter marks.
stringH3K4me3Reference genome related files and options required for the workflow.
Name of iGenomes reference.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Path to GTF gene annotation file.
string^\S+\.gtf(\.gz)?$Path to blacklist regions file.
string^\S+\.bed(\.gz)?$Path to transcription factor motifs file.
string^\S+\.(cisbp|homer|jaspar|meme|transfac|uniprobe)?$File containing SNPs for organism.
string^\S+\.(bed.gz)?$NCBI Taxonomy ID.
integerDo not load the iGenomes reference config.
booleanThe 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/masterInstitutional 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.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanDo not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringBoolean 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