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tfactivity_help.txt
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$ NXF_SYNTAX_PARSER=v2 nextflow run . --help
N E X T F L O W ~ version 26.03.2-edge
Launching `./main.nf` [serene_franklin] revision: 7e2b36e487
WARN: Unrecognized config option 'validation.defaultIgnoreParams'
WARN: Unrecognized config option 'validation.monochromeLogs'
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tfactivity 0.0.1dev
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Typical pipeline command:
nextflow run nf-core/tfactivity -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>
help message of that parameter will be printed.
or `--helpFull`.
Input/output options
--input [string] Path to comma-separated file containing information about the samples in the experiment.
--input_bam [string] Path to comma-separated file containing information about the BAM files in the experiment.
--counts [string] 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.
--counts_design [string] Path to comma-separated file containing information about the counts file.
--outdir [string] The output directory where the results will be saved. You have to use absolute paths to storage on
Cloud infrastructure.
--email [string] Email address for completion summary.
Expression options
--expression_aggregation [string] Method to aggregate expression values. [default: mean]
--min_count [integer] Minimum number of total counts to keep a gene in the analysis. [default: 50]
--min_tpm [number] Minimum TPM to keep a gene in the analysis. [default: 1]
--min_count_tf [integer] Minimum number of total counts to keep a transcription factor in the analysis. [default: 50]
--min_tpm_tf [number] Minimum TPM to keep a transcription factor in the analysis. [default: 1]
Motif options
--duplicate_motifs [string] 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). (accepted: remove, merge, keep) [default: remove]
Peak merging
--merge_samples [boolean] Merge samples with the same condition and assay.
--min_peak_occurrence [integer] Minimum number of samples that a peak has to occur in to keep it while merging. [default: 1]
Ranking options
--alpha [number] Alpha value for the Mann-Whitney U test. [default: 0.05]
STARE options
--window_size [integer] Size of the window to search for binding sites. [default: 50000]
--decay [boolean] Use decay in STARE [default: true]
--affinity_aggregation [string] Method to aggregate affinity values. (accepted: mean, max, sum) [default: max]
ROSE options
--rose_tss_window [integer] TSS window in base pairs [default: 2500]
--rose_stitching_window [integer] Stichting window in base pairs [default: 12500]
SNEEP options
--sneep_scale_file [string] Path to SNEEP scale file.
--sneep_motif_file [string] Path to SNEEP motif file.
Optional steps
--skip_chromhmm [boolean] Skip chromhmm. This also skips rose automatically since rose requires chromhmm input.
--skip_rose [boolean] Skip rose.
--skip_fimo [boolean] Skip fimo. This also skips sneep automatically since sneep requires fimo input.
--skip_sneep [boolean] Skip sneep.
FIMO options
--fimo_qvalue_threshold [number] Q-value threshold for filtering significant FIMO results. [default: 0.05]
DYNAMITE options
--dynamite_ofolds [integer] Number of outer folds for dynamite. [default: 3]
--dynamite_ifolds [integer] Number of inner folds for dynamite. [default: 6]
--dynamite_alpha [number] Alpha value for dynamite. [default: 0.1]
--dynamite_randomize [boolean] Randomize the data for dynamite. [default: false]
--dynamite_min_regression [number] Minimum regression value for dynamite. [default: 0.1]
ChromHMM options
--chromhmm_states [integer] Number of ChromHMM states. [default: 10]
--chromhmm_threshold [number] Threshold for ChromHMM enhancer detection. [default: 0.75]
--chromhmm_enhancer_marks [string] Comma-separated ChromHMM enhancer marks. [default: H3K27ac,H3K4me1]
--chromhmm_promoter_marks [string] Comma-separated ChromHMM promoter marks. [default: H3K4me3]
Reference genome options
--genome [string] Name of iGenomes reference.
--fasta [string] Path to FASTA genome file.
--gtf [string] Path to GTF gene annotation file.
--blacklist [string] Path to blacklist regions file.
--motifs [string] Path to transcription factor motifs file.
--snps [string] File containing SNPs for organism.
--tflink_file [string] Path to TFLink TF-target interaction table used for annotation.
--taxon_id [integer] NCBI Taxonomy ID.
Generic options
--help [boolean, string] Display the help message.
--help_full [boolean] Display the full detailed help message.
--show_hidden [boolean] Display hidden parameters in the help message (only works when --help or --help_full are provided).
!! Hiding 17 param(s), use the `--showHidden` parameter to show them !!
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* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/tfactivity/blob/master/CITATIONS.md