curl -fsSL get.nextflow.io | bash

$ nextflow pull guigolab/chip-nf
Checking guigolab/chip-nf ...
 downloaded from https://github.com/guigolab/chip-nf.git

$ nextflow run chip-nf --help

N E X T F L O W  ~  version 0.24.1
Launching `guigolab/chip-nf` [nostalgic_franklin] - revision: 974a45c356 [master]

C H I P - N F ~ ChIP-seq Pipeline
---------------------------------
Run ChIP-seq analyses on a set of data.

Usage:
    chipseq-pipeline.nf --index TSV_FILE --genome GENOME_FILE [OPTION]...

Options:
    --help                              Show this message and exit.
    --index TSV_FILE                    Tab separted file containing information about the data.
    --genome GENOME_FILE                Reference genome file.
    --genome-index GENOME_INDEX_ FILE   Reference genome index file.
    --genome-size GENOME_SIZE           Reference genome size for MACS2 callpeaks. Must be one of
                                        MACS2 precomputed sizes: hs, mm, dm, ce. (Default: hs)
    --mismatches MISMATCHES             Sets the maximum number/percentage of mismatches allowed for a read (Default: 2).
    --multimaps MULTIMAPS               Sets the maximum number of mappings allowed for a read (Default: 10).
    --min-matched-bases BASES           Sets the minimum number/percentage of bases that have to match with the reference (Default: 0.80).
    --quality-threshold THRESHOLD       Sets the sequence quality threshold for a base to be considered as low-quality (Default: 26).
    --fragment-length LENGTH            Sets the fragment length globally for all samples (Default: 200).
    --remove-duplicates                 Remove duplicate alignments instead of just flagging them (Default: false).
    --rescale                           Rescale peak scores to conform to the format supported by the
                                        UCSC genome browser (score must be <1000) (Default: false).
    --shift                             Move fragments ends and apply global extsize in peak calling. (Default: false).

sample1    sample1_run1     /path/to/sample1_run1.fastq.gz    -           H3
sample1    sample1_run2     /path/to/sample1_run2.fastq.gz    -           H3
sample1    sample1_run3     /path/to/sample1_run3.fastq.gz    -           H3
sample1    sample1_run4     /path/to/sample1_run4.fastq.gz    -           H3
sample2    sample2_run1     /path/to/sample2_run1.fastq.gz    control1    H3K4me2
control1   control1_run1    /path/to/control1_run1.fastq.gz   control1    input

sample1   /path/to/results/peakOut/sample1.pileup_signal.bw    H3         255     pileupSignal    0.9960   0.4393
sample1   /path/to/results/peakOut/sample1_peaks.narrowPeak    H3         255     narrowPeak      0.9960   0.4393
sample1   /path/to/results/sample1.bam                         H3         255     Alignments      0.9960   0.4393
sample1   /path/to/results/peakOut/sample1_peaks.gappedPeak    H3         255     gappedPeak      0.9960   0.4393
sample1   /path/to/results/peakOut/sample1_peaks.broadPeak     H3         255     broadPeak       0.9960   0.4393
sample2   /path/to/results/peakOut/sample2_peaks.gappedPeak    H3K4me2    200     gappedPeak      0.9995   0.7216
sample2   /path/to/results/peakOut/sample2.fc_signal.bw        H3K4me2    200     fcSignal        0.9995   0.7216
sample2   /path/to/results/peakOut/sample2.pval_signal.bw      H3K4me2    200     pvalueSignal    0.9995   0.7216
sample2   /path/to/results/peakOut/sample2_peaks.broadPeak     H3K4me2    200     broadPeak       0.9995   0.7216
sample2   /path/to/results/peakOut/sample2.pileup_signal.bw    H3K4me2    200     pileupSignal    0.9995   0.7216
sample2   /path/to/results/peakOut/sample2_peaks.narrowPeak    H3K4me2    200     narrowPeak      0.9995   0.7216
sample2   /path/to/results/sample2_GCCAAT_primary.bam          H3K4me2    200     Alignments      0.9995   0.7216