PEPATAC usage reference

PEPATAC command-line usage instructions:

python pipelines/ --help

usage: [-h] [-R] [-N] [-D] [-F] [-T] [--silent] [--verbosity V]
                  [--logdev] [-C CONFIG_FILE] [-O PARENT_OUTPUT_FOLDER]
                  [-M MEMORY_LIMIT] [-P NUMBER_OF_CORES] [-S SAMPLE_NAME] -I
                  INPUT_FILES [INPUT_FILES ...]
                  [-I2 [INPUT_FILES2 [INPUT_FILES2 ...]]] -G GENOME_ASSEMBLY
                  [-Q SINGLE_OR_PAIRED]
                  [--trimmer {trimmomatic,pyadapt,skewer}]
                  [--aligner {bowtie2,bwa}]
                  [--deduplicator {picard,samblaster,samtools}]
                  [--peak-caller {fseq,fseq2,genrich,hmmratac,homer,macs2}]
                  [-gs GENOME_SIZE] [--peak-type {fixed,variable}]
                  [--extend EXTEND] [--frip-ref-peaks FRIP_REF_PEAKS]
                  [--motif] [--sob] [--no-scale] [--prioritize] [--keep]
                  [--noFIFO] [--lite] [--skipqc]
                  [--prealignment-names PREALIGNMENT_NAMES [PREALIGNMENT_NAMES ...]]
                  [--prealignment-index PREALIGNMENT_INDEX [PREALIGNMENT_INDEX ...]]
                  --genome-index GENOME_INDEX --chrom-sizes CHROM_SIZES
                  [--TSS-name TSS_NAME] [--blacklist BLACKLIST]
                  [--anno-name ANNO_NAME] [--search-file SEARCH_FILE] [-V]

PEPATAC version 0.10.3

optional arguments:
  -h, --help            show this help message and exit
  -R, --recover         Overwrite locks to recover from previous failed run
  -N, --new-start       Overwrite all results to start a fresh run
  -D, --dirty           Don't auto-delete intermediate files
  -F, --force-follow    Always run 'follow' commands
  -T, --testmode        Only print commands, don't run
  --silent              Silence logging. Overrides verbosity.
  --verbosity V         Set logging level (1-5 or logging module level name)
  --logdev              Expand content of logging message format.
                        Pipeline configuration file (YAML). Relative paths are
                        with respect to the pipeline script.
                        Parent output directory of project
                        Memory limit for processes accepting such. Default
                        units are megabytes unless specified using the suffix
                        Number of cores for parallelized processes
  -S SAMPLE_NAME, --sample-name SAMPLE_NAME
                        Name for sample to run
  -I2 [INPUT_FILES2 [INPUT_FILES2 ...]], --input2 [INPUT_FILES2 [INPUT_FILES2 ...]]
                        Secondary input files, such as read2
  -Q SINGLE_OR_PAIRED, --single-or-paired SINGLE_OR_PAIRED
                        Single- or paired-end sequencing protocol
  --trimmer {trimmomatic,pyadapt,skewer}
                        Name of read trimming program.
  --aligner {bowtie2,bwa}
                        Name of read aligner.
  --deduplicator {picard,samblaster,samtools}
                        Name of deduplicator program.
  --peak-caller {fseq,fseq2,genrich,hmmratac,homer,macs2}
                        Name of peak caller.
  -gs GENOME_SIZE, --genome-size GENOME_SIZE
                        Effective genome size. It can be 1.0e+9 or 1000000000:
                        e.g. human (2.7e9), mouse (1.87e9), C. elegans (9e7),
                        fruitfly (1.2e8). Default:2.7e9
  --peak-type {fixed,variable}
                        Call variable or fixed width peaks. Fixed width
                        requires MACS2.
  --extend EXTEND       How far to extend fixed width peaks up and downstream.
  --frip-ref-peaks FRIP_REF_PEAKS
                        Path to reference peak set (BED format) for
                        calculating FRiP.
  --motif               Perform motif enrichment analysis.
  --sob                 Use seqOutBias to produce signal tracks, incorporate
                        mappability information, and account for Tn5 bias.
  --no-scale            Do not scale signal tracks: Default is to scale by
                        read count. If using seqOutBias, scales by the
                        expected/observed cut frequency.
  --prioritize          Plot cFRiF/FRiF using mutually exclusive priority
                        ranked features based on the order of feature
                        appearance in the feature annotation asset.
  --keep                Enable this flag to keep prealignment BAM files.
  --noFIFO              Do NOT use named pipes during prealignments.
  --lite                Only keep minimal, essential output to conserve disk
  --skipqc              Skip FastQC. Useful for bugs in FastQC that appear
                        with some sequence read files.
                        Space-delimited list of prealignment genome names to
                        align to before primary alignment.
                        Space-delimited list of prealignment genome name and
                        index files delimited by an equals sign to align to
                        before primary alignment. e.g.
  --genome-index GENOME_INDEX
                        Path to primary genome index file. Either a bowtie2 or
                        bwa index.
  --chrom-sizes CHROM_SIZES
                        Path to primary genome chromosome sizes file.
  --TSS-name TSS_NAME   Path to TSS annotation file.
  --blacklist BLACKLIST
                        Path to genomic region blacklist file.
  --anno-name ANNO_NAME
                        Path to reference annotation file (BED format) for
                        calculating FRiF.
  --search-file SEARCH_FILE
                        Required for seqOutBias (--sob). Path to tallymer
                        index search file built with the same read length as
                        the input.
  -V, --version         show program's version number and exit

required named arguments:
                        One or more primary input files
                        Identifier for genome assembly