PEPPRO usage reference

PEPPRO 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
                 INPUT_FILES [INPUT_FILES ...]
                 [-I2 [INPUT_FILES2 [INPUT_FILES2 ...]]] -G GENOME_ASSEMBLY
                 [-Q SINGLE_OR_PAIRED]
                 [--protocol {PRO,pro,PRO-SEQ,PRO-seq,proseq,PROSEQ,GRO,gro,groseq,GROSEQ,GRO-SEQ,GRO-seq}]
                 [--adapter-tool {cutadapt,fastp}]
                 [--dedup-tool {seqkit,fqdedup}]
                 [--trimmer-tool {seqtk,fastx}] [--umi-len UMI_LEN]
                 [--max-len MAX_LEN] [--sob] [--scale]
                 [--prealignment-names PREALIGNMENT_NAMES [PREALIGNMENT_NAMES ...]]
                 [--prealignment-index PREALIGNMENT_INDEX [PREALIGNMENT_INDEX ...]]
                 --genome-index GENOME_INDEX [--fasta FASTA] --chrom-sizes
                 CHROM_SIZES [--TSS-name TSS_NAME] [--pi-tss ENSEMBL_TSS]
                 [--pi-body ENSEMBL_GENE_BODY] [--pre-name PRE_NAME]
                 [--anno-name ANNO_NAME] [--exon-name EXON_NAME]
                 [--intron-name INTRON_NAME] [--search-file SEARCH_FILE]
                 [--coverage] [--keep] [--keep-mito] [--noFIFO]
                 [--no-complexity] [--prioritize] [-V]

PEPPRO version 0.10.1

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.
                        Memory limit for processes accepting such. Default
                        units are megabytes unless specified using the suffix
                        Number of cores for parallelized processes
  -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
  --protocol {PRO,pro,PRO-SEQ,PRO-seq,proseq,PROSEQ,GRO,gro,groseq,GROSEQ,GRO-SEQ,GRO-seq}
                        Run on sequencing type.
  --adapter-tool {cutadapt,fastp}
                        Name of adapter removal program. Default: cutadapt
  --dedup-tool {seqkit,fqdedup}
                        Program to use to duplicate reads. Default: seqkit
  --trimmer-tool {seqtk,fastx}
                        Name of read trimming program. Default: seqtk
  --umi-len UMI_LEN     Specify the length of the UMI.If your data does not
                        utilize UMIs, set to 0. Default: 0
  --max-len MAX_LEN     Trim reads to maximum length. Set to -1 to disable
                        length trimming. Default: -1
  --sob                 Use seqOutBias to produce signal tracks and
                        incorporate mappability information.
  --scale               Scale signal tracks: Default is to scale by read
                        count. If using seqOutBias, scales by the
                        expected/observed cut frequency.
                        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 bowtie2 primary genome index file.
  --fasta FASTA         Path to primary genome fasta file. Required with
  --chrom-sizes CHROM_SIZES
                        Path to primary genome chromosome sizes file.
  --TSS-name TSS_NAME   file_name of TSS annotation file.
  --pi-tss ENSEMBL_TSS  file_name of pause index TSS annotation file.
                        file_name of pause index gene body annotation file.
  --pre-name PRE_NAME   file_name of pre-mRNA annotation file.
  --anno-name ANNO_NAME
                        file_name of genomic annotation file.
  --exon-name EXON_NAME
                        file_name of exon annotation file.
  --intron-name INTRON_NAME
                        file_name of intron annotation file.
  --search-file SEARCH_FILE
                        Required for seqOutBias (--sob). Path to tallymer
                        index search file built with the same read length as
                        the input.
  --coverage            Report library complexity using coverage: reads /
                        (bases in genome / read length)
  --keep                Keep prealignment BAM files.
  --keep-mito           Keep mitochondrial aligning reads.
  --noFIFO              Do NOT use named pipes during prealignments.
  --no-complexity       Disable library complexity calculation (faster).
  --prioritize          Plot cFRiF/FRiF using mutually exclusive priority
                        ranked features based on the order of feature
                        appearance in the feature annotation asset.
  -V, --version         show program's version number and exit

required named arguments:
                        Parent output directory of project
  -S SAMPLE_NAME, --sample-name SAMPLE_NAME
                        Name for sample to run
                        One or more primary input files
                        Identifier for genome assembly