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usage.txt
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usage.txt
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usage: peppro.py [-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]
[--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 PI_TSS]
[--pi-body PI_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 0.10.2
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.
-C CONFIG_FILE, --config CONFIG_FILE
Pipeline configuration file (YAML). Relative paths are
with respect to the pipeline script.
-M MEMORY_LIMIT, --mem MEMORY_LIMIT
Memory limit for processes accepting such. Default
units are megabytes unless specified using the suffix
[K|M|G|T].
-P NUMBER_OF_CORES, --cores NUMBER_OF_CORES
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.
--prealignment-names PREALIGNMENT_NAMES [PREALIGNMENT_NAMES ...]
Space-delimited list of prealignment genome names to
align to before primary alignment.
--prealignment-index PREALIGNMENT_INDEX [PREALIGNMENT_INDEX ...]
Space-delimited list of prealignment genome name and
index files delimited by an equals sign to align to
before primary alignment. e.g.
rCRSd=/path/to/bowtie2_index/.
--genome-index GENOME_INDEX
Path to bowtie2 primary genome index file.
--fasta FASTA Path to primary genome fasta file. Required with
--sob.
--chrom-sizes CHROM_SIZES
Path to primary genome chromosome sizes file.
--TSS-name TSS_NAME file_name of TSS annotation file.
--pi-tss PI_TSS file_name of pause index TSS annotation file.
--pi-body PI_BODY 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:
-O PARENT_OUTPUT_FOLDER, --output-parent PARENT_OUTPUT_FOLDER
Parent output directory of project
-S SAMPLE_NAME, --sample-name SAMPLE_NAME
Name for sample to run
-I INPUT_FILES [INPUT_FILES ...], --input INPUT_FILES [INPUT_FILES ...]
One or more primary input files
-G GENOME_ASSEMBLY, --genome GENOME_ASSEMBLY
Identifier for genome assembly