forked from databio/pepatac
-
Notifications
You must be signed in to change notification settings - Fork 0
/
usage.txt
executable file
·113 lines (110 loc) · 6.33 KB
/
usage.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
usage: pepatac.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]
[--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.
-C CONFIG_FILE, --config CONFIG_FILE
Pipeline configuration file (YAML). Relative paths are
with respect to the pipeline script.
-O PARENT_OUTPUT_FOLDER, --output-parent PARENT_OUTPUT_FOLDER
Parent output directory of project
-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
-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
space.
--skipqc Skip FastQC. Useful for bugs in FastQC that appear
with some sequence read files.
--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 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:
-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