CLI Reference¶
pycashier¶
Usage: pycashier [OPTIONS] COMMAND [ARGS]...
Cash in on DNA Barcode Tags
See `pycashier COMMAND -h` for more information.
Options:
--version Show the version and exit.
-h, --help Show this message and exit.
Commands:
extract extract DNA barcodes from a directory of fastq files
merge merge overlapping paired-end reads using fastp
receipt combine and summarize outputs of extract
scrna extract expressed DNA barcodes from scRNA-seq
pycashier extract¶
Usage: pycashier extract [OPTIONS]
extract DNA barcodes from a directory of fastq files
Sample names should be delimited with a ".", such as `<sample>.raw.fastq`,
anything succeeding the first period will be ignored by `pycashier`.
If your data is paired-end with overlapping barcodes, see `pycashier merge`.
Input/Output Options:
-i, --input DIRECTORY source directory containing fastq files [required]
-o, --output DIRECTORY output directory [default: ./outs]
-p, --pipeline DIRECTORY pipeline directory [default: ./pipeline]
-s, --samples TEXT comma separated list of samples to process
Quality (Fastp) Options:
-q, --quality INTEGER minimum PHRED quality for filtering reads [default: 30]
-up, --unqualified-percent INTEGER
minimum percent of bases which can be below quality threshold
[default: 20]
-fa, --fastp-args TEXT additional arguments passed to fastp [default:
--dont_eval_duplication]
Trim (Cutadapt) Options:
-ca, --cutadapt-args TEXT additional arguments passed to cutadapt [default: --max-n=0 -n 2
--trimmed-only]
-e, --error FLOAT error tolerance supplied to cutadapt [default: 0.1]
-l, --length INTEGER target length of extracted barcode [default: 20]
-ua, --upstream-adapter TEXT 5' sequence flanking barcode
-da, --downstream-adapter TEXT 3' sequence flanking barcode
--unlinked-adapters run cutadapt using unlinked adapters
--skip-trimming skip cutadapt trimming entirely and use reads as-is
Cluster (Starcode) Options:
-r, --ratio INTEGER ratio to use for message passing clustering [default: 3]
-d, --distance INTEGER RANGE levenshtein distance for clustering [default: 1; 1<=x<=8]
Filter Options:
-fc, --filter-count INTEGER minium nominal number of reads
-fp, --filter-percent FLOAT minimum percentage of total reads [default: 0.005]
--offset INTEGER length offset from target barcode length post-clustering [default: 1]
General Options:
-t, --threads INTEGER number of cpu cores to use [default: 1]
-y, --yes answer yes to prompts
-v, --verbose show more output, set log level to debug
-c, --config FILE read parameter values from config file [default: pycashier.toml]
--save-config [explicit|full] save current params to file specified by `--config`
--log-file FILE path to log file [default: <pipeline-dir>/pycashier.log]
-h, --help Show this message and exit.
pycashier merge¶
Usage: pycashier merge [OPTIONS]
merge overlapping paired-end reads using fastp
Simple wrapper over `fastp` to combine R1 and R2 from PE fastq files.
Input/Output Options:
-i, --input DIRECTORY source directory containing gzipped R1 and R2 fastq files [required]
-o, --output DIRECTORY output directory [default: ./mergedfastqs]
-p, --pipeline DIRECTORY pipeline directory [default: ./pipeline]
-s, --samples TEXT comma separated list of samples to process
Merge Options:
-fa, --fastp-args TEXT additional arguments passed to fastp [default: -m -c -G -Q -L]
General Options:
-t, --threads INTEGER number of cpu cores to use [default: 1]
-y, --yes answer yes to prompts
-v, --verbose show more output, set log level to debug
-c, --config FILE read parameter values from config file [default: pycashier.toml]
--save-config [explicit|full] save current params to file specified by `--config`
--log-file FILE path to log file [default: <pipeline-dir>/pycashier.log]
-h, --help Show this message and exit.
pycashier receipt¶
Usage: pycashier receipt [OPTIONS]
combine and summarize outputs of extract
Input/Output Options:
-i, --input DIRECTORY source directory containing sam files from scRNA-seq [default: ./outs;
required]
-o, --output FILE combined tsv of all samples found in input directory [default:
./combined.tsv]
-p, --pipeline DIRECTORY pipeline directory [default: ./pipeline]
-s, --samples TEXT comma separated list of samples to process
Receipt Options:
--no-overlap skip per lineage overlap column
General Options:
-v, --verbose show more output, set log level to debug
-c, --config FILE read parameter values from config file [default: pycashier.toml]
--save-config [explicit|full] save current params to file specified by `--config`
--log-file FILE path to log file [default: <pipeline-dir>/pycashier.log]
-h, --help Show this message and exit.
pycashier scrna¶
Usage: pycashier scrna [OPTIONS]
extract expressed DNA barcodes from scRNA-seq
Designed for interoperability with 10X scRNA-seq workflow.
After processing samples with `cellranger` resulting
bam files should be converted to sam files using `samtools`.
NOTE: You can speed this up by providing a sam file with only the unmapped reads.
Input/Output Options:
-i, --input DIRECTORY source directory containing sam files from scRNA-seq [required]
-o, --output DIRECTORY output directory [default: ./outs]
-p, --pipeline DIRECTORY pipeline directory [default: ./pipeline]
-s, --samples TEXT comma separated list of samples to process
Trim (Cutadapt) Options:
-e, --error FLOAT error tolerance supplied to cutadapt [default: 0.1]
-l, --length INTEGER target length of extracted barcode [default: 20]
-ua, --upstream-adapter TEXT 5' sequence flanking barcode
-da, --downstream-adapter TEXT 3' sequence flanking barcode
-ca, --cutadapt-args TEXT additional arguments passed to cutadapt [default: --max-n=0 -n 2
--trimmed-only]
-ml, --minimum-length INTEGER minimum length of extracted barcode [default: 10]
General Options:
-t, --threads INTEGER number of cpu cores to use [default: 1]
-y, --yes answer yes to prompts
-v, --verbose show more output, set log level to debug
-c, --config FILE read parameter values from config file [default: pycashier.toml]
--save-config [explicit|full] save current params to file specified by `--config`
--log-file FILE path to log file [default: <pipeline-dir>/pycashier.log]
-h, --help Show this message and exit.