FACTCAT

This eponymous tool concatenates .fastq(.gz) files whilst creating a summary of the sequences. Can also demultiplex reads according to Guppy/MinKNOW .fastq record headers.

URL: https://github.com/epi2me-labs/fastcat

Example

This wrapper can be used in the following way:

test/Snakefile not found.

Note that input, output and log file paths can be chosen freely.

When running with

snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.

Input/Output

Input:

• fq_or_path: fastq files or path. If path set, automative give -x.

Output:

• out_fq: output fastq file. if ends with gz, auto compressed. (optional)

• file_summary: file summary output. (optional)

• read_summary: read summary outout. (optional)

Params

• extras: extra arguments to program.

• fastcat: fastcat path. default is fastcat.

Authors

• yangqun

Code

# fastcat wrapper.

__author__ = "yangqun"

import sys
import os
from snakemake.shell import shell

data = snakemake.input.get('fq_or_path')
out_fq = snakemake.output.get('out_fq')
file_summary = snakemake.output.get('file_summary')
read_summary = snakemake.output.get('read_summary')
extras = snakemake.params.get('extras', '')
fastcat = snakemake.params.get('fastcat', 'fastcat')

# input data
if not data:
    sys.exit("Please give fastq files or path.")

if os.path.isdir(data):
    extras += ' -x'

# output data
out_cmd = ''
if out_fq:
    if out_fq.endswith('gz'):
        # compressed fastq.
        out_cmd = " | gzip >{}".format(out_fq)
    else:
        # fastq.
        out_cmd = " >{}".format(out_fq)
else:
    # do not output fastq.
    out_cmd = " >/dev/null"

cmds = ""
# summary
if file_summary:
    cmds += ' -f ' + file_summary
if read_summary:
    cmds += ' -r ' + read_summary

# run
shell(
    "{fastcat} {cmds} {extras} {data} {out_cmd}"
)