Usage

To use merge_fastq in a project:

import merge_fastq
merge_fastq(fastq1,fastq2)

To use merge_fastq for command line:

> merge_fastq --help

Usage: merge_fastq [OPTIONS]

Console script for merge_fastq.

Options:
-fp1, --fastq1 PATH      Full path to gziped READ1 fastq files, can be
                        specified multiple times for example: --fastq1
                        test_part1_R1.fastq.gz --fastq1
                        test_part2_R1.fastq.gz  [required]
-fp2, --fastq2 PATH      Full path to gziped READ2 fastq files, can be
                        specified multiple times for example: --fastq2
                        test_part1_R2.fastq.gz --fastq2
                        test_part2_R2.fastq.gz  [required]
-op, --output-path PATH  Full path to write the output files (default:
                        Current working directory)
-of1, --out-fastq1 TEXT  Name of the merged output READ1 fastq file
                        (default: merged_fastq_R1.fastq.gz)
-of2, --out-fastq2 TEXT  Name of the merged output READ2 fastq file
                        (default: merged_fastq_R2.fastq.gz)
--help                   Show this message and exit.

Example commandline:

• Using default option for multiple fastq1 and fastq2 files

  $ merge_fastq \
  --fastq1 test_part1_R1.fastq.gz \
  --fastq1 test_part2_R1.fastq.gz \
  --fastq2 test_part1_R2.fastq.gz \
  --fastq2 test_part2_R2.fastq.gz \
  

• Using custom option for multiple fastq1 and fastq2 files

  $ merge_fastq \
  --fastq1 test_part1_R1.fastq.gz \
  --fastq1 test_part2_R1.fastq.gz \
  --fastq2 test_part1_R2.fastq.gz \
  --fastq2 test_part2_R2.fastq.gz \
  --output-path /path/to/where/you/want/output
  --out-fastq1 test_merged_R1.fastq.gz
  --out-fastq2 test_merged_R2.fastq.gz