Usage

To use process_fastq in a project:

import process_fastq
process_fastq.run(sample_id, request_id, run_id, fastq_path, output_path, cutadapt_path)

To use process_fastq from cli:

Usage: process_fastq [OPTIONS]

    Options:
    -s, --sample-id TEXT            Sample id to get the fastq files can be
                                    either IGO sample id or Investigator sample
                                    id (eg: -s EDD_ret_pt049_cf02)  [required]
    -p, --request-id TEXT           IGO request id to get the fastq files.
                                    (eg:-p Project_05500_GB or -p 05500_GB)
    -r, --run-id TEXT               Run id to get the fastq files, can be
                                    specified multiple times (eg:-r PITT_0376 -r
                                    PITT_0378)
    -fp, --fastq-path PATH          Full path to fastq files  [required]
    -op, --output-path PATH         Full path to where we link the output files
                                    [required]
    -cp, --cutadapt-path PATH       Full path to location of cutadapt executable
                                    [required]
    -l, --expected-read-length INTEGER
                                    Expected read length from the fastq file
    --version                       Show the version and exit.
    -v, --verbosity LVL             Either CRITICAL, ERROR, WARNING, INFO or
                                    DEBUG
    --help                          Show this message and exit.

Example commandline:

$ process_fastq \
-p request_id \
-s smaple_name \
-r RunID \
-fp /path/to/fastq/directory \
-op /path/to/output/directory \
-cp /path/to/cutadapt

To use link_fastq_juno.py from cli:

Usage: link_fastq_juno.py [OPTIONS]

Options:

-m, --manifest-file PATH

Manifest file having information about run id and sample id to get the fastq files (eg: -m Project_05500_GB_manifest.xslx) [required]

-p, --request-id TEXT

IGO request id to get the fastq files. (eg:-p Project_05500_GB or -p 05500_GB) [required]

-fp, --fastq-path PATH

Full path to fastq files [required]

-op, --output-path PATH

Full path to where we link the output files [required]

-cp, --cutadapt-path PATH

Full path to location of cutadapt executable [required]

-pfp, --process-fastq-path PATH

Full path to location of cutadapt executable [required]

-l, --expected-read-length INTEGER

Expected read length from the fastq file

--version

Show the version and exit.

-v, --verbosity LVL

Either CRITICAL, ERROR, WARNING, INFO or DEBUG

--help

Show this message and exit.

Example commandline:

$ python3 link_fastq_juno.py \
-p request_id \
-m /path/to/manifest.xlsx \
-pfp /path/to/process_fastq \
-fp /path/to/fastq/directory \
-op /path/to/output/directory \
-cp /path/to/cutadapt