.. _examples:

CLI usage Examples
******************

.. warning::

  **Remember:** the pipeline does not concatenate the reads. Whenever you use a pattern such as \* with unpaired reads the pipeline will process each read separately.

Illumina paired end reads.
""""""""""""""""""""""""""

This command will select all the read pairs that match the pattern "path-to/SRR*_{1,2}.fastq.gz" and process each pair separately.

.. code-block:: bash

      ./nextflow run fmalmeida/ngs-preprocess \
        --max_cpus 3 \
        --output illumina_paired \
        --shortreads "path-to/SRR*_{1,2}.fastq.gz" \
        --shortreads_type "paired" \
        --fastp_merge_pairs

.. note::

  Since ``--shortreads`` will always be a pattern match, example "illumina/SRR9847694_{1,2}.fastq.gz", it MUST ALWAYS be double quoted as the example below.

.. note::

  When using paired end reads it is required that inputs are set with the "{1,2}" pattern. For example: "SRR6307304_{1,2}.fastq". This will properly load reads "SRR6307304_1.fastq" and "SRR6307304_2.fastq"

.. note::

  ``--fastp_merge_pairs`` triggers the Fastp module to merge read pairs.

Illumina single end reads.
""""""""""""""""""""""""""

This command will select all the reads that match the pattern "path-to/SRR*.fastq.gz" and process each one separately.

.. code-block:: bash

      ./nextflow run fmalmeida/ngs-preprocess \
        --max_cpus 3 \
        --output illumina_single \
        --shortreads "path-to/SRR*.fastq.gz" \
        --shortreads_type "single" \
        --fastp_additional_parameters " --trim_front1 5 --trim_tail1 5 "

.. note::

  In this example, we pass on an additional parameter (``--trim_front1 5 --trim_tail1 5``) to Fastp so it trims the reads using a fixed number of bases from the head and tail of reads.
  
.. note::
  
  If multiple unpaired reads are given as input at once, pattern MUST be double quoted: "SRR9696*.fastq.gz"

ONT reads (fastq)
"""""""""""""""""

This command will select all the reads that match the pattern "path-to/SRR*.fastq.gz" and process each one separately.

.. code-block:: bash

  ./nextflow run fmalmeida/ngs-preprocess \
    --max_cpus 3 \
    --output ONT \
    --nanopore_fastq "path-to/SRR*.fastq.gz" \
    --lreads_min_length 1000

.. note::

  The parameter ``--lreads_min_length`` applies a minimum read length threshold to filter the reads.

Pacbio raw (subreads.bam) reads
"""""""""""""""""""""""""""""""

This command will select all the reads that match the pattern "path-to/m140905_*.subreads.bam" and process each one separately.

.. code-block:: bash

  ./nextflow run fmalmeida/ngs-preprocess \
    --max_cpus 3 \
    --output pacbio_subreads \
    --pacbio_bam "path-to/m140905_*.subreads.bam" \
    --pacbio_get_hifi \
    -with-report

.. note::

  The parameter ``--pacbio_get_hifi`` will make the pipeline **try** to produce the high fidelity pacbio ccs reads.

.. note::

  ``-with-report`` will generate nextflow execution reports.

.. note::
  
  If multiple reads are given as input at once, pattern MUST be double quoted: "SRR9696*.fastq.gz"

Pacbio raw (legacy .bas.h5 to subreads.bam) reads
"""""""""""""""""""""""""""""""""""""""""""""""""

.. code-block:: bash

  ./nextflow run fmalmeida/ngs-preprocess \
    --pacbio_h5 E01_1/Analysis_Results/ \
    --output E01_1/Analysis_Results/preprocessed \
    --max_cpus 3

.. note::

  This example refers to the SMRT Cell data files available at: https://github.com/PacificBiosciences/DevNet/wiki/E.-coli-Bacterial-Assembly. The path ``E01_1/Analysis_Results/`` is the directory where the legacy \*.bas.h5 and \*.bax.h5 files are located. The pipeline will load the bas files available in the directory.

.. note::

  Pacbio bas.h5 file and its related bax.h5 files MUST be in the same directory

Running with a nf-core interactive graphical interface
""""""""""""""""""""""""""""""""""""""""""""""""""""""

.. code-block:: bash

  ./nf-core launch fmalmeida/ngs-preprocess


Running with a configuration file
"""""""""""""""""""""""""""""""""

.. code-block:: bash

  ./nextflow run fmalmeida/ngs-preprocess -c nextflow.config