#!/usr/bin/env bash
#
# Copyright (c) 2016 10x Genomics, Inc. All rights reserved.
#
# Run BASIC_CS with mrp.
#

source $TENX_SCRIPTDIR/common/_includes

DOCOPT_SPEC="$(cat <<EOF
$DOCOPT_PREAMBLE_FASTQS

Options:
# Output Files
    --bam               Output barcoded reads as unaligned BAM instead of FASTQ.
    --readgroup=TEXT    RG data to be inserted into BAM. Optional.

# Sample Specification
    $DOCOPT_OPTIONS_FASTQS

# Martian Runtime
    $DOCOPT_OPTIONS_MRP_CLUSTER
EOF
)"

function implement_process_options {
    process_options_fastqs

    # --bam
    output_format=\"fastq\"
    if [ "$bam" == "true" ]; then
        output_format=\"bam\"
    fi

    # --readgroup
    if [ -n "$readgroup" ]; then
        read_group=\"$readgroup\"
    else
        read_group=\"None\"
    fi
}

function implement_generate_sample_defs {
    generate_sample_defs_fastqs_crg
}

function implement_generate_mro {
    cat <<EOF > $mro
@include "basic_cs.mro"

call BASIC_CS(
    fastq_mode = $fastq_mode,
    sample_id = $sample_id,
    sample_def = $sample_def,
    output_format = $output_format,
    read_group = $read_group,
)
EOF
}

source $TENX_SCRIPTDIR/../tenkit/bin/common/_subcmd_mrp