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

source $TENX_SCRIPTDIR/common/_includes

DOCOPT_SPEC="$(cat <<EOF
$DOCOPT_PREAMBLE_FASTQS

Options:
# Genome
    $DOCOPT_OPTIONS_REFERENCE

# Sample Specification
    $DOCOPT_OPTIONS_FASTQS

# Martian Runtime
    $DOCOPT_OPTIONS_MRP_CLUSTER 
EOF
)"

function implement_process_options {
    process_options_fastqs
    process_options_reference
}

function implement_generate_sample_defs {
    generate_sample_defs_fastqs_crg
}

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

call ALIGNER_CS(
    fastq_mode = $fastq_mode,
    sample_id = $sample_id,
    sample_def = $sample_def,
    reference_path = $reference_path,
)
EOF
}

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