# -*- coding: utf-8 -*-
"""Wrapper for running Melt preprocessing
"""

from snakemake.shell import shell

__author__ = "<NAME>"
__email__ = "<EMAIL>"

shell(
    r"""
# -----------------------------------------------------------------------------
# Redirect stderr to log file by default and enable printing executed commands
exec 2> >(tee -a "{snakemake.log}")
set -x
# -----------------------------------------------------------------------------

ln -sr {snakemake.input.bam} {snakemake.output.orig_bam}
ln -sr {snakemake.input.bai} {snakemake.output.orig_bai}

melt_mei -Xmx2G Preprocess \
    Preprocess \
    -bamfile {snakemake.output.orig_bam} \
    -h {snakemake.config[static_data_config][reference][path]}
"""
)

# -*- coding: utf-8 -*-
"""Wrapper for running Melt preprocessing
"""

from snakemake.shell import shell

__author__ = "<NAME>"
__email__ = "<EMAIL>"

shell(
    r"""
# -----------------------------------------------------------------------------
# Redirect stderr to log file by default and enable printing executed commands
exec 2> >(tee -a "{snakemake.log}")
set -x
# -----------------------------------------------------------------------------

ln -sr {snakemake.input.bam} {snakemake.output.orig_bam}
ln -sr {snakemake.input.bai} {snakemake.output.orig_bai}

melt_mei -Xmx2G Preprocess \
    Preprocess \
    -bamfile {snakemake.output.orig_bam} \
    -h {snakemake.config[static_data_config][reference][path]}
"""
)

# -*- coding: utf-8 -*- Wrapper for running Melt preprocessing # ----------------------------------------------------------------------------- # Redirect stderr to log file by default and enable printing executed commands exec 2> >(tee -a "{snakemake.log}") set -x # -----------------------------------------------------------------------------  ln -sr {snakemake.input.bam} {snakemake.output.orig_bam} ln -sr {snakemake.input.bai} {snakemake.output.orig_bai}  melt_mei -Xmx2G Preprocess \     Preprocess \     -bamfile {snakemake.output.orig_bam} \     -h {snakemake.config[static_data_config][reference][path]}