def to_cram(data):
"""Convert BAM archive files into indexed CRAM.
"""
ref_file = utils.get_in(data, ("reference", "fasta", "base"))
cram_file = cram.compress(data["work_bam"], ref_file, data["config"])
data["work_bam"] = cram_file
return [[data]]
def to_cram(data):
"""Convert BAM archive files into indexed CRAM.
"""
data = utils.to_single_data(data)
cram_file = cram.compress(dd.get_work_bam(data) or dd.get_align_bam(data), data)
out_key = "archive_bam" if cwlutils.is_cwl_run(data) else "work_bam"
data[out_key] = cram_file
return [[data]]
def to_cram(data):
"""Convert BAM archive files into indexed CRAM.
"""
data = utils.to_single_data(data)
cram_file = cram.compress(
dd.get_work_bam(data) or dd.get_align_bam(data), data)
out_key = "archive_bam" if cwlutils.is_cwl_run(data) else "work_bam"
data[out_key] = cram_file
return [[data]]
def to_cram(data):
"""Convert BAM archive files into indexed CRAM.
"""
cram_file = cram.compress(data["work_bam"], data)
data["work_bam"] = cram_file
return [[data]]
def to_cram(data):
"""Convert BAM archive files into indexed CRAM.
"""
cram_file = cram.compress(data["work_bam"], data)
data["work_bam"] = cram_file
return [[data]]