@@ -63,6 +63,7 @@ def run_star( # pylint:disable=too-many-branches
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) -> None :
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"""
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Run STAR alignment on list of short read data.
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+
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:param genome_file: Genome file path.
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:type genome_file: Path
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:param output_dir: Working directory path.
@@ -81,15 +82,11 @@ def run_star( # pylint:disable=too-many-branches
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:type subsample_read_limit:int, default 100000000,
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:param subsample_percentage: Maximun percentage of reads to subsample.
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:type subsample_percentage: int, default 0.25,
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- :param sampling_via_read_limit: If True will subsample an input dataset of \
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- fastq files using --subsample_read_limit value.
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+ :param sampling_via_read_limit: subsample fastq files using --subsample_read_limit.
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:type sampling_via_read_limit : boolean, False,
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- :param sampling_via_percentage: If True will subsample an input dataset of \
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- fastq files using --subsample_percentage value.
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+ :param sampling_via_percentage: subsample fastq files using --subsample_percentage.
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:type sampling_via_percentage : boolean, False,
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- :param sampling_via_read_limit_percentage: If True will subsample an input dataset \
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- of fastq files using --subsample_read_limit and --subsample_percentage value; \
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- the lowest number of reads is taken.
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+ :param sampling_via_read_limit_percentage: use max read limit and percentage value.
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:type sampling_via_read_limit_percentage : boolean, False,
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:param num_threads: Number of available threads.
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:type num_threads: int, default 1
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