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ChristianOertlin
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fix(find downsample fastq files) (#2878)
# Description fix parsing sample id downsample store cli
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cg/apps/downsample/utils.py

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Original file line numberDiff line numberDiff line change
@@ -38,7 +38,7 @@ def store_downsampled_fastq_files_from_dir(
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"""
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fastq_file_paths: list[Path] = get_files_matching_pattern(
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directory=Path(fastq_file_output_directory),
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pattern=f"*{sample_id.split(sep='_')[0]}*.{SequencingFileTag.FASTQ}.gz",
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pattern=f"*{sample_id.split(sep='DS')[0]}*.{SequencingFileTag.FASTQ}.gz",
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)
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if not fastq_file_paths:
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raise FileNotFoundError(

cg/cli/downsample.py

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@@ -70,7 +70,7 @@ def downsample_sample(
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"store",
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help="Store the downsampled fastq files in housekeeper.\n "
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"Make sure the downsample sbtach job has finished before using this command! \n"
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"Usage: cg downsample store ACC123145_2.0M ACC1231_30.0M",
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"Usage: cg downsample store ACC123145DS2C0M ACC1231DS30C0M",
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)
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@click.argument("sample_ids", type=str, nargs=-1)
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@click.pass_obj

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