test/test_add_samples_for_joint_calling.py
def _add_samples(run_id: str, project: str):
    """
    Add 3 samples: one with fastq input, one with CRAM input, one with GVCF input.
    :param run_id: to suffix sample names for uniqueness
    """
    s1 = NewSample(
        external_id=f'NA12878-from-fq-{run_id}',
        type=SampleType('blood'),
        meta={
            'reads': [
                [
                    'gs://cpg-seqr-test/batches/NA12878-trio-tiny/NA12878_L001_R1.fq',
                    'gs://cpg-seqr-test/batches/NA12878-trio-tiny/NA12878_L002_R1.fq',
                ],
                [
                    'gs://cpg-seqr-test/batches/NA12878-trio-tiny/NA12878_L001_R2.fq',
                    'gs://cpg-seqr-test/batches/NA12878-trio-tiny/NA12878_L002_R2.fq',
                ],
            ]
        },
    )
    s2 = NewSample(
        external_id=f'NA12878-from-cram-{run_id}',
        type=SampleType('blood'),
        meta={'reads': 'gs://cpg-seqr-test/batches/NA12878-trio-tiny/NA12878.cram'},
    )
    s3 = NewSample(
        external_id=f'NA12878-from-gvcf-{run_id}',
        type=SampleType('blood'),
        meta={'reads': 'gs://cpg-seqr-test/batches/NA12878-trio/NA12878.g.vcf.gz'},
    )
    sample_ids = [sapi.create_new_sample(project, s) for s in (s1, s2, s3)]
    print(f'Added samples {", ".join(sample_ids)}')
    return sample_ids

    Add 3 samples: one with fastq input, one with CRAM input, one with GVCF input.
    :param run_id: to suffix sample names for uniqueness
    
Add 3 samples: one with fastq input, one with CRAM input, one with GVCF input.
Add 3 samples : one with fastq input one with CRAM input one with GVCF input .
def _add_samples(run_id: str, project: str):
    s1 = NewSample(
        external_id=f'NA12878-from-fq-{run_id}',
        type=SampleType('blood'),
        meta={
            'reads': [
                [
                    'gs://cpg-seqr-test/batches/NA12878-trio-tiny/NA12878_L001_R1.fq',
                    'gs://cpg-seqr-test/batches/NA12878-trio-tiny/NA12878_L002_R1.fq',
                ],
                [
                    'gs://cpg-seqr-test/batches/NA12878-trio-tiny/NA12878_L001_R2.fq',
                    'gs://cpg-seqr-test/batches/NA12878-trio-tiny/NA12878_L002_R2.fq',
                ],
            ]
        },
    )
    s2 = NewSample(
        external_id=f'NA12878-from-cram-{run_id}',
        type=SampleType('blood'),
        meta={'reads': 'gs://cpg-seqr-test/batches/NA12878-trio-tiny/NA12878.cram'},
    )
    s3 = NewSample(
        external_id=f'NA12878-from-gvcf-{run_id}',
        type=SampleType('blood'),
        meta={'reads': 'gs://cpg-seqr-test/batches/NA12878-trio/NA12878.g.vcf.gz'},
    )
    sample_ids = [sapi.create_new_sample(project, s) for s in (s1, s2, s3)]
    print(f'Added samples {", ".join(sample_ids)}')
    return sample_ids
def _add_samples ( run_id : str , project : str ) : s1 = NewSample ( external_id = f'NA12878-from-fq-{run_id}' , type = SampleType ( 'blood' ) , meta = { 'reads' : [ [ 'gs://cpg-seqr-test/batches/NA12878-trio-tiny/NA12878_L001_R1.fq' , 'gs://cpg-seqr-test/batches/NA12878-trio-tiny/NA12878_L002_R1.fq' , ] , [ 'gs://cpg-seqr-test/batches/NA12878-trio-tiny/NA12878_L001_R2.fq' , 'gs://cpg-seqr-test/batches/NA12878-trio-tiny/NA12878_L002_R2.fq' , ] , ] } , ) s2 = NewSample ( external_id = f'NA12878-from-cram-{run_id}' , type = SampleType ( 'blood' ) , meta = { 'reads' : 'gs://cpg-seqr-test/batches/NA12878-trio-tiny/NA12878.cram' } , ) s3 = NewSample ( external_id = f'NA12878-from-gvcf-{run_id}' , type = SampleType ( 'blood' ) , meta = { 'reads' : 'gs://cpg-seqr-test/batches/NA12878-trio/NA12878.g.vcf.gz' } , ) sample_ids = [ sapi . create_new_sample ( project , s ) for s in ( s1 , s2 , s3 ) ] print ( f'Added samples {", ".join(sample_ids)}' ) return sample_ids
Add 3 samples: one with fastq input, one with CRAM input, one with GVCF input.
Add 3 samples : one with fastq input one with CRAM input one with GVCF input .
"""
    Add 3 samples: one with fastq input, one with CRAM input, one with GVCF input.
    :param run_id: to suffix sample names for uniqueness
    """
run_id
str
to suffix sample names for uniqueness
to suffix sample names for uniqueness
project
str