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Bugfix, fix compression outputs for single indexed samples #738

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Dec 1, 2024
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Bugfix, fix compression outputs for single indexed samples #738

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83 changes: 80 additions & 3 deletions ...n-manager/lambdas/merge_rgids_with_fastq_list_rows_py/merge_rgids_with_fastq_list_rows.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,8 +34,7 @@

# Constants
# index.index2.lane.rgsm.instrument_run_id
RGID_PARTIAL_REGEX = re.compile(r"\w+\.\w+\.(\d+.\w+).\w+")

RGID_PARTIAL_REGEX = re.compile(r"\w+\.(?:\w+\.)?(\d+.\w+).\w+")

# AWS things
def get_ssm_client() -> 'SSMClient':
Expand Down Expand Up @@ -231,4 +230,82 @@ def handler(event, context):
# # ]



# if __name__ == "__main__":
# # Test the handler function
# import json
# environ["AWS_PROFILE"] = "umccr-production"
# environ["ICAV2_ACCESS_TOKEN_SECRET_ID"] = "ICAv2JWTKey-umccr-prod-service-production"
# print(
# json.dumps(
# handler(
# {
# "rgids_list": [
# "AACGTGAT.1.NTC_SsCRE211028VD_L2101268.211104_A00130_0182_BHLNYCDSX2",
# "AACTGTAG.TGCGGCGT.4.PRJ210975_L2101293.211104_A00130_0182_BHLNYCDSX2",
# "AAGATACT.ATGTAAGT.1.PRJ210951_L2101226.211104_A00130_0182_BHLNYCDSX2",
# "ACGACTACCA.TTAGGGTCGT.1.PRJ211018_LPRJ211018.211104_A00130_0182_BHLNYCDSX2",
# "ACTCGTGT.GTTCCAAT.4.PRJ210972_L2101283.211104_A00130_0182_BHLNYCDSX2",
# "ATAACGCC.TGAACCTG.1.MDX210286_L2101126_topup.211104_A00130_0182_BHLNYCDSX2",
# "ATGGCATG.GGTACCTT.2.PRJ210954_L2101228.211104_A00130_0182_BHLNYCDSX2",
# "ATGGCTTGTG.CACAACATTC.1.PRJ211015_LPRJ211015.211104_A00130_0182_BHLNYCDSX2",
# "ATTGTGAA.GCAATGCA.3.PRJ210969_L2101282.211104_A00130_0182_BHLNYCDSX2",
# "CAATCCCGAC.TACTACTCGG.1.PRJ211014_LPRJ211014.211104_A00130_0182_BHLNYCDSX2",
# "CCTTCACC.GGAGCGTC.3.PRJ210948_L2101280.211104_A00130_0182_BHLNYCDSX2",
# "CGCGCACTTA.AGAATACAGG.1.PRJ211019_LPRJ211019.211104_A00130_0182_BHLNYCDSX2",
# "GATCTATC.AGCCTCAT.2.PRJ210963_L2101234.211104_A00130_0182_BHLNYCDSX2",
# "GCCACAGG.ATGGCATG.3.PRJ210968_L2101281.211104_A00130_0182_BHLNYCDSX2",
# "GCGCAAGC.CGGCGTGA.1.PRJ210950_L2101225.211104_A00130_0182_BHLNYCDSX2",
# "GCTACAAAGC.AGGGCACGTG.1.PRJ211020_LPRJ211020.211104_A00130_0182_BHLNYCDSX2",
# "GGAGCGTC.GCACGGAC.2.PRJ210953_L2101227.211104_A00130_0182_BHLNYCDSX2",
# "GTCTACAC.ACCTTGGC.4.PRJ210973_L2101284.211104_A00130_0182_BHLNYCDSX2",
# "GTCTGTCA.2.MDX210310_L2101265.211104_A00130_0182_BHLNYCDSX2",
# "TCCGTTGGAT.GCGAGAACGT.1.PRJ211017_LPRJ211017.211104_A00130_0182_BHLNYCDSX2",
# "TGAAGAGA.2.MDX210311_L2101266.211104_A00130_0182_BHLNYCDSX2",
# "TGCGCGGTTT.TTTATCCTTG.1.PRJ211013_LPRJ211013.211104_A00130_0182_BHLNYCDSX2",
# "TTCACGCA.4.PTC_SsCRE211028VD_L2101267.211104_A00130_0182_BHLNYCDSX2",
# "TTCCTGTT.AAGATACT.3.PRJ210947_L2101279.211104_A00130_0182_BHLNYCDSX2",
# "TTCTCGATGA.GTGCCCGACA.1.PRJ211016_LPRJ211016.211104_A00130_0182_BHLNYCDSX2"
# ],
# "instrument_run_folder_uri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/ora-compression/211104_A00130_0182_BHLNYCDSX2/20241122ab8a58de/"
# },
# None,
# ),
# indent=4
# )
# )
#
# # [
# # {
# # "rglb": "UnknownLibrary",
# # "rgsm": "PRJ211015_LPRJ211015",
# # "lane": 1,
# # "rgid": "ATGGCTTGTG.CACAACATTC.1.PRJ211015_LPRJ211015.211104_A00130_0182_BHLNYCDSX2",
# # "read_1_file_uri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/ora-compression/211104_A00130_0182_BHLNYCDSX2/20241122ab8a58de/10X_10X-5prime-expression/PRJ211015_LPRJ211015_S3_L001_R1_001.fastq.ora",
# # "read_2_file_uri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/ora-compression/211104_A00130_0182_BHLNYCDSX2/20241122ab8a58de/10X_10X-5prime-expression/PRJ211015_LPRJ211015_S3_L001_R2_001.fastq.ora"
# # },
# # {
# # "rglb": "UnknownLibrary",
# # "rgsm": "PRJ211018_LPRJ211018",
# # "lane": 1,
# # "rgid": "ACGACTACCA.TTAGGGTCGT.1.PRJ211018_LPRJ211018.211104_A00130_0182_BHLNYCDSX2",
# # "read_1_file_uri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/ora-compression/211104_A00130_0182_BHLNYCDSX2/20241122ab8a58de/10X_10X-5prime-expression/PRJ211018_LPRJ211018_S6_L001_R1_001.fastq.ora",
# # "read_2_file_uri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/ora-compression/211104_A00130_0182_BHLNYCDSX2/20241122ab8a58de/10X_10X-5prime-expression/PRJ211018_LPRJ211018_S6_L001_R2_001.fastq.ora"
# # },
# # ...
# # {
# # "rglb": "UnknownLibrary",
# # "rgsm": "NTC_SsCRE211028VD_L2101268",
# # "lane": 1,
# # "rgid": "AACGTGAT.1.NTC_SsCRE211028VD_L2101268.211104_A00130_0182_BHLNYCDSX2",
# # "read_1_file_uri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/ora-compression/211104_A00130_0182_BHLNYCDSX2/20241122ab8a58de/exome_AgSsCRE/NTC_SsCRE211028VD_L2101268_S4_L001_R1_001.fastq.ora",
# # "read_2_file_uri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/ora-compression/211104_A00130_0182_BHLNYCDSX2/20241122ab8a58de/exome_AgSsCRE/NTC_SsCRE211028VD_L2101268_S4_L001_R2_001.fastq.ora"
# # },
# # {
# # "rglb": "UnknownLibrary",
# # "rgsm": "PTC_SsCRE211028VD_L2101267",
# # "lane": 4,
# # "rgid": "TTCACGCA.4.PTC_SsCRE211028VD_L2101267.211104_A00130_0182_BHLNYCDSX2",
# # "read_1_file_uri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/ora-compression/211104_A00130_0182_BHLNYCDSX2/20241122ab8a58de/exome_AgSsCRE/PTC_SsCRE211028VD_L2101267_S3_L004_R1_001.fastq.ora",
# # "read_2_file_uri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/ora-compression/211104_A00130_0182_BHLNYCDSX2/20241122ab8a58de/exome_AgSsCRE/PTC_SsCRE211028VD_L2101267_S3_L004_R2_001.fastq.ora"
# # }
# # ]