diff --git a/lib/workload/stateless/stacks/ora-compression-manager/deploy/index.ts b/lib/workload/stateless/stacks/ora-compression-manager/deploy/index.ts index ff8e9f1e2..553802e0d 100644 --- a/lib/workload/stateless/stacks/ora-compression-manager/deploy/index.ts +++ b/lib/workload/stateless/stacks/ora-compression-manager/deploy/index.ts @@ -228,6 +228,7 @@ export class OraCompressionIcav2PipelineManagerStack extends cdk.Stack { ICAV2_ACCESS_TOKEN_SECRET_ID: icav2AccessTokenSecretObj.secretName, }, timeout: Duration.seconds(60), + memorySize: 1024, }); // Give the lambda function access to the secret icav2AccessTokenSecretObj.grantRead(setMergeSizesLambdaObj.currentVersion); @@ -270,7 +271,7 @@ export class OraCompressionIcav2PipelineManagerStack extends cdk.Stack { detailType: [props.detailType], detail: { workflowName: [{ 'equals-ignore-case': props.workflowName }], - state: [{ 'equals-ignore-case': 'SUCCEEDED' }], + status: [{ 'equals-ignore-case': 'SUCCEEDED' }], }, }, } diff --git a/lib/workload/stateless/stacks/ora-compression-manager/lambdas/merge_file_sizes_for_fastq_list_rows_py/merge_file_sizes_for_fastq_list_rows.py b/lib/workload/stateless/stacks/ora-compression-manager/lambdas/merge_file_sizes_for_fastq_list_rows_py/merge_file_sizes_for_fastq_list_rows.py index a8f57f850..a6844d78b 100644 --- a/lib/workload/stateless/stacks/ora-compression-manager/lambdas/merge_file_sizes_for_fastq_list_rows_py/merge_file_sizes_for_fastq_list_rows.py +++ b/lib/workload/stateless/stacks/ora-compression-manager/lambdas/merge_file_sizes_for_fastq_list_rows_py/merge_file_sizes_for_fastq_list_rows.py @@ -28,7 +28,6 @@ read_icav2_file_contents ) - # Type checking if typing.TYPE_CHECKING: from mypy_boto3_ssm import SSMClient @@ -37,6 +36,7 @@ # Globals ICAV2_BASE_URL = "https://ica.illumina.com/ica/rest" + # AWS things def get_ssm_client() -> 'SSMClient': """ @@ -86,20 +86,20 @@ def read_md5sum(project_data: ProjectData) -> pd.DataFrame: :param project_data: :return: """ - with read_icav2_file_contents(project_data.project_id, project_data.data.id) as file_contents: + with StringIO(read_icav2_file_contents(project_data.project_id, project_data.data.id)) as file_contents: return pd.read_csv( - StringIO(file_contents), + file_contents, header=None, - names=["md5sum", "file_name"], + names=["md5sum", "fastqPath"], sep=" ", engine="python" ) def read_file_sizes(project_data: ProjectData) -> pd.DataFrame: - with read_icav2_file_contents(project_data.project_id, project_data.data.id) as file_contents: + with StringIO(read_icav2_file_contents(project_data.project_id, project_data.data.id)) as file_contents: return pd.read_csv( - StringIO(file_contents), + file_contents, sep="\t" ) @@ -110,8 +110,17 @@ def read_fastq_list_csv(project_data: ProjectData) -> pd.DataFrame: :param project_data: :return: """ - with read_icav2_file_contents(project_data.project_id, project_data.data.id) as file_contents: - return pd.read_csv(StringIO(file_contents)) + with StringIO(read_icav2_file_contents(project_data.project_id, project_data.data.id)) as file_contents: + return pd.read_csv(file_contents).rename( + columns={ + "RGID": "rgid", + "RGLB": "rglb", + "RGSM": "rgsm", + "Lane": "lane", + "Read1File": "read1File", + "Read2File": "read2File" + } + ) def get_icav2_file_from_folder(project_data_list: typing.List[ProjectData], file_name: str) -> ProjectData: @@ -125,8 +134,8 @@ def get_icav2_file_from_folder(project_data_list: typing.List[ProjectData], file return next( filter( lambda project_data_iter: ( - project_data_iter.data.details.name == file_name and - DataType[project_data_iter.data.details.data_type] == DataType.FILE + project_data_iter.data.details.name == file_name and + DataType[project_data_iter.data.details.data_type] == DataType.FILE ), project_data_list ) @@ -153,21 +162,25 @@ def merge_fastq_list_rows_with_md5sums_and_filesizes( """ # Extend the gzipped md5s to the fastq list rows fastq_list_ora_df = fastq_list_ora_df.merge( - fastq_gzipped_md5_df, + fastq_gzipped_md5_df.assign( + fastqPath=lambda row_iter_: row_iter_.fastqPath.str.rstrip(".gz") + ".ora" + ), how="left", left_on="read1File", - right_on="fileName" + right_on="fastqPath" ).drop( - columns='fileName' + columns='fastqPath' ).rename( columns={"md5sum": "read1FileGzippedMd5sum"} ).merge( - fastq_gzipped_md5_df, + fastq_gzipped_md5_df.assign( + fastqPath=lambda row_iter_: row_iter_.fastqPath.str.rstrip(".gz") + ".ora" + ), how="left", left_on="read2File", - right_on="fileName" + right_on="fastqPath" ).drop( - columns='fileName' + columns='fastqPath' ).rename( columns={"md5sum": "read2FileGzippedMd5sum"} ) @@ -177,61 +190,65 @@ def merge_fastq_list_rows_with_md5sums_and_filesizes( fastq_ora_md5_df, how="left", left_on="read1File", - right_on="fileName" + right_on="fastqPath" ).drop( - columns='fileName' + columns='fastqPath' ).rename( columns={"md5sum": "read1FileOraMd5sum"} ).merge( fastq_ora_md5_df, how="left", left_on="read2File", - right_on="fileName" + right_on="fastqPath" ).drop( - columns='fileName' + columns='fastqPath' ).rename( columns={"md5sum": "read2FileOraMd5sum"} ) # Extend the gzipped file sizes to the fastq list rows fastq_list_ora_df = fastq_list_ora_df.merge( - fastq_gzipped_filesizes_df, + fastq_gzipped_filesizes_df.assign( + fastqPath=lambda row_iter_: row_iter_.fastqPath.str.rstrip(".gz") + ".ora" + ), how="left", left_on="read1File", - right_on="fileName" + right_on="fastqPath" ).drop( - columns='fileName' + columns='fastqPath' ).rename( - columns={"fileSize": "read1GzippedFileSize"} + columns={"fileSizeInBytes": "read1GzippedFileSizeInBytes"} ).merge( - fastq_gzipped_filesizes_df, + fastq_gzipped_filesizes_df.assign( + fastqPath=lambda row_iter_: row_iter_.fastqPath.str.rstrip(".gz") + ".ora" + ), how="left", left_on="read2File", - right_on="fileName" + right_on="fastqPath" ).drop( - columns='fileName' + columns='fastqPath' ).rename( - columns={"fileSize": "read2GzippedFileSize"} + columns={"fileSizeInBytes": "read2GzippedFileSizeInBytes"} ) fastq_list_ora_df = fastq_list_ora_df.merge( fastq_ora_filesizes_df, how="left", left_on="read1File", - right_on="fileName" + right_on="fastqPath" ).drop( - columns='fileName' + columns='fastqPath' ).rename( - columns={"fileSize": "read1OraFileSize"} + columns={"fileSizeInBytes": "read1OraFileSizeInBytes"} ).merge( fastq_ora_filesizes_df, how="left", left_on="read2File", - right_on="fileName" + right_on="fastqPath" ).drop( - columns='fileName' + columns='fastqPath' ).rename( - columns={"fileSize": "read2OraFileSize"} + columns={"fileSizeInBytes": "read2OraFileSizeInBytes"} ) # Return the fastq files @@ -296,21 +313,21 @@ def handler(event, context): fastq_gzipped_md5_file_obj = read_md5sum( get_icav2_file_from_folder( output_dir_project_data_list, - "fastq_gzipped_md5.txt") + "fastq_gzipped.md5.txt") ) # Get the file sizes for the new ora compressed tsv fastq_ora_md5_file_obj = read_md5sum( get_icav2_file_from_folder( output_dir_project_data_list, - "fastq_ora_md5.txt") + "fastq_ora.md5.txt") ) # Get the original gzipped tsv file size fastq_gzipped_filesizes_file_obj = read_file_sizes( get_icav2_file_from_folder( output_dir_project_data_list, - "fastq_gzipped_filesizes.tsv" + "fastq_gzipped.filesizes.tsv" ) ) @@ -318,7 +335,7 @@ def handler(event, context): fastq_ora_filesizes_file_obj = read_file_sizes( get_icav2_file_from_folder( output_dir_project_data_list, - "fastq_ora_filesizes.tsv" + "fastq_ora.filesizes.tsv" ) ) @@ -345,5 +362,427 @@ def handler(event, context): inplace=True ) + # FIXME Drop rgid and rglb since we don't + # FIXME accurately have these values yet + # FIXME this will be possible once the fastq manager exists + fastq_list_ora_df.drop( + columns=["rgid", "rglb"], + inplace=True + ) + # Return the merged file as a json list return fastq_list_ora_df.to_dict(orient="records") + + +# if __name__ == "__main__": +# import json +# +# environ['AWS_PROFILE'] = 'umccr-development' +# environ['AWS_REGION'] = 'ap-southeast-2' +# environ['ICAV2_ACCESS_TOKEN_SECRET_ID'] = "ICAv2JWTKey-umccr-prod-service-dev" +# print( +# json.dumps( +# handler( +# { +# "output_dir_uri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/" +# }, +# None +# ), +# indent=4 +# ) +# ) +# +# # [ +# # { +# # "rgsm": "L2401526", +# # "lane": 1, +# # "read1FileGzippedMd5sum": "ff9f75053fd5dfe34ac011fd679c62dd", # pragma: allowlist secret +# # "read2FileGzippedMd5sum": "18a267c2c5ca2f71e272815cd7508fd8", # pragma: allowlist secret +# # "read1FileOraMd5sum": "bb26321f461de85419c95131ce73f0a5", # pragma: allowlist secret +# # "read2FileOraMd5sum": "986ef94789f76d7a5e510d34b465033b", # pragma: allowlist secret +# # "read1GzippedFileSizeInBytes": 42630072057, # pragma: allowlist secret +# # "read2GzippedFileSizeInBytes": 43902595265, # pragma: allowlist secret +# # "read1OraFileSizeInBytes": 8647052933, +# # "read2OraFileSizeInBytes": 9265337812, +# # "read1FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401526/L2401526_S1_L001_R1_001.fastq.ora", +# # "read2FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401526/L2401526_S1_L001_R2_001.fastq.ora" +# # }, +# # { +# # "rgsm": "L2401532", +# # "lane": 1, +# # "read1FileGzippedMd5sum": "7ec0a49be2a3c0a049b7593d00474cdb", # pragma: allowlist secret +# # "read2FileGzippedMd5sum": "af902803801285d3475ef1c8776ad611", # pragma: allowlist secret +# # "read1FileOraMd5sum": "6e2c5ce6e3014fd5f8be78bf9d769b26", # pragma: allowlist secret +# # "read2FileOraMd5sum": "54c5a6787ab80f07c25fc4abd5eb6bbc", # pragma: allowlist secret +# # "read1GzippedFileSizeInBytes": 4870, # pragma: allowlist secret +# # "read2GzippedFileSizeInBytes": 5969, # pragma: allowlist secret +# # "read1OraFileSizeInBytes": 4189, +# # "read2OraFileSizeInBytes": 4914, +# # "read1FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401532/L2401532_S7_L001_R1_001.fastq.ora", +# # "read2FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401532/L2401532_S7_L001_R2_001.fastq.ora" +# # }, +# # { +# # "rgsm": "L2401528", +# # "lane": 1, +# # "read1FileGzippedMd5sum": "6de45d4c93afcf310d45c0edb0361427", # pragma: allowlist secret +# # "read2FileGzippedMd5sum": "c9a3dfed465b4053e1bacbc9e1b6bc70", # pragma: allowlist secret +# # "read1FileOraMd5sum": "1b947ed0f912f5dc0d5246cf0cbe63b9", # pragma: allowlist secret +# # "read2FileOraMd5sum": "16e8dc8d559dd8dd9515946c5112021c", # pragma: allowlist secret +# # "read1GzippedFileSizeInBytes": 43357314992, # pragma: allowlist secret +# # "read2GzippedFileSizeInBytes": 44092409731, # pragma: allowlist secret +# # "read1OraFileSizeInBytes": 8541275179, +# # "read2OraFileSizeInBytes": 8863424337, +# # "read1FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401528/L2401528_S3_L001_R1_001.fastq.ora", +# # "read2FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401528/L2401528_S3_L001_R2_001.fastq.ora" +# # }, +# # { +# # "rgsm": "L2401531", +# # "lane": 1, +# # "read1FileGzippedMd5sum": "6dd394650558c4a93e2e2dd0322eaf08", # pragma: allowlist secret +# # "read2FileGzippedMd5sum": "f8ccf03414fc374903b1a2a5302ac517", # pragma: allowlist secret +# # "read1FileOraMd5sum": "1c61d4cca313a29dab5a05c2b9173a93", # pragma: allowlist secret +# # "read2FileOraMd5sum": "14583d8caca26fda8fac0701c0588292", # pragma: allowlist secret +# # "read1GzippedFileSizeInBytes": 43818023110, # pragma: allowlist secret +# # "read2GzippedFileSizeInBytes": 44844382192, # pragma: allowlist secret +# # "read1OraFileSizeInBytes": 8589773627, +# # "read2OraFileSizeInBytes": 9065337736, +# # "read1FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401531/L2401531_S6_L001_R1_001.fastq.ora", +# # "read2FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401531/L2401531_S6_L001_R2_001.fastq.ora" +# # }, +# # { +# # "rgsm": "L2401527", +# # "lane": 1, +# # "read1FileGzippedMd5sum": "0953e17b02574f3167abbaba37dcd4ef", # pragma: allowlist secret +# # "read2FileGzippedMd5sum": "4d7f065b4ba5f7a702a469d566403bc6", # pragma: allowlist secret +# # "read1FileOraMd5sum": "70e9b68355b87e6fc3d96871def6e881", # pragma: allowlist secret +# # "read2FileOraMd5sum": "f3d0b90486c6f77fd78832777972b1be", # pragma: allowlist secret +# # "read1GzippedFileSizeInBytes": 37685523375, # pragma: allowlist secret +# # "read2GzippedFileSizeInBytes": 39255037633, # pragma: allowlist secret +# # "read1OraFileSizeInBytes": 7599984647, +# # "read2OraFileSizeInBytes": 8409290279, +# # "read1FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401527/L2401527_S2_L001_R1_001.fastq.ora", +# # "read2FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401527/L2401527_S2_L001_R2_001.fastq.ora" +# # }, +# # { +# # "rgsm": "L2401530", +# # "lane": 1, +# # "read1FileGzippedMd5sum": "cd9e0018d17f119871e3b34ee5c6cf78", # pragma: allowlist secret +# # "read2FileGzippedMd5sum": "b4d9ab7d12e752eef790f27dd7d68aa5", # pragma: allowlist secret +# # "read1FileOraMd5sum": "9f2eb09791defb77c40e54693301d327", # pragma: allowlist secret +# # "read2FileOraMd5sum": "81434c21c81358e2d454750d428912ac", # pragma: allowlist secret +# # "read1GzippedFileSizeInBytes": 40837628477, # pragma: allowlist secret +# # "read2GzippedFileSizeInBytes": 41771419794, # pragma: allowlist secret +# # "read1OraFileSizeInBytes": 8127751530, +# # "read2OraFileSizeInBytes": 8567645785, +# # "read1FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401530/L2401530_S5_L001_R1_001.fastq.ora", +# # "read2FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401530/L2401530_S5_L001_R2_001.fastq.ora" +# # }, +# # { +# # "rgsm": "L2401529", +# # "lane": 1, +# # "read1FileGzippedMd5sum": "69b4f91a0c87e52a5f02186d61f58f5d", # pragma: allowlist secret +# # "read2FileGzippedMd5sum": "5c42766421250fcbb97944d7e0920cc0", # pragma: allowlist secret +# # "read1FileOraMd5sum": "26cd69ff20668ca692f4fbc043bbfba6", # pragma: allowlist secret +# # "read2FileOraMd5sum": "09442fbd28bbf53778b71eeed1223027", # pragma: allowlist secret +# # "read1GzippedFileSizeInBytes": 40964945004, # pragma: allowlist secret +# # "read2GzippedFileSizeInBytes": 41736727855, # pragma: allowlist secret +# # "read1OraFileSizeInBytes": 8158884285, +# # "read2OraFileSizeInBytes": 8535009518, +# # "read1FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401529/L2401529_S4_L001_R1_001.fastq.ora", +# # "read2FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401529/L2401529_S4_L001_R2_001.fastq.ora" +# # }, +# # { +# # "rgsm": "L2401539", +# # "lane": 2, +# # "read1FileGzippedMd5sum": "1cf861134c39c7a1fe885396de951fd9", # pragma: allowlist secret +# # "read2FileGzippedMd5sum": "8f97bf9c1fcbb364d7779d9bdaba7e12", # pragma: allowlist secret +# # "read1FileOraMd5sum": "833cd38bea126e644627694af39e551b", # pragma: allowlist secret +# # "read2FileOraMd5sum": "31bda754f678a2c1d39cb7484eafc28b", # pragma: allowlist secret +# # "read1GzippedFileSizeInBytes": 76151725499, # pragma: allowlist secret +# # "read2GzippedFileSizeInBytes": 81298319647, # pragma: allowlist secret +# # "read1OraFileSizeInBytes": 13777362811, +# # "read2OraFileSizeInBytes": 17019842335, +# # "read1FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_2/L2401539/L2401539_S9_L002_R1_001.fastq.ora", +# # "read2FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_2/L2401539/L2401539_S9_L002_R2_001.fastq.ora" +# # }, +# # { +# # "rgsm": "L2401544", +# # "lane": 2, +# # "read1FileGzippedMd5sum": "a6e1b6243503bfdffb15389be16a8300", # pragma: allowlist secret +# # "read2FileGzippedMd5sum": "6e08a07e72f14a59b663bec92d060960", # pragma: allowlist secret +# # "read1FileOraMd5sum": "6acbc7678701e00a7918932729a76d9c", # pragma: allowlist secret +# # "read2FileOraMd5sum": "71fc9c563ab6b1292a60a63919fe47b8", # pragma: allowlist secret +# # "read1GzippedFileSizeInBytes": 4479234306, # pragma: allowlist secret +# # "read2GzippedFileSizeInBytes": 4788152749, # pragma: allowlist secret +# # "read1OraFileSizeInBytes": 836174432, +# # "read2OraFileSizeInBytes": 1029001113, +# # "read1FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_2/L2401544/L2401544_S12_L002_R1_001.fastq.ora", +# # "read2FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_2/L2401544/L2401544_S12_L002_R2_001.fastq.ora" +# # }, +# # { +# # "rgsm": "L2401540", +# # "lane": 2, +# # "read1FileGzippedMd5sum": "c45c22d932e8c2d4501663779f0b745a", # pragma: allowlist secret +# # "read2FileGzippedMd5sum": "3b4c5bc5b1001bd171302d01e676eb0b", # pragma: allowlist secret +# # "read1FileOraMd5sum": "0de3746eab5f548936fb5d1708e0e329", # pragma: allowlist secret +# # "read2FileOraMd5sum": "e52be348378672ca5929e4a27a0f4d88", # pragma: allowlist secret +# # "read1GzippedFileSizeInBytes": 37104673601, # pragma: allowlist secret +# # "read2GzippedFileSizeInBytes": 39140876826, # pragma: allowlist secret +# # "read1OraFileSizeInBytes": 6782972169, +# # "read2OraFileSizeInBytes": 8108052715, +# # "read1FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_2/L2401540/L2401540_S10_L002_R1_001.fastq.ora", +# # "read2FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_2/L2401540/L2401540_S10_L002_R2_001.fastq.ora" +# # 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} +# # ] \ No newline at end of file diff --git a/lib/workload/stateless/stacks/ora-compression-manager/step_functions_templates/fastq_list_row_compression_event.asl.json b/lib/workload/stateless/stacks/ora-compression-manager/step_functions_templates/fastq_list_row_compression_event.asl.json index 6450c5a49..52f34f2ec 100644 --- a/lib/workload/stateless/stacks/ora-compression-manager/step_functions_templates/fastq_list_row_compression_event.asl.json +++ b/lib/workload/stateless/stacks/ora-compression-manager/step_functions_templates/fastq_list_row_compression_event.asl.json @@ -7,7 +7,9 @@ "Resource": "arn:aws:states:::lambda:invoke", "OutputPath": "$.Payload", "Parameters": { - "Payload.$": "$", + "Payload": { + "output_dir_uri.$": "$.payload.data.outputs.instrumentRunOraOutputUri" + }, "FunctionName": "${__merge_sizes_lambda_function_arn__}" }, "Retry": [ diff --git a/lib/workload/stateless/stacks/ora-compression-manager/step_functions_templates/set_compression_outputs.asl.json b/lib/workload/stateless/stacks/ora-compression-manager/step_functions_templates/set_compression_outputs.asl.json index 492c8fb85..fb11e337a 100644 --- a/lib/workload/stateless/stacks/ora-compression-manager/step_functions_templates/set_compression_outputs.asl.json +++ b/lib/workload/stateless/stacks/ora-compression-manager/step_functions_templates/set_compression_outputs.asl.json @@ -25,7 +25,7 @@ "Parameters": { "FunctionName": "${__set_outputs_json_lambda_function_arn__}", "Payload": { - "instrument_run_id.$": "$.ready_event_data_inputs.instrumentRunId", + "instrument_run_id.$": "$.get_db_attributes_step.ready_event_data_inputs.instrumentRunId", "analysis_output_uri.$": "$.get_db_attributes_step.analysis_output_uri" } },