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Merge pull request #774 from umccr/enhancement/allow-gzip-and-ora-com…
…pression Decompress ora files prior to running if gzip files are also present
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170 changes: 170 additions & 0 deletions
170
...ateless/stacks/transcriptome-pipeline-manager/lambdas/has_ora_inputs_py/has_ora_inputs.py
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,170 @@ | ||
| #!/usr/bin/env python3 | ||
|
|
||
| """ | ||
| Add ora reference | ||
| """ | ||
| from pathlib import Path | ||
| from typing import Dict, Optional, List | ||
|
|
||
|
|
||
| def handler(event, context) -> Dict[str, bool]: | ||
| """ | ||
| Get the boolean parameters from the event input | ||
| :param event: | ||
| :param context: | ||
| :return: Dictionary of boolean parameters | ||
| """ | ||
|
|
||
| # Collect the event data input | ||
| event_data_input: Dict = event['event_data_input'] | ||
|
|
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| # Get the fastq list rows | ||
| tumor_fastq_list_rows: Optional[List] = event_data_input.get('tumorFastqListRows', None) | ||
| normal_fastq_list_rows: Optional[List] = event_data_input.get('fastqListRows', None) | ||
|
|
||
| # If tumorFastqListRows is None and fastqListRows is None, return false | ||
| if tumor_fastq_list_rows is None and normal_fastq_list_rows is None: | ||
| return { | ||
| "add_ora_step": False, | ||
| "is_hybrid": False | ||
| } | ||
|
|
||
| add_ora_step = False | ||
| for fastq_list_row_iter in [tumor_fastq_list_rows, normal_fastq_list_rows]: | ||
| if fastq_list_row_iter is not None: | ||
| # If fastqListRows is not None, return true | ||
| # Iterate over each of the fastq list rows, if one of the read1FileUri or read2FileUri end with .fastq.ora | ||
| # return true | ||
| if any( | ||
| [ | ||
| row.get('read1FileUri', '').endswith('.fastq.ora') or | ||
| row.get('read2FileUri', '').endswith('.fastq.ora') | ||
| for row in fastq_list_row_iter | ||
| ] | ||
| ): | ||
| add_ora_step = True | ||
|
|
||
| # Check if hybrid | ||
| endings = [] | ||
| for fastq_list_row_iter in [tumor_fastq_list_rows, normal_fastq_list_rows]: | ||
| if fastq_list_row_iter is not None: | ||
| endings.extend( | ||
| list(set(list(map( | ||
| lambda fastq_list_row_: Path(fastq_list_row_.get("read1FileUri")).suffix, | ||
| fastq_list_row_iter | ||
| )))) | ||
| ) | ||
|
|
||
| if len(list(set(endings))) > 1: | ||
| # Don't need ora when hybrid since ora samples will be dropped | ||
| is_hybrid = True | ||
| add_ora_step = False | ||
| else: | ||
| is_hybrid = False | ||
|
|
||
| # Got to here? Return false | ||
| return { | ||
| "add_ora_step": add_ora_step, | ||
| "is_hybrid": is_hybrid | ||
| } | ||
|
|
||
|
|
||
| # if __name__ == "__main__": | ||
| # import json | ||
| # | ||
| # print( | ||
| # json.dumps( | ||
| # handler( | ||
| # { | ||
| # "event_data_input": { | ||
| # "tumorFastqListRows": [ | ||
| # { | ||
| # "rgid": "ATGAGGCC.CAATTAAC.2", | ||
| # "rgsm": "L2400195", | ||
| # "rglb": "L2400195", | ||
| # "lane": 2, | ||
| # "read1FileUri": "icav2://ea19a3f5-ec7c-4940-a474-c31cd91dbad4/primary/240229_A00130_0288_BH5HM2DSXC/2024071110689063/Samples/Lane_2/L2400195/L2400195_S9_L002_R1_001.fastq.gz", | ||
| # "read2FileUri": "icav2://ea19a3f5-ec7c-4940-a474-c31cd91dbad4/primary/240229_A00130_0288_BH5HM2DSXC/2024071110689063/Samples/Lane_2/L2400195/L2400195_S9_L002_R2_001.fastq.gz" | ||
| # }, | ||
| # { | ||
| # "rgid": "ATGAGGCC.CAATTAAC.3", | ||
| # "rgsm": "L2400195", | ||
| # "rglb": "L2400195", | ||
| # "lane": 3, | ||
| # "read1FileUri": "icav2://ea19a3f5-ec7c-4940-a474-c31cd91dbad4/primary/240229_A00130_0288_BH5HM2DSXC/2024071110689063/Samples/Lane_3/L2400195/L2400195_S9_L003_R1_001.fastq.gz", | ||
| # "read2FileUri": "icav2://ea19a3f5-ec7c-4940-a474-c31cd91dbad4/primary/240229_A00130_0288_BH5HM2DSXC/2024071110689063/Samples/Lane_3/L2400195/L2400195_S9_L003_R2_001.fastq.gz" | ||
| # } | ||
| # ], | ||
| # "fastqListRows": [ | ||
| # { | ||
| # "rgid": "GCACGGAC.TGCGAGAC.4", | ||
| # "rgsm": "L2400191", | ||
| # "rglb": "L2400191", | ||
| # "lane": 4, | ||
| # "read1FileUri": "icav2://ea19a3f5-ec7c-4940-a474-c31cd91dbad4/primary/240229_A00130_0288_BH5HM2DSXC/2024071110689063/Samples/Lane_4/L2400191/L2400191_S17_L004_R1_001.fastq.gz", | ||
| # "read2FileUri": "icav2://ea19a3f5-ec7c-4940-a474-c31cd91dbad4/primary/240229_A00130_0288_BH5HM2DSXC/2024071110689063/Samples/Lane_4/L2400191/L2400191_S17_L004_R2_001.fastq.gz" | ||
| # } | ||
| # ], | ||
| # "dragenReferenceVersion": "v9-r3" | ||
| # } | ||
| # }, | ||
| # None | ||
| # ), | ||
| # indent=4 | ||
| # ) | ||
| # ) | ||
| # | ||
| # # { | ||
| # # "add_ora_step": false, | ||
| # # "is_hybrid": false | ||
| # # } | ||
| # | ||
| # if __name__ == "__main__": | ||
| # import json | ||
| # | ||
| # print( | ||
| # json.dumps( | ||
| # handler( | ||
| # { | ||
| # "event_data_input": { | ||
| # "tumorFastqListRows": [ | ||
| # { | ||
| # "rgid": "ATGAGGCC.CAATTAAC.2", | ||
| # "rgsm": "L2400195", | ||
| # "rglb": "L2400195", | ||
| # "lane": 2, | ||
| # "read1FileUri": "icav2://ea19a3f5-ec7c-4940-a474-c31cd91dbad4/primary/240229_A00130_0288_BH5HM2DSXC/2024071110689063/Samples/Lane_2/L2400195/L2400195_S9_L002_R1_001.fastq.gz", | ||
| # "read2FileUri": "icav2://ea19a3f5-ec7c-4940-a474-c31cd91dbad4/primary/240229_A00130_0288_BH5HM2DSXC/2024071110689063/Samples/Lane_2/L2400195/L2400195_S9_L002_R2_001.fastq.gz" | ||
| # }, | ||
| # { | ||
| # "rgid": "ATGAGGCC.CAATTAAC.3", | ||
| # "rgsm": "L2400195", | ||
| # "rglb": "L2400195", | ||
| # "lane": 3, | ||
| # "read1FileUri": "icav2://ea19a3f5-ec7c-4940-a474-c31cd91dbad4/primary/240229_A00130_0288_BH5HM2DSXC/2024071110689063/Samples/Lane_3/L2400195/L2400195_S9_L003_R1_001.fastq.gz", | ||
| # "read2FileUri": "icav2://ea19a3f5-ec7c-4940-a474-c31cd91dbad4/primary/240229_A00130_0288_BH5HM2DSXC/2024071110689063/Samples/Lane_3/L2400195/L2400195_S9_L003_R2_001.fastq.gz" | ||
| # } | ||
| # ], | ||
| # "fastqListRows": [ | ||
| # { | ||
| # "rgid": "GCACGGAC.TGCGAGAC.4", | ||
| # "rgsm": "L2400191", | ||
| # "rglb": "L2400191", | ||
| # "lane": 4, | ||
| # "read1FileUri": "icav2://ea19a3f5-ec7c-4940-a474-c31cd91dbad4/primary/240229_A00130_0288_BH5HM2DSXC/2024071110689063/Samples/Lane_4/L2400191/L2400191_S17_L004_R1_001.fastq.ora", | ||
| # "read2FileUri": "icav2://ea19a3f5-ec7c-4940-a474-c31cd91dbad4/primary/240229_A00130_0288_BH5HM2DSXC/2024071110689063/Samples/Lane_4/L2400191/L2400191_S17_L004_R2_001.fastq.ora" | ||
| # } | ||
| # ], | ||
| # "dragenReferenceVersion": "v9-r3" | ||
| # } | ||
| # }, | ||
| # None | ||
| # ), | ||
| # indent=4 | ||
| # ) | ||
| # ) | ||
| # | ||
| # # { | ||
| # # "add_ora_step": true, | ||
| # # "is_hybrid": true | ||
| # # } |
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