Paired tumor normal calling #5
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caalo
commented
Mar 12, 2024
•
caalo
commented
- Added parameter_meta
- Reduced the number of private variables for MarkDuplicates
- Removed old comments
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Our final version is paired tumor normal calling: tumor1-normal1, tumor2-normal2 calling. |
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| { | |||
| "mutation_calling.tumorFastq": ["/fh/fast/paguirigan_a/pub/ReferenceDataSets/workflow_testing_data/WDL/wdl_101/HCC4006_final.fastq", "/fh/fast/paguirigan_a/pub/ReferenceDataSets/workflow_testing_data/WDL/wdl_101/CALU1_combined_final.fastq"], | |||
| "mutation_calling.normalFastq": "/fh/fast/paguirigan_a/pub/ReferenceDataSets/workflow_testing_data/WDL/wdl_101/MOLM13_combined_final.fastq", | |||
| "mutation_calling.samples": [{"tumorSample": "/fh/fast/paguirigan_a/pub/ReferenceDataSets/workflow_testing_data/WDL/wdl_101/HCC4006_final.fastq", | |||
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We decided that the path will be required to be put in by the reader?
Maybe for testing we can keep this but for the final one we maybe want to say something like /path/to/tumor/1/fastq or something?
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That's the Fred Hutch json! There's a separate one for non-Fred Hutch (although there is still FH paths in it). I think you created these files so you can make any changes to them if you desire!
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| # Align fastq file to the reference genome | ||
| task BwaMem { | ||
| input { | ||
| File input_fastq | ||
| referenceGenome refGenome | ||
| Int threads = 16 | ||
| } | ||
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| String base_file_name = basename(input_fastq, ".fastq") | ||
| String ref_fasta_local = basename(refGenome.ref_fasta) | ||
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| String read_group_id = "ID:" + base_file_name | ||
| String sample_name = "SM:" + base_file_name |
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I had put SM but we can change to anything
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Sure. Feel free to make any commits to change that
| } | ||
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| String base_file_name = basename(input_fastq, ".fastq") | ||
| String ref_fasta_local = basename(refGenome.ref_fasta) | ||
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| String read_group_id = "ID:" + base_file_name | ||
| String sample_name = "SM:" + base_file_name | ||
| String platform = "illumina" | ||
| String platform_info = "PL:" + platform # Create the platform information | ||
| String platform_info = "PL:illumina" | ||
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I kept that platform variable so that people can add as they please? But i guess for this guide it is okay to expect illumina.
