Add --input_variant parameter for handling single variant #112
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Can you find why the smoke test failed. @jylee-bcm |
hyunhwan-jeong
suggested changes
Dec 18, 2024
bin/generate_input_vcf.py
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| ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> | ||
| ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> | ||
| ##FILTER=<ID=PASS,Description="All filters passed"> | ||
| ##reference=file:///staging/human/reference/b37/b37.fa.default/reference.bin |
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does it only handle hg19? not hg38?
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it just works regardless of it.
It even works without the line.
would you prefer to remove it?
| } | ||
| } | ||
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| showUsage() | ||
| showVersion() | ||
| validateInputParams() | ||
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| process GENERATE_INPUT_VCF { |
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no need to process for both hg19/hg38?
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it just works regardless of that.
nextflow.config
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| @@ -1,4 +1,7 @@ | |||
| params { | |||
| input_vcf = null | |||
| input_variant = null | |||
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| run_id = 1 | |||
| ref_ver = "hg19" | |||
| ref_dir = " " | |||
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better to do null instead of " "
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I will apply that
we can't see the error message but i am pretty sure that's related with the docker version problem. |
hyunhwan-jeong
approved these changes
Dec 18, 2024
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