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Wire Glimpse phasing runtime params into outer workflow #207

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Mar 3, 2025
Merged

Wire Glimpse phasing runtime params into outer workflow #207

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6 changes: 5 additions & 1 deletion GlimpseImputationPipeline/Glimpse2ImputationAndCheckQC.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,8 @@ workflow Glimpse2ImputationAndCheckQC {
String? check_qc_docker
Int? check_qc_cpu
Int? check_qc_mem_gb
Int? glimpse_phase_cpu
Int? glimpse_phase_mem_gb
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In our local change I called these cpu_phase and mem_gb_phase to mirror the values in Glimpse2Imputaiton but for this PR thought it'd be good to better match check_qc_[cpu|mem_gb]. Happy to update however desired

}

call Glimpse2Imputation.Glimpse2Imputation {
Expand All @@ -62,7 +64,9 @@ workflow Glimpse2ImputationAndCheckQC {
docker_extract_num_sites_from_reference_chunk = docker_extract_num_sites_from_reference_chunk,
mem_scaling_factor_phase = mem_scaling_factor_phase,
cpu_ligate = cpu_ligate,
mem_gb_ligate = mem_gb_ligate
mem_gb_ligate = mem_gb_ligate,
cpu_phase = glimpse_phase_cpu,
mem_gb_phase = glimpse_phase_mem_gb
}

call Glimpse2CheckQC.Glimpse2CheckQC {
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