From f2d760cec0564f8f5cd8d40622ca001aca936368 Mon Sep 17 00:00:00 2001 From: seppinho Date: Thu, 7 Mar 2024 14:49:04 +0100 Subject: [PATCH] Set 2000x subsampling to default --- cloudgene.yaml | 8 +++++--- nextflow.config | 3 ++- workflows/mtdna_server_2.nf | 4 ++-- 3 files changed, 9 insertions(+), 6 deletions(-) diff --git a/cloudgene.yaml b/cloudgene.yaml index 19ccbcb..139267a 100644 --- a/cloudgene.yaml +++ b/cloudgene.yaml @@ -101,7 +101,7 @@ workflow: 0.1: 0.1 - id: coverage_estimation - description: Apply Coverage Estimate + description: Apply VAF Coverage Estimation type: list value: off values: @@ -109,10 +109,12 @@ workflow: off: Off - id: subsampling - description: Coverage Subsampling (0 means deactivated) + description: Subsample to 2000x type: number visible: true - value: 0 + values: + on: On + off: Off - id: myseparator0 type: separator diff --git a/nextflow.config b/nextflow.config index a1d60c8..fe65cdc 100644 --- a/nextflow.config +++ b/nextflow.config @@ -23,7 +23,8 @@ params { alignQ = 30 coverage_estimation = "on" max_samples = 0 - subsampling = 0 + subsampling = "on" + subsampling_coverage = 2000 service = [ diff --git a/workflows/mtdna_server_2.nf b/workflows/mtdna_server_2.nf index eadbdaf..8b8bf68 100644 --- a/workflows/mtdna_server_2.nf +++ b/workflows/mtdna_server_2.nf @@ -84,10 +84,10 @@ workflow MTDNA_SERVER_2 { validated_files = INPUT_VALIDATION.out.validated_files.flatten() - if(params.subsampling != 0) { + if(params.subsampling.equals("on") ) { SUBSAMPLING ( validated_files, - params.subsampling + params.subsampling_coverage ) validated_files = SUBSAMPLING.out.subsampled_bam_ch }