From 9903f191c0460f7e9293081375d5f06cd6437fc2 Mon Sep 17 00:00:00 2001 From: seppinho Date: Tue, 13 Aug 2019 22:24:13 +0200 Subject: [PATCH] Improve RefPanel logging and refactor eagle map check --- .../imputationserver/steps/Imputation.java | 27 ++++++++++++++++--- 1 file changed, 23 insertions(+), 4 deletions(-) diff --git a/src/main/java/genepi/imputationserver/steps/Imputation.java b/src/main/java/genepi/imputationserver/steps/Imputation.java index 78113a52..b3f3b3c4 100644 --- a/src/main/java/genepi/imputationserver/steps/Imputation.java +++ b/src/main/java/genepi/imputationserver/steps/Imputation.java @@ -91,13 +91,22 @@ public boolean run(WorkflowContext context) { context.println("Reference Panel: "); context.println(" Name: " + reference); + context.println(" ID: " + panel.getId()); + context.println(" Build: " + panel.getBuild()); context.println(" Location: " + panel.getHdfs()); context.println(" Legend: " + panel.getLegend()); context.println(" Version: " + panel.getVersion()); - - if (!panel.checkEagleMap()) { - context.error("Eagle map file not found."); - return false; + context.println(" Eagle Map: " + panel.getMapEagle()); + context.println(" Eagle BCFs: " + panel.getRefEagle()); + context.println(" Minimac Map: " + panel.getMapMinimac()); + for (Map.Entry entry : panel.getPopulations().entrySet()) { + context.println(" Populations: " + entry.getKey() + "/" + entry.getValue()); + } + for (Map.Entry entry : panel.getSamples().entrySet()) { + context.println(" Samples: " + entry.getKey() + "/" + entry.getValue()); + } + for (Map.Entry entry : panel.getQcFilter().entrySet()) { + context.println(" QC Filters: " + entry.getKey() + "/" + entry.getValue()); } // execute one job per chromosome @@ -158,6 +167,16 @@ protected void readConfigFile() { if (result.needsPhasing) { context.println("Input data is unphased."); + if (!panel.checkEagleMap()) { + context.error("Eagle map file not found."); + return false; + } + + if (!panel.checkEagleBcf()) { + context.error("Eagle bcf files not found."); + return false; + } + // eagle context.println(" Setting up eagle reference and map files..."); job.setMapEagleHdfs(panel.getMapEagle());