Fixes/lift over

files/rsq-report.Rmd

@@ -20,6 +20,7 @@ params:
 
 library(ggplot2)
 library(dplyr)
+library(knitr)
 ```
 
 ## Parameters
@@ -29,7 +30,7 @@ library(dplyr)
 | Job             | `r params$name`            |
 | Date             | `r params$date`             |
 
-## RSQ Plot
+## RSQ Table
 ```{r echo=FALSE}
 dataset = read.csv(params$input, row.names=NULL, sep = '\t')
 dataset_weighted = dataset %>%
@@ -42,8 +43,13 @@ dataset_weighted = dataset %>%
         weighted_R2 = weighted.mean(Imputation.R2,X.Variants)
     )
 
-ggplot() + geom_line(data = dataset_weighted, mapping = aes(x = mean_MAF, y= weighted_R2))  +  scale_x_log10() +  expand_limits(x = 0, y = 0) 
+kable(dataset_weighted)
+```
 
+## RSQ Plot
+
+```{r echo=FALSE}
+ggplot() + geom_line(data = dataset_weighted, mapping = aes(x = mean_MAF, y= weighted_R2))  +  scale_x_log10() +  expand_limits(x = 0, y = 0) 
 ```
 
 <small>

modules/local/lift_over.nf

@@ -3,10 +3,10 @@ process LIFT_OVER {
 //publishDir "${params.outdir}/aggRSquare", mode: 'copy', pattern: '*aggRSquare'
 
     input:
-    tuple val(chr), val(array_name), path(dosage_data), path(sequence_data)
+    tuple val(chr), path(dosage_data), path(sequence_data)
 
     output:
-    tuple val(chr), val(array_name), path(dosage_data), path("${sequence_data.baseName}.liftover.vcf.gz"), emit: sequence_data_lifted
+    tuple val(chr), path(dosage_data), path("${sequence_data.baseName}.liftover.vcf.gz"), emit: sequence_data_lifted
 
     script:
     def chain_file = (params.sequence_build == 'hg19' ? "/opt/imputationserver/chains/hg19ToHg38.over.chain.gz" : '/opt/imputationserver/chains/hg38ToHg19.over.chain.gz')

nextflow.config

@@ -42,7 +42,6 @@ profiles {
 
     development {
         docker.enabled                    = true
-        docker.userEmulation              = true
         singularity.enabled               = false
     }
 

tests/microarray.nf.test

@@ -71,4 +71,23 @@ nextflow_pipeline {
 
     }
 
+    test("Rsq calculation for hg19/hg38") {
+
+        when {
+            params {
+               project          = "r2_calculation_hg19"
+               workflow_name    = "r2"
+               imputation_build = "hg19"
+               sequence_build   = "hg38"
+               imputed_data     = "$projectDir/tests/data/imputed_data/hg19/*vcf.gz"
+               sequence_data    = "$projectDir/tests/data/sequence_data/hg38/*vcf.gz"
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+
+    }
+
 }