Merge branch 'main' into fixes/liftover-index-creation

Dockerfile

@@ -48,7 +48,7 @@ RUN wget https://github.com/lukfor/pgs-calc/releases/download/v${PGS_CALC_VERSIO
 ENV PATH="/opt/pgs-calc:${PATH}"
 
 # Install imputationserver-utils
-ENV IMPUTATIONSERVER_UTILS_VERSION=v1.5.0
+ENV IMPUTATIONSERVER_UTILS_VERSION=v1.5.1
 RUN mkdir /opt/imputationserver-utils
 WORKDIR "/opt/imputationserver-utils"
 #COPY files/imputationserver-utils.tar.gz .

README.md

@@ -23,7 +23,7 @@ If you encounter any problems, feel free to open an issue [here](https://github.
 
 ## Version History
 
-[Version 2.0.4](https://github.com/genepi/imputationserver2/releases/tag/v2.0.4) - Fix QC issues and remove HTSJDK index creation for a smoother input validation.
+[Version 2.0.3 - Version 2.0.6](https://github.com/genepi/imputationserver2/releases/tag/v2.0.6)  - Fix QC issues and remove HTSJDK index creation for input validation and QC.
 
 [Version 2.0.2](https://github.com/genepi/imputationserver2/releases/tag/v2.0.2) - Set minimac4 tmp directory (required for larger sample sizes).
 

cloudgene.hla.yaml

@@ -3,7 +3,7 @@ name: HLA Imputation
 description: "<p> Thank you for using our multi-ethnic HLA imputation panel, built from ~20,000 whole genome sequencing samples from five global populations.  </p> <p>
 Please cite this manuscript if you would like to include imputed results from the panel in your work: </p> <p>
 Luo, Y., Kanai, M., Choi, W., Li, X., Yamamoto, K., Ogawa, K., Gutierrez-Arcelus, M., Gregersen, P. K., Stuart, P. E., Elder, J. T., Fellay, J., Carrington, M., Haas, D. W., Guo, X., Palmer, N. D., Chen, Y.-D. I., Rotter, J. I., Taylor, K. D., Rich, S., … Raychaudhuri, S. (2020). <b> A high-resolution HLA reference panel capturing global population diversity enables multi-ethnic fine-mapping in HIV host response</b>. https://doi.org/10.1101/2020.07.16.20155606 <br><br>If your input data is <b>GRCh37/hg19</b> please ensure chromosomes are encoded without prefix  (e.g. <b>20</b>).<br>If your input data is <b>GRCh38hg38</b> please ensure chromosomes are encoded with prefix 'chr' (e.g. <b>chr20</b>). </p>"
-version: 2.0.5
+version: 2.0.6
 website: https://imputationserver.readthedocs.io
 category: Application
 submitButton: Start Imputation

cloudgene.pgs.yaml

@@ -1,7 +1,7 @@
 id: imputationserver2-pgs
 name: Polygenic Score Calculation
 description: "You can upload genotyped data and the application imputes your genotypes, performs ancestry estimation and finally calculates Polygenic Risk Scores.<br><br>No dataset at hand? No problem, download our example dataset: <a href=\"https://imputationserver.sph.umich.edu/resources/50-samples.zip\" class=\"btn btn-sm btn-secondary\" style=\"color:#ffffff !important\"><i class=\"fa fa-file\"></i> 50-samples.zip</a><br><br>"
-version: 2.0.5
+version: 2.0.6
 website: https://imputationserver.readthedocs.io
 category: Application
 submitButton: Start Calculation

cloudgene.yaml

@@ -1,7 +1,7 @@
 id: imputationserver2
 name: Genotype Imputation
 description: This is the new Michigan Imputation Server Pipeline using <a href="https://github.com/statgen/Minimac4">Minimac4</a>. Documentation can be found <a href="http://imputationserver.readthedocs.io/en/latest/">here</a>.<br><br>If your input data is <b>GRCh37/hg19</b> please ensure chromosomes are encoded without prefix  (e.g. <b>20</b>).<br>If your input data is <b>GRCh38hg38</b> please ensure chromosomes are encoded with prefix 'chr' (e.g. <b>chr20</b>).
-version: 2.0.5
+version: 2.0.6
 website: https://imputationserver.readthedocs.io
 category: Application
 submitButton: Start Imputation

modules/local/quality_control/quality_control_vcf.nf

@@ -66,6 +66,7 @@ process QUALITY_CONTROL_VCF {
         --statistics-out ${statisticsDir} \
         --metafiles-out ${metaFilesDir} \
         --report qc_report.txt \
+        --no-index \
         $chain \
         $vcf_files 
 

nextflow.config

@@ -1,6 +1,6 @@
 manifest {
     name                                  = 'imputationserver2'
-    version                               = 'v2.0.5'
+    version                               = 'v2.0.6'
     description                           = 'Genotype Imputation Server 2'
     author                                = 'Lukas Forer & Sebastian Schönherr'
     homePage                              = 'https://github.com/genepi/imputationserver2'
@@ -96,7 +96,7 @@ profiles {
 
     docker.enabled                    = true
     singularity.enabled               = false
-    process.container                 = 'quay.io/genepi/imputationserver2:v2.0.5'
+    process.container                 = 'quay.io/genepi/imputationserver2:v2.0.6'
 
     test  {
          includeConfig 'conf/test.config'

tests/main.qc.nf.test

@@ -37,6 +37,26 @@ nextflow_pipeline {
 
     }
 
+    test("Should run QC-only including VCF 4.3 and indels") {
+
+        when {
+            params {
+                project  = "test-job"
+                build = "hg19"
+                files = "$projectDir/tests/data/input/chr20-phased/with_indels/*.vcf.gz"
+                allele_frequency_population = "eur"
+                mode = "qc-only"
+                refpanel_yaml = "$projectDir/tests/data/refpanels/hapmap2-hg38/cloudgene.yaml"
+                output = "${outputDir}"
+            }   
+        }
+
+        then {
+            assert workflow.success
+        }
+
+    }
+
     test("Should fail QC-only but publish files") {
 
         when {