diff --git a/README.md b/README.md index 8da9089..f14970f 100644 --- a/README.md +++ b/README.md @@ -27,7 +27,7 @@ If you encounter any problems, feel free to open an issue [here](https://github. ## Version History -[Version 2.0.3 - Version 2.0.6](https://github.com/bystrogenomics/imputationserver2/releases/tag/v2.0.7) - Fix QC issues and remove HTSJDK index creation for input validation and QC. +[Version 2.0.3 - Version 2.0.6](https://github.com/bystrogenomics/imputationserver2/releases/tag/v2.0.8) - Fix QC issues and remove HTSJDK index creation for input validation and QC. [Version 2.0.2](https://github.com/bystrogenomics/imputationserver2/releases/tag/v2.0.2) - Set minimac4 tmp directory (required for larger sample sizes). diff --git a/modules/local/input_validation/input_validation_vcf.nf b/modules/local/input_validation/input_validation_vcf.nf index 54b2509..66b8cff 100644 --- a/modules/local/input_validation/input_validation_vcf.nf +++ b/modules/local/input_validation/input_validation_vcf.nf @@ -10,7 +10,7 @@ process INPUT_VALIDATION_VCF { output: path("validated_vcfs/*.vcf.gz"), emit: validated_files - path("skipped_vcfs/*.vcf.gz"), emit: skipped_files + path("skipped_vcfs/*.vcf.gz"), emit: skipped_files, optional: true path("validation_report.txt"), emit: validation_report script: @@ -161,17 +161,23 @@ EOF vcf_files_to_validate+=("\$f") mv "\$f" validated_vcfs/ - if [ -f "\$f.csi" ] || [ -f "\$f.tbi" ]; then - mv "\$f".csi validated_vcfs/ - mv "\$f".tbi validated_vcfs/ + if [ -f "\$f.csi" ] ; then + mv "\$f.csi" validated_vcfs/ + fi + + if [ -f "\$f.tbi" ]; then + mv "\$f.tbi" validated_vcfs/ fi else skipped_vcfs+=("\$f") mv "\$f" skipped_vcfs/ - if [ -f "\$f.csi" ] || [ -f "\$f.tbi" ]; then - mv "\$f".csi skipped_vcfs/ - mv "\$f".tbi skipped_vcfs/ + if [ -f "\$f.csi" ] ; then + mv "\$f.csi" skipped_vcfs/ + fi + + if [ -f "\$f.tbi" ]; then + mv "\$f.tbi" skipped_vcfs/ fi fi done diff --git a/nextflow.config b/nextflow.config index 1fdd5b0..89b7062 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,6 +1,6 @@ manifest { name = 'imputationserver2' - version = 'v2.0.7' + version = 'v2.0.8' description = 'Genotype Imputation Server 2' author = 'Lukas Forer & Sebastian Schönherr' homePage = 'https://github.com/bystrogenomics/imputationserver2' @@ -98,7 +98,7 @@ profiles { docker.enabled = true singularity.enabled = false - process.container = 'bystrogenomics/imputationserver2:v2.0.7' + process.container = 'bystrogenomics/imputationserver2:v2.0.8' test { includeConfig 'conf/test.config'