ext-tools: add pydnatic

opencga-app/app/cloud/docker/opencga-ext-tools/Dockerfile

@@ -14,9 +14,9 @@ RUN apt-get update -y && \
     libssl-dev libssh-dev libxml2-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev \
     gnuplot pandoc samtools bcftools tabix fastqc plink1.9 bwa r-base wget libopenblas0-openmp libcholmod3 libsuitesparse-dev && \
     apt-get remove libopenblas0-pthread && \
+    pip3 install pydantic && \
 
     ## 2. Install samtools and bcftools 1.21 and plugins
-#     apt-get update -y && apt-get install -y wget && \
     wget https://github.com/samtools/samtools/releases/download/1.21/samtools-1.21.tar.bz2 && \
     tar xjvf samtools-1.21.tar.bz2 && \
     cd samtools-1.21 && \

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java

@@ -1486,10 +1486,10 @@ public class RunLiftoverCommandOptions {
         @Parameter(names = {"--files"}, description = "List of VCF files to lift over", required = false, arity = 1)
         public String files;
 
-        @Parameter(names = {"--target-assembly"}, description = "Target assembly for lift over. Valid values: GRCh38 (for Ensembl) or hg38 (for NCBI)", required = false, arity = 1)
+        @Parameter(names = {"--target-assembly"}, description = "Target assembly for lift over. Valid values: GRCH38 (for Ensembl) or HG38 (for NCBI)", required = false, arity = 1)
         public String targetAssembly;
 
-        @Parameter(names = {"--vcf-destination"}, description = "Destination path where the lifted-over VCF files will be stored. If left empty, the VCF files will be stored in the job folder. If the keyword OPENCGA_VCF_INPUT_FOLDER is used, they will be stored in the same folder as the input VCF files. Otherwise, they will be stored in the specified destination path", required = false, arity = 1)
+        @Parameter(names = {"--vcf-destination"}, description = "Destination path where the lifted-over VCF files will be stored. If left empty, the VCF files will be stored in the job folder. If the keyword OPENCGA_VCF_INPUT_FOLDER is used, then VCF files be stored in the same folder as the input VCF files. Otherwise, they will be stored in the specified destination path", required = false, arity = 1)
         public String vcfDestination;
 
         @Parameter(names = {"--outdir"}, description = "Output dir for the job.", required = false, arity = 1)

opencga-client/src/main/R/R/Variant-methods.R

@@ -389,7 +389,7 @@ setMethod("variantClient", "OpencgaR", function(OpencgaR, endpointName, params=N
         #' @param jobScheduledStartTime Time when the job is scheduled to start.
         #' @param jobPriority Priority of the job.
         #' @param jobDryRun Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
-        #' @param data BCFtools +liftover plugin parameterss.
+        #' @param data BCFtools +liftover plugin parameters.
         runLiftover=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL, subcategory="variant/liftover",
                 subcategoryId=NULL, action="run", params=params, httpMethod="POST", as.queryParam=NULL, ...),
 

opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java

@@ -552,7 +552,7 @@ public RestResponse<Job> runKnockout(KnockoutAnalysisParams data, ObjectMap para
 
     /**
      * BCFtools liftover plugin maps coordinates from assembly 37 to 38.
-     * @param data BCFtools +liftover plugin parameterss.
+     * @param data BCFtools +liftover plugin parameters.
      * @param params Map containing any of the following optional parameters.
      *       study: study.
      *       jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.

opencga-client/src/main/javascript/Variant.js

@@ -445,7 +445,7 @@ export default class Variant extends OpenCGAParentClass {
     }
 
     /** BCFtools liftover plugin maps coordinates from assembly 37 to 38.
-    * @param {Object} data - BCFtools +liftover plugin parameterss.
+    * @param {Object} data - BCFtools +liftover plugin parameters.
     * @param {Object} [params] - The Object containing the following optional parameters:
     * @param {String} [params.study] - study.
     * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not

opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py

@@ -575,7 +575,7 @@ def run_liftover(self, data=None, **options):
         BCFtools liftover plugin maps coordinates from assembly 37 to 38.
         PATH: /{apiVersion}/analysis/variant/liftover/run
 
-        :param dict data: BCFtools +liftover plugin parameterss. (REQUIRED)
+        :param dict data: BCFtools +liftover plugin parameters. (REQUIRED)
         :param str study: study.
         :param str job_id: Job ID. It must be a unique string within the
             study. An ID will be autogenerated automatically if not provided.