removed everything but sample from Fetch_SRA_to_BAM_BAM_only

broadinstitute · Jul 14, 2024 · c60daa7 · c60daa7
1 parent deb4065
commit c60daa7
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/pipes/WDL/tasks/tasks_ncbi_tools.wdl b/pipes/WDL/tasks/tasks_ncbi_tools.wdl
@@ -184,13 +184,13 @@ task Fetch_SRA_to_BAM_BAM_only {
 #        CENTER=$(jq -r .EXPERIMENT_PACKAGE_SET.EXPERIMENT_PACKAGE.SUBMISSION.center_name SRA.json)
 #        PLATFORM=$(jq -r '.EXPERIMENT_PACKAGE_SET.EXPERIMENT_PACKAGE.EXPERIMENT.PLATFORM | keys[] as $k | "\($k)"' SRA.json)
 #        MODEL=$(jq -r ".EXPERIMENT_PACKAGE_SET.EXPERIMENT_PACKAGE.EXPERIMENT.PLATFORM.$PLATFORM.INSTRUMENT_MODEL" SRA.json)
-#        SAMPLE=$(jq -r '.EXPERIMENT_PACKAGE_SET.EXPERIMENT_PACKAGE.SAMPLE.IDENTIFIERS.EXTERNAL_ID|select(.namespace == "BioSample")|.content' SRA.json)
+        SAMPLE=$(jq -r '.EXPERIMENT_PACKAGE_SET.EXPERIMENT_PACKAGE.SAMPLE.IDENTIFIERS.EXTERNAL_ID|select(.namespace == "BioSample")|.content' SRA.json)
 #        LIBRARY=$(jq -r .EXPERIMENT_PACKAGE_SET.EXPERIMENT_PACKAGE.EXPERIMENT.alias SRA.json)
 #        RUNDATE=$(jq -r '(.EXPERIMENT_PACKAGE_SET.EXPERIMENT_PACKAGE.RUN_SET | (if (.RUN|type) == "object" then (.RUN) else (.RUN[] | select(any(.; .accession == "~{SRA_ID}"))) end) | .SRAFiles) | if (.SRAFile|type) == "object" then .SRAFile.date else [.SRAFile[]|select(.supertype == "Original" or .supertype=="Primary ETL")][0].date end' SRA.json | cut -f 1 -d ' ')
 
-#        if [[ -n "~{sample_name}" ]]; then
-#            SAMPLE="~{sample_name}"
-#        fi
+        if [[ -n "~{sample_name}" ]]; then
+            SAMPLE="~{sample_name}"
+        fi
 
 #        if [ "$PLATFORM" = "OXFORD_NANOPORE" ]; then
 #            # per the SAM/BAM specification