drop_file.js

// mongo opencga_user_project

/*
var studyId = ??;
var fileIds = [??];
var sampleIds = [??];
*/
function dropFiles(studyId, fileIds, sampleIds) {
  db.variants.update(
    {
      "studies" : {
        $elemMatch: { 
          "sid" : studyId,
          "files.fid" : { $in : fileIds }
        }
      }
    }, {
      $pull:{
        "studies.$.files":{fid:{$in:fileIds}}, 
        "studies.$.gt.?/?" : {$in:sampleIds},
        "studies.$.gt.0/1" : {$in:sampleIds},
        "studies.$.gt.1/1" : {$in:sampleIds} // Add other genotypes
      }
    } , {multi:true})

  db.studies.update({"_id":studyId},{$pull:{"indexedFiles":{$in:fileIds}}})
  db.files.drop({"fileId":{$in:fileIds}})
  // Remove from stage collection
}
// mongo opencga_catalog

db.file.update({"_id":{$in:fileIds}}, {$set:{"index.status":"NONE"}}, {multi:true})