Changeset 6003


Ignore:
Timestamp:
Sep 14, 2020, 9:45:04 AM (12 months ago)
Author:
Nicklas Nordborg
Message:

References #1266: Run prepDE.py in the StringTie? pipeline

Better to use the name of the StringTie item instead of the alignment.

File:
1 edited

Legend:

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  • extensions/net.sf.basedb.reggie/branches/4.27-stable/src/net/sf/basedb/reggie/grid/StringTieJobCreator.java

    r6001 r6003  
    228228
    229229      // Create raw bioassay
    230       String rawName = as.getNextRawBioAssayName(dc, stringTieType);
     230      String stringTieName = as.getNextRawBioAssayName(dc, stringTieType);
    231231      RawBioAssay raw = stringTieType.createRawBioAssay(dc);
    232232      Pipeline.RNASEQ_HISAT_STRINGTIE.setAnnotation(dc, raw);
    233233      raw.setArrayDesign(arrayDesign);
    234234      raw.setJob(stringTieJob);
    235       raw.setName(rawName);
     235      raw.setName(stringTieName);
    236236      raw.setParentExtract(lib.getExtract());
    237237      raw.setSoftware(software);
     
    308308      prepDECmd += " -g stringtie/gene_count.csv";
    309309      prepDECmd += " -t stringtie/transcript_count.csv";
    310       script.cmd("echo " + alignedName + " ./stringtie/transcript.gtf > input.lst");
     310      script.cmd("echo " + stringTieName + " ./stringtie/transcript.gtf > input.lst");
    311311      script.cmd(prepDECmd + " > stringtie/prepde.out");
    312312      script.newLine();
     
    318318      if (externalGroup != null)
    319319      {
    320         ScriptUtil.addChgrp(externalGroup, "${StringTieFolder}", rawName, null, script);
     320        ScriptUtil.addChgrp(externalGroup, "${StringTieFolder}", stringTieName, null, script);
    321321      }
    322322      script.cmd("ls -1 ${StringTieFolder}/* >> ${WD}/files.out");
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