setupFileCreator regex bug

[Mario Giovacchini]

I've got four samples:

• NA10860_Nano
• NA10860_PCR-free
• NA11993_Nano
• NA11993_PCR-free

When processing them with the ngi_pipeline I get a failure for the two samples which end with PCR-free whereas the samples ending with Nano have no trouble; thus I suspect the hyphen is causing the regex to fail.

The traceback:

[2014-09-05 09:49] INFO: ngi_pipeline.piper_ngi: Building Piper setup.xml file for project "ND-0522" sample "NA10860_PCR-free", libprep "A", seqrun "140821_D00458_0029_AC45JGANXX"
[2014-09-05 09:49] INFO: ngi_pipeline.piper_ngi: Executing command line: setupFileCreator --output /proj/a2010002/nobackup/NGI/analysis_ready/ANALYSIS/ND-0522/ND-0522-NA10860_PCR-free-140821_D00458_0029_AC45JGANXX_setup.xml --project_name ND-0522 --sequencing_platform Illumina --sequencing_center NGI --uppnex_project
_id a2010002 --reference /proj/a2009002/piper_references/gatk_bundle/2.8/b37/human_g1k_v37.fasta  --input_fastq /proj/a2010002/nobackup/NGI/analysis_ready/DATA/ND-0522/NA10860_PCR-free/A/140821_D00458_0029_AC45JGANXX/NA10860_PCR-free_ATCACG_L001_R1_001.fastq.gz --input_fastq /proj/a2010002/nobackup/NGI/analysis_ready
/DATA/ND-0522/NA10860_PCR-free/A/140821_D00458_0029_AC45JGANXX/NA10860_PCR-free_ATCACG_L001_R2_001.fastq.gz --input_fastq /proj/a2010002/nobackup/NGI/analysis_ready/DATA/ND-0522/NA10860_PCR-free/A/140821_D00458_0029_AC45JGANXX/NA10860_PCR-free_ATCACG_L002_R1_001.fastq.gz --input_fastq /proj/a2010002/nobackup/NGI/anal
ysis_ready/DATA/ND-0522/NA10860_PCR-free/A/140821_D00458_0029_AC45JGANXX/NA10860_PCR-free_ATCACG_L002_R2_001.fastq.gz
Exception in thread "main" java.lang.IllegalArgumentException: requirement failed: Just one sample hit should be possible for regexp, found: 0
        at scala.Predef$.require(Predef.scala:233)
        at molmed.apps.Sthlm2UUSNP$.parseSampleInfoFromFileHierarchy(Sthlm2UUSNP.scala:172)
        at molmed.apps.setupcreator.SetupUtils$.molmed$apps$setupcreator$SetupUtils$$parseInfoFromFile$1(SetupUtils.scala:310)
        at molmed.apps.setupcreator.SetupUtils$$anonfun$5.apply(SetupUtils.scala:314)
        at molmed.apps.setupcreator.SetupUtils$$anonfun$5.apply(SetupUtils.scala:314)
        at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
        at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
        at scala.collection.immutable.Set$Set4.foreach(Set.scala:137)
        at scala.collection.TraversableLike$class.map(TraversableLike.scala:244)
        at scala.collection.AbstractSet.scala$collection$SetLike$$super$map(Set.scala:47)
        at scala.collection.SetLike$class.map(SetLike.scala:93)
        at scala.collection.AbstractSet.map(Set.scala:47)
        at molmed.apps.setupcreator.SetupUtils$.createXMLFromIGNHierarchy(SetupUtils.scala:314)
        at molmed.apps.setupcreator.SetupFileCreator$.createSetupFile(SetupFileCreator.scala:92)
        at molmed.apps.setupcreator.SetupFileCreator$$anonfun$10.apply(SetupFileCreator.scala:65)
        at molmed.apps.setupcreator.SetupFileCreator$$anonfun$10.apply(SetupFileCreator.scala:58)
        at scala.Option.map(Option.scala:145)
        at molmed.apps.setupcreator.SetupFileCreator$delayedInit$body.apply(SetupFileCreator.scala:58)
        at scala.Function0$class.apply$mcV$sp(Function0.scala:40)
        at scala.runtime.AbstractFunction0.apply$mcV$sp(AbstractFunction0.scala:12)
        at scala.App$$anonfun$main$1.apply(App.scala:71)
        at scala.App$$anonfun$main$1.apply(App.scala:71)
        at scala.collection.immutable.List.foreach(List.scala:318)
        at scala.collection.generic.TraversableForwarder$class.foreach(TraversableForwarder.scala:32)
        at scala.App$class.main(App.scala:71)
        at molmed.apps.setupcreator.SetupFileCreator$.main(SetupFileCreator.scala:13)
        at molmed.apps.setupcreator.SetupFileCreator.main(SetupFileCreator.scala)

The directory tree:

mario@nestor1 /proj/a2010002/nobackup/NGI/analysis_ready/DATA/ND-0522 $ tree
.
├── NA10860_Nano
│   └── A
│       └── 140821_D00458_0029_AC45JGANXX
│           ├── NA10860_Nano_GATCAG_L005_R1_001.fastq.gz
│           ├── NA10860_Nano_GATCAG_L005_R2_001.fastq.gz
│           ├── NA10860_Nano_GATCAG_L006_R1_001.fastq.gz
│           └── NA10860_Nano_GATCAG_L006_R2_001.fastq.gz
├── NA10860_PCR-free
│   └── A
│       └── 140821_D00458_0029_AC45JGANXX
│           ├── NA10860_PCR-free_ATCACG_L001_R1_001.fastq.gz
│           ├── NA10860_PCR-free_ATCACG_L001_R2_001.fastq.gz
│           ├── NA10860_PCR-free_ATCACG_L002_R1_001.fastq.gz
│           └── NA10860_PCR-free_ATCACG_L002_R2_001.fastq.gz
├── NA11993_Nano
│   └── A
│       └── 140821_D00458_0029_AC45JGANXX
│           ├── NA11993_Nano_TAGCTT_L007_R1_001.fastq.gz
│           ├── NA11993_Nano_TAGCTT_L007_R2_001.fastq.gz
│           ├── NA11993_Nano_TAGCTT_L008_R1_001.fastq.gz
│           └── NA11993_Nano_TAGCTT_L008_R2_001.fastq.gz
└── NA11993_PCR-free
    └── A
        └── 140821_D00458_0029_AC45JGANXX
            ├── NA11993_PCR-free_TTAGGC_L003_R1_001.fastq.gz
            ├── NA11993_PCR-free_TTAGGC_L003_R2_001.fastq.gz
            ├── NA11993_PCR-free_TTAGGC_L004_R1_001.fastq.gz
            └── NA11993_PCR-free_TTAGGC_L004_R2_001.fastq.gz

[Johan Dahlberg]

Hey @mariogiov! Try this out now.