workflows not submitting properly

[GoogleCodeExporter]

same problem as before, sort of.  Got this on some but not all samples:

Submitting Sample: #Sample: ESR-13 (Gruber Sequencing of Homo sapiens)
java.lang.NullPointerException
    at java.io.File.<init>(File.java:265)
    at edu.usc.epigenome.workflow.generator.RNAseqV2Workflow.createWorkFlow(RNAseqV2Workflow.java:153)
    at edu.usc.epigenome.workflow.SequencingPipeline.main(SequencingPipeline.java:78)

Worked for whole flow cell (C4YC8ACXX) except the last two lanes.  These two 
lanes also had edits done by hand, maybe not a coincidence?

Original issue reported on code.google.com by cmnico...@gmail.com on 8 Jul 2014 at 12:00

[GoogleCodeExporter]

ahh, i see it:

notice that the genome is on a separate line after the "=" . I should make my 
submitWorkflow.pl check for this.

This is vi's fault though, for some reason it likes to throw in linebreaks. the 
work around is to put vi into "paste mode" by typeing
:set paste

then doing your paste into the terminal.

#Sample: ESR-9 (Gruber Sequencing of Homo sapiens)
Sample.41.SampleID = SAN1706A32
Sample.41.Lane = 8
Sample.41.Input = ESR-9_AACCAG_L008_R1_001.fastq.gz
Sample.41.Workflow = rnaseqv2
Sample.41.Reference =
/home/uec-00/shared/production/genomes/encode_hg19_mf/male.hg19

Original comment by zack...@gmail.com on 8 Jul 2014 at 4:40

[GoogleCodeExporter]

Thanks!  I COULD NOT get rid of those line breaks, really weird.  Had to do
it by hand in vi.  All is well now

Original comment by cmnico...@gmail.com on 8 Jul 2014 at 4:17

[GoogleCodeExporter]

Original comment by zack...@gmail.com on 8 Jul 2014 at 11:34

• Changed state: Done