Re: unbound variable error

[Paolo Di Tommaso]

Hello, 

Note the difference between single quote and double quote multi-line strings. Check here and here.

Also you you provide all SAM inputs using a proper process definition without using absolute paths, otherwise you script won't be portable. See for example this and this. 

Hope it helps.

Cheers, Paolo

On Mon, Jun 20, 2016 at 4:30 AM, Brandon <brandon.k...@gmail.com> wrote:

Hello, All

I'm the newbie in nextflow. so I confused.

 

[2d/07cf59] Cached process > seqcluster_prepare (1)
[be/3f6b6f] Submitted process > mapping (1)
Error executing process > 'mapping (1)'
Caused by:
  Process 'mapping (1)' terminated with an error exit status
Command executed:
  /BiO/BioTools/bcbio/data/anaconda/bin/STAR --genomeDir /BiO/BioTools/bcbio/data/genomes/Hsapiens/hg19/star --readFilesIn ${read} --runThreadN 1 --outFileNamePrefix --outReadsUnmapped Fastx --outFilterMultimapNmax 1000 --outStd SAM --alignIntronMax 1 --outSAMunmapped Within --outSAMattributes NH HI NM MD AS  --sjdbGTFfile /BiO/BioTools/bcbio/data/genomes/Hsapiens/hg19/rnaseq/ref-transcripts.gtf  --sjdbOverhang 39  --outSAMattrRGline ID:miRQC_A PL:illumina PU:1_2016-04-08_mirqc_bcbio SM:miRQC_A
Command exit status:
  1
Command output:
  (empty)
Command error:
  .command.sh: line 2: read: unbound variable
  .command.run.1: line 90: 40546 Terminated              nxf_trace "$pid" .command.trace
Work dir:
  /BiO/BioPeople/brandon/test_nextflow/smrna/work/be/3f6b6f6cdb8fb3974696f4bf25cb06
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named: '.command.sh'

process mapping{

        input:

        set read from seqs_fa

        script:

        '''

        /BiO/BioTools/bcbio/data/anaconda/bin/STAR --genomeDir /BiO/BioTools/bcbio/data/genomes/Hsapiens/hg19/star --readFilesIn ${read} --runThreadN 1 --outFileNamePrefix --outReadsUnmapped Fastx --outFilterMultimapNmax 1000 --outStd SAM --alignIntronMax 1 --outSAMunmapped Within --outSAMattributes NH HI NM MD AS  --sjdbGTFfile /BiO/BioTools/bcbio/data/genomes/Hsapiens/hg19/rnaseq/ref-transcripts.gtf  --sjdbOverhang 39  --outSAMattrRGline ID:miRQC_A PL:illumina PU:1_2016-04-08_mirqc_bcbio SM:miRQC_A

        '''

Why is not converting for ${read}  in this script ?

please check this.

Thanks. 

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