nextflow test script

test.nf

import groovy.json.JsonSlurper

def jsonSlurper = new JsonSlurper()

res = jsonSlurper.parse(new URL('https://api-omicidx.cancerdatasci.org/sra/1.0/search/run?q=experiment_accession:' + params.experiment + '&size=500'))

l = res.hits.hits.collect {
    [ it._source.experiment_accession, it._source.accession ]
}

params.transcript_fa = "transcripts.fa"

transcript_fa = file(params.transcript_fa)

srrs = Channel.from( l )

process salmonIndex {
    cpus 4
    memory '12 GB'
    
  input:
  file transcript_fa
  
  output:
  file 'index' into index
  
  """
  /home/ubuntu/salmon-0.11.3-linux_x86_64/bin/salmon index -p 4 --gencode -i index --transcripts $transcript_fa
  """

}

process produceSequences {
    tag { srr }

    // publishDir "s3://starbuck1/tmp/${srr}", mode: 'copy'

    input:
    set srx, srr from srrs
    

    output:
    set srx, file("SRR*.fastq.gz") into (records, records2)


    """
    /home/ubuntu/sratoolkit.2.9.2-ubuntu64/bin/fastq-dump --split-files --gzip $srr
    """

}


collated = records2.groupTuple()

// paired = records2.filter { it.get(1) instanceof List }
// single = records3.filter { !(it.get(1) instanceof List) }

// single.subscribe { println("single: $it")}

process align {
    tag { srx }
    cpus 4
    memory '12 GB'

    publishDir "s3://starbuck1/tmp/${srx}", mode: 'copy'

    input: 
    set srx, file(f) from collated
    file index from index
    
    output:
    file('quants')
    
    """
    /home/ubuntu/salmon-0.11.3-linux_x86_64/bin/salmon quant \
        --numGibbsSamples 25 -o quants -p 4 -l A -i index -r ${f}
    gzip quants/quant.sf
    """
}



/* records.subscribe { println(it.get(0)) } */
index.subscribe { println(it) }