// ch1 = Channel.value( 'GRCh38' )
// ch2 = Channel.value( ['chr1', 'chr2', 'chr3', 'chr4', 'chr5'] )
// ch3 = Channel.value( ['chr1' : 248956422, 'chr2' : 242193529, 'chr3' : 198295559] )
// ch1.view()
// ch2.view()
// ch3.view()


// chromosome_ch = Channel.of(1..22, 'X', 'Y')
// chromosome_ch.view()

// ch_vl = Channel.value('GRCh38')
// ch_qu = Channel.of(1..4)

// ch_vl.view()
// ch_qu.view()

// aligner_list = ['salmon', 'kallisto']

// aligner_ch = Channel.fromList(aligner_list)

// aligner_ch.view()

// ids = ['ERR908507', 'ERR908506', 'ERR908505']

// q_ids = Channel.fromList(ids)
// q_ids.view()

// q_val = Channel.value(ids)
// q_val.view()

// read_ch = Channel.fromPath( '../**.png', hidden: true )
// read_ch.view()

// read_ch = Channel.fromPath( 'data/chicken/reads/*.fq.gz', checkIfExists: true, hidden: true )
// read_ch.view()


// -process.debug


// params.chr = "chr2"

// process CHR_COUNT {

//   script:
//   """
//   printf "Number of sequences for chromosome ${params.chr} :"
//   grep -c '>'${params.chr} ${projectDir}/../Downloads/dm6.fa
//   """
// }

// workflow {
//     CHR_COUNT()
// }

process NUM_IDS {

  script:
  """
  #set bash variable NUMIDS
  NUMIDS=`grep -c '^>' $params.transcriptome`

  echo 'Number of sequences'
  printf "%'d\n" \$NUMIDS
  """
}

params.transcriptome = "${projectDir}/../Downloads/dm6.fa"

workflow {
  NUM_IDS()
}