prj init

hello_world.nf

@@ -0,0 +1,73 @@
+// 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()
+}