emase-zero: add count workflow

src/nf_modules/emase-zero/main.nf

+version = "0.3.1"
+container_url = "lbmc/emase-zero:${version}"
+
+include { tr2g } from "./../kb/main.nf"
+
+
+params.count = "-m 2"
+params.count_out = ""
+workflow count {
+  take:
+    bin
+    transcript_length
+    gtf
+
+  main:
+    tr2g(gtf, channel.of(["NO T2G", ""]))
+    emase(bin, transcript_length, tr2g.out.t2g)
+
+  emit:
+    count: emase.count
+}
+
+process emase {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "$file_id"
+  if (params.count_out != "") {
+    publishDir "results/${params.count_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(bin)
+    tuple val(transcript_length_id), path(transcript_length)
+    tuple val(transcript_to_gene_id), path(transcript_to_gene)
+
+  output:
+    tuple val(file_id), path("${bin.simpleName}.quantified"), emit: count
+
+  script:
+"""
+emase-zero ${params.count} \
+  -b ${bin} \
+  -o ${bin.simpleName}.quantified \
+  -l ${transcript_length} \
+  -g ${transcript_to_gene}
+"""
+}
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