alntools: add bam2ec process

src/nf_modules/alntools/main.nf

+version = "dd69682"
+container_url = "lbmc/alntools:${version}"
+
+process bam2ec {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "$file_id"
+
+  input:
+    tuple val(file_id), path(bam)
+    tuple val(gtf_id), path(gtf)
+
+  output:
+    tuple val(file_id), path("${bam.simpleName}.bin"), emit: bin
+    tuple val(gtf_id), path("${gtf.simpleName}_transcripts_lengths.tsv"), emit: tsv
+
+  script:
+"""
+awk -F"\t" '
+$3=="exon" 
+    {
+        ID=substr($9, length($9)-16, 15); 
+        L[ID]+=$5-$4+1
+    } 
+END{
+    for(i in L)
+        {print i"\t"L[i]}
+    }
+' ${gtf} ${gtf.simpleName}_transcripts_lengths.tsv
+alntools bam2ec -t ${gtf.simpleName}_transcripts_lengths.tsv -c 8 ${bam} ${bam.simpleName}.bin
+"""
+}
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