gffread: add main.nf

src/nf_modules/gffread/main.nf

+version = "0.12.2"
+container_url = "lbmc/gffread:${version}"
+
+params.gffread = ""
+params.gffread_out = ""
+process gffread {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "$file_prefix"
+  if (params.gffread_out != "") {
+    publishDir "results/${params.gffread_out}", mode: 'copy'
+  }
+
+  input:
+  tuple val(file_id), path(gtf)
+  tuple val(fasta_id), path(fasta)
+
+  output:
+    tuple val(fasta_id), path("${file_prefix}.fasta"), emit: fasta
+
+  script:
+  if (file_id instanceof List){
+    file_prefix = file_id[0]
+  } else {
+    file_prefix = file_id
+  }
+  """
+  gffread ${gtf} -g ${fasta} -o ${file_prefix}.fasta
+  """
+}
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