agat: add main.nf

src/nf_modules/agat/main.nf

+version = "0.8.0"
+container_url = "lbmc/agat:${version}"
+
+params.gff_to_bed = ""
+params.gff_to_bed_out = ""
+process gff_to_bed {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "$file_id"
+  if (params.gff_to_bed_out != "") {
+    publishDir "results/${params.gff_to_bed_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(gff)
+  output:
+    tuple val(file_id), path("*.bed"), emit: bed
+
+  script:
+"""
+agat_convert_sp_gff2bed.pl --gff ${gff} -o ${gff.simpleName}.bed
+"""
+}
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