initial nextflow

pinf_genome_annotation.nf

+/* Concept for the genome annotation pipeline
+
+1. Parse genome to protein using gff2prot util from funannotate
+2. Remove everything after stop codon in protein fasta with:
+    seqkit -> sed
+3. 
+
+
+*/
+
+// Script parameters
+params.genome = "genome_basename"
+
+process extractProteins {
+    input:
+    path genomeFasta
+    path genomeGFF
+
+    output:
+    path "${genome}_protein.fa"
+    """
+    funannotate util gff2prot -g $genomeGFF -f $genomeFasta --no_stop |\
+     seqkit seq -w 0 |\
+     sed 's/\*.*//' >\
+     ${genome}_protein.fa
+    """
+}