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comparison nf/subworkflows/ncbi/default/annotwriter/main.nf @ 0:d9c5c5b87fec draft

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planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
author fubar
date Sat, 03 Aug 2024 11:16:53 +0000
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-1:000000000000 0:d9c5c5b87fec
1 #!/usr/bin/env nextflow
2 nextflow.enable.dsl=2
3
4
5 workflow annotwriter {
6 take:
7 accept_asn_file // Channel: accept.asn file
8 parameters // Map : extra parameter and parameter update
9 main:
10 c = run_annotwriter(accept_asn_file)
11 emit:
12 annoted_file = c
13 }
14
15
16 process run_annotwriter {
17 input:
18 path accept_asn_file
19 output:
20 path ('output/accept.gff'), emit: 'annoted_file'
21
22 script:
23 """
24 mkdir -p output
25 if [ -s ${accept_asn_file} ]; then
26 annotwriter -i ${accept_asn_file} -nogenbank -format gff3 -o output/accept.gff
27 else
28 touch output/accept.gff
29 fi
30 """
31
32 stub:
33 """
34 mkdir -p output
35 echo "1" > output/accept.gff
36 """
37 }