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Simeon Rossmann
DivGene-genome-annotation
Commits
fc911927
Commit
fc911927
authored
1 year ago
by
Simeon
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working minimal nextflow script
parent
379a671f
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nextflow.config
+1
-0
1 addition, 0 deletions
nextflow.config
pinf_genome_annotation.nf
+14
-11
14 additions, 11 deletions
pinf_genome_annotation.nf
with
15 additions
and
11 deletions
nextflow.config
0 → 100644
+
1
−
0
View file @
fc911927
params
.
genome
=
"MP1831"
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pinf_genome_annotation.nf
+
14
−
11
View file @
fc911927
/* Concept for the genome annotation pipeline
/* Concept for the genome annotation pipeline
1. Parse genome to protein using gff2prot util from funannotate
1. Parse genome to protein using gff2prot util from funannotate
2. Remove everything after stop codon in protein fasta with:
2. Remove everything after stop codon in protein fasta with:
seqkit -> sed
seqkit -> sed
3.
3. */
*/
// Script parameters
// Script parameters
params
.
project
=
"/home/nibio/Documents/Erik_NCBI_tbl_test/Simeon_annotering/table2asn/"
params
.
genome
=
"genome_basename"
params
.
genome
=
"genome_basename"
params
.
genomeGFF
=
"${params.project}${params.genome}.gff"
params
.
genomeFasta
=
"${params.project}${params.genome}.fsa"
process
extractProteins
{
process
extractProteins
{
input:
input:
...
@@ -17,11 +16,15 @@ process extractProteins {
...
@@ -17,11 +16,15 @@ process extractProteins {
path
genomeGFF
path
genomeGFF
output:
output:
path
"${genome}_protein.fa"
path
"${params.genome}_protein.fa"
"""
"""
funannotate util gff2prot -g $genomeGFF -f $genomeFasta --no_stop |\
funannotate util gff2prot -g $genomeGFF -f $genomeFasta --no_stop | seqkit seq -w 0 | sed 's/\\*.*//' > "${params.genome}_protein.fa"
seqkit seq -w 0 |\
sed 's/\*.*//' >\
${genome}_protein.fa
"""
"""
}
}
workflow
{
def
genome_ch
=
Channel
.
fromPath
(
params
.
genomeFasta
)
extractProteins
(
genome_ch
,
params
.
genomeGFF
)
}
\ No newline at end of file
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