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SOaAS
psot.repository
Commits
8a98d304
Commit
8a98d304
authored
8 years ago
by
Lukas Jelonek
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Added nextflow driver script that runs signalp and blast
parent
ded79224
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8a98d304
params
.
file
=
"example/proteins.fas"
Channel
.
fromPath
(
params
.
file
).
into
{
for_blast
;
for_signalp
}
process
blast_swissprot
{
input:
file
fasta
from
for_blast
output:
file
"${fasta}.blast_swissprot.tsv"
into
blast_results
script:
"""
module_blast_swissprot.py --fasta $fasta > ${fasta}.blast_swissprot.tsv
"""
}
process
convert_blast_swissprot
{
input:
file
result
from
blast_results
output:
file
"${result}.json"
into
converted_blast_results
script:
"""
convert_blast_swissprot.py ${result} > ${result}.json
"""
}
process
signalp
{
input:
file
fasta
from
for_signalp
output:
file
"${fasta}.signalp.tsv"
into
signalp_results
script:
"""
module_signalp.py --fasta $fasta > ${fasta}.signalp.tsv
"""
}
process
convert_signalp
{
input:
file
result
from
signalp_results
output:
file
"${result}.json"
into
converted_signalp_results
script:
"""
convert_signalp.py ${result} > ${result}.json
"""
}
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