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MORICE Jérôme
panBrass
Commits
c5469a84
Commit
c5469a84
authored
1 month ago
by
MORICE Jérôme
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Pipeline/panBrass.nf
+3
-3
3 additions, 3 deletions
Pipeline/panBrass.nf
scripts/PrepareChrSizeFile/src/PrepareChrSizeFile.py
+1
-1
1 addition, 1 deletion
scripts/PrepareChrSizeFile/src/PrepareChrSizeFile.py
with
4 additions
and
4 deletions
Pipeline/panBrass.nf
+
3
−
3
View file @
c5469a84
...
...
@@ -184,18 +184,18 @@ process prepareChrSize {
tuple val(nameInputChannel), file(correspondanceChromosomeFileInputChannel), file(chrFastaFileInputChannel)
output:
path "${nameInputChannel}.
{
chr.size
}
"
path "${nameInputChannel}.chr.size
.txt
"
// copy the prepareChrSize output files located in the work folder and paste them in a folder of my choice
//publishDir "$prepareChrSizeOutputDir", mode: 'copy'
publishDir "$prepareChrSizeOutputDir", mode: 'copy', pattern: '*.chr.size'
publishDir "$prepareChrSizeOutputDir", mode: 'copy', pattern: '*.chr.size
.txt
'
script:
"""
#echo $nameInputChannel $correspondanceChromosomeFileInputChannel $chrFastaFileInputChannel
#head -5 $correspondanceChromosomeFileInputChannel
#head -5 $chrFastaFileInputChannel
python3 /panbrass/scripts/PrepareChrSizeFile/src/PrepareChrSizeFile.py --fasta $chrFastaFileInputChannel --rename $correspondanceChromosomeFileInputChannel --chr_size_output ${nameInputChannel}.chr.size
python3 /panbrass/scripts/PrepareChrSizeFile/src/PrepareChrSizeFile.py --fasta $chrFastaFileInputChannel --rename $correspondanceChromosomeFileInputChannel --chr_size_output ${nameInputChannel}.chr.size
.txt
"""
}
...
...
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scripts/PrepareChrSizeFile/src/PrepareChrSizeFile.py
+
1
−
1
View file @
c5469a84
...
...
@@ -20,5 +20,5 @@ with gzip.open(args['fasta'],'rt') as handle:
for
record
in
SeqIO
.
parse
(
handle
,
"
fasta
"
):
if
(
record
.
id
in
conv
):
# On l'ecrit dans le fichier
os
.
write
(
conv
[
record
.
id
]
+
"
\t
"
+
str
(
len
(
record
))
+
"
\n
"
)
os
.
write
(
conv
[
record
.
id
]
+
"
"
+
str
(
len
(
record
))
+
"
\n
"
)
os
.
close
()
\ No newline at end of file
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