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genotoul-bioinfo
metagWGS
Commits
21c9ebdf
Commit
21c9ebdf
authored
Sep 16, 2021
by
MARTIN Pierre
Browse files
main.nf assembly refac
parent
c6be9c97
Changes
1
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main.nf
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21c9ebdf
...
...
@@ -551,9 +551,10 @@ process assembly {
script:
if
(
params
.
assembly
==
'metaspades'
)
"""
metaspades.py -t ${task.cpus} -m ${spades_mem} -1 ${preprocessed_reads_R1} -2 ${preprocessed_reads_R2} -o ${params.assembly}
metaspades.py -t ${task.cpus} -m ${spades_mem} -1 ${preprocessed_reads_R1} -2 ${preprocessed_reads_R2} -o ${params.assembly}
mv ${params.assembly}/scaffolds.fasta ${params.assembly}/${sampleId}.contigs.fa
mv ${params.assembly}/spades.log ${params.assembly}/${sampleId}.log
mv ${params.assembly}/params.txt ${params.assembly}/${sampleId}.params.txt
"""
else
if
(
params
.
assembly
==
'megahit'
)
"""
...
...
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