Commit 21c9ebdf authored by MARTIN Pierre's avatar MARTIN Pierre
Browse files

main.nf assembly refac

parent c6be9c97
......@@ -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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