From d7a746149bd8667e1602795e47d09a1306e7f168 Mon Sep 17 00:00:00 2001 From: Abhinav Sharma Date: Sat, 18 Jul 2020 14:30:40 +0530 Subject: [PATCH] save only the scaffolds fasta file --- main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/main.nf b/main.nf index cb265a0..2658fa4 100644 --- a/main.nf +++ b/main.nf @@ -29,14 +29,14 @@ process spades { tuple genomeName, file(genomeReads) from ch_in_spades output: - path """${genomeName}""" into ch_out_spades + path """${genomeName}_scaffolds.fasta""" into ch_out_spades script: """ spades.py -k 21,33,55,77 --careful --only-assembler --pe1-1 ${genomeReads[0]} --pe1-2 ${genomeReads[1]} -o ${genomeName} -t 2 + cp ${genomeName}/scaffolds.fasta ${genomeName}_scaffolds.fasta """ } -// TODO we only need to store the genomeName/scaffolds.fasta as genomeName_scaffolds.fasta