Commit bdc2326e authored by Midoux Cedric's avatar Midoux Cedric
Browse files

seqkit for filter

parent b0ea3a92
......@@ -13,6 +13,5 @@ snakemake \
--jobs 80 \
--wait-for-files \
--latency-wait 150 \
--use-conda \
--verbose \
--printshellcmds
......@@ -74,8 +74,7 @@ rule metaspades:
input:
unpack(assembly_input)
output:
contigs = "work/metaSPADES/{reads}/{reads}.contigs.fasta",
log = "work/metaSPADES/{reads}/{reads}-filter.log"
contigs = "work/metaSPADES/{reads}/{reads}.contigs.fasta"
threads:
20
params:
......@@ -92,11 +91,15 @@ rule metaspades:
"{params.input} "
"-o {params.output} "
" ; "
"filterSeq.py "
"-i work/metaSPADES/{wildcards.reads}/contigs.fasta "
"-o {output.contigs} "
"-l {output.log} "
"--min-length {params.min_len} "
"conda activate seqkit-0.10.1 "
" ; "
"seqkit "
"seq "
"--min-len {params.min_len} "
"--out-file {output.contigs} "
"work/metaSPADES/{wildcards.reads}/contigs.fasta "
" ; "
"conda deactivate"
def contigs_input(wildcards):
if wildcards.sample == "catalogue":
......
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