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

seqkit for filter

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