seqkit for filter

RunSnake.sh

@@ -13,6 +13,5 @@ snakemake \
 --jobs 80 \
 --wait-for-files \
 --latency-wait 150 \
---use-conda \
 --verbose \
 --printshellcmds

assembly.smk

@@ -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":