From 2c58d9fb22fad14c03e2c8a848a2c2f10b20ed29 Mon Sep 17 00:00:00 2001 From: ctbus Date: Mon, 16 Oct 2023 12:32:19 -0400 Subject: [PATCH] Try unzipping inputs --- sbx_virus_id.smk | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/sbx_virus_id.smk b/sbx_virus_id.smk index 9915745..b7b501a 100755 --- a/sbx_virus_id.smk +++ b/sbx_virus_id.smk @@ -116,7 +116,9 @@ rule virus_id_spades_paired: shell: """ mkdir -p {params.out_fp} - spades.py -1 {input.r1} -2 {input.r2} -t {threads} -o {params.out_fp} --continue 2>&1 | tee {log} + gzip -d < {input.r1} > {params.out_fp}/{wildcards.sample}_1.fastq + gzip -d < {input.r2} > {params.out_fp}/{wildcards.sample}_2.fastq + spades.py -1 {params.out_fp}/{wildcards.sample}_1.fastq -2 {params.out_fp}/{wildcards.sample}_1.fastq -t {threads} -o {params.out_fp} --continue 2>&1 | tee {log} """