From 2714dfbc82fc5f58b7efbbcb1c2d648f3b3bc154 Mon Sep 17 00:00:00 2001
From: seehagec01 <seehagec01@mi.fu-berlin.de>
Date: Thu, 28 Apr 2022 16:08:37 +0200
Subject: [PATCH] =?UTF-8?q?IVA=20produziert=20contigs=20f=C3=BCr=203/6=20s?=
=?UTF-8?q?amples?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
---
project/workflow/rules/IVA.smk | 6 +++---
project/workflow/snakefile | 7 ++++---
2 files changed, 7 insertions(+), 6 deletions(-)
diff --git a/project/workflow/rules/IVA.smk b/project/workflow/rules/IVA.smk
index 15b05e7..2d299c3 100644
--- a/project/workflow/rules/IVA.smk
+++ b/project/workflow/rules/IVA.smk
@@ -3,13 +3,13 @@ rule IVA:
"results/unmapped_fastq/{sample}_1_unmapped.fastq",
"results/unmapped_fastq/{sample}_2_unmapped.fastq"
output:
- "results/IVA/{sample}"
+ "results/IVA/{sample}/"
log:
"workflow/report/IVA/{sample}.log"
- threads:20
+ #threads:20
conda:
"../envs/yourenv.yaml"
shell:
- "iva --threads {threads} -f {input[0]} -r {input[1]} {output} 2> {log}"
+ "iva -f {input[0]} -r {input[1]} {output} 2> {log}"
\ No newline at end of file
diff --git a/project/workflow/snakefile b/project/workflow/snakefile
index 3644c24..1c2ed9a 100644
--- a/project/workflow/snakefile
+++ b/project/workflow/snakefile
@@ -5,9 +5,10 @@ samples = pd.read_table(config["samples"], index_col="sample")
rule all:
input:
- "results/krakendb/db",
- expand("results/kraken/{sample}_report.txt", sample=samples.index)
- #expand("results/IVA/{sample}", sample=samples.index)
+ #"results/krakendb/db"
+ #"results/kraken/ERR4181713_report.txt"
+ #expand("results/kraken/{sample}_report.txt", sample=samples.index)
+ expand("results/IVA/{sample}", sample=samples.index)
include: "rules/fastp.smk"
include: "rules/bowtie2.smk"
--
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