From 5888ef2f47f02c2e3a2a2f068bf65ab9a8939e83 Mon Sep 17 00:00:00 2001 From: seehagec01 <seehagec01@mi.fu-berlin.de> Date: Thu, 28 Apr 2022 12:38:01 +0200 Subject: [PATCH] push vor branchwechsel --- project/workflow/rules/IVA.smk | 2 +- project/workflow/rules/kraken.smk | 6 ++++-- project/workflow/snakefile | 6 ++++-- 3 files changed, 9 insertions(+), 5 deletions(-) diff --git a/project/workflow/rules/IVA.smk b/project/workflow/rules/IVA.smk index 46fa482..15b05e7 100644 --- a/project/workflow/rules/IVA.smk +++ b/project/workflow/rules/IVA.smk @@ -3,7 +3,7 @@ rule IVA: "results/unmapped_fastq/{sample}_1_unmapped.fastq", "results/unmapped_fastq/{sample}_2_unmapped.fastq" output: - "results/IVA/{sample}.trim.good.iva" + "results/IVA/{sample}" log: "workflow/report/IVA/{sample}.log" threads:20 diff --git a/project/workflow/rules/kraken.smk b/project/workflow/rules/kraken.smk index 3d5310a..0e4197a 100644 --- a/project/workflow/rules/kraken.smk +++ b/project/workflow/rules/kraken.smk @@ -11,13 +11,15 @@ rule build: rule report: input: - db="results/krakendb/db", + db="/buffer/ag_bsc/pmsb_workflows_2022/virus/swp-workflows/project/results/krakendb/db", sample=["results/fastp/trimmed/{sample}.1.fastq", "results/fastp/trimmed/{sample}.2.fastq"] output: + "results/kraken/{sample}.kreprt2", "results/kraken/{sample}_report.txt" + threads: 8 conda: "../envs/yourenv.yaml" log: "workflow/report/kraken_report/{sample}.log" shell: - "kraken2 --report --db {input.db} {input.sample} > {output} 2> {log}" \ No newline at end of file + "kraken2 --threads {threads} --db {input[0]} --paired {input.sample} --output {output[0]} --report {output[1]} 2> {log}" \ No newline at end of file diff --git a/project/workflow/snakefile b/project/workflow/snakefile index 9ba3b7d..3644c24 100644 --- a/project/workflow/snakefile +++ b/project/workflow/snakefile @@ -5,13 +5,15 @@ samples = pd.read_table(config["samples"], index_col="sample") rule all: input: - expand("results/IVA/{sample}.trim.good.iva", sample=samples.index) + "results/krakendb/db", + expand("results/kraken/{sample}_report.txt", sample=samples.index) + #expand("results/IVA/{sample}", sample=samples.index) include: "rules/fastp.smk" include: "rules/bowtie2.smk" include: "rules/samtools.smk" include: "rules/IVA.smk" -#include: "rules/kraken.smk" +include: "rules/kraken.smk" -- GitLab