From 57e1a31993a846e60e98f3b33faad327a9c1c65e Mon Sep 17 00:00:00 2001 From: Anna Mauti Gelbe <annamaug01@compute04.imp.fu-berlin.de> Date: Wed, 27 Apr 2022 13:15:04 +0200 Subject: [PATCH] Kraken db, Iva --- project/workflow/envs/yourenv.yaml | 1 + project/workflow/rules/IVA.smk | 11 ++++++----- project/workflow/rules/kraken.smk | 7 +++---- project/workflow/snakefile | 5 ++--- 4 files changed, 12 insertions(+), 12 deletions(-) diff --git a/project/workflow/envs/yourenv.yaml b/project/workflow/envs/yourenv.yaml index d337846..ccc3e2b 100644 --- a/project/workflow/envs/yourenv.yaml +++ b/project/workflow/envs/yourenv.yaml @@ -19,4 +19,5 @@ dependencies: - snakemake-wrapper-utils=0.3 - kmc=3.2.1 - Trimmomatic=0.32 + - kraken2=2.1.2 prefix: /buffer/ag_bsc/pmsb_workflows_2022/virus/anna-swp-workflows/project/workflow/envs/yourenv.yaml diff --git a/project/workflow/rules/IVA.smk b/project/workflow/rules/IVA.smk index 27fcd97..46fa482 100644 --- a/project/workflow/rules/IVA.smk +++ b/project/workflow/rules/IVA.smk @@ -1,14 +1,15 @@ rule IVA: input: - "results/unmapped_fastq/ERR4082860_1_unmapped.fastq", - "results/unmapped_fastq/ERR4082860_2_unmapped.fastq" + "results/unmapped_fastq/{sample}_1_unmapped.fastq", + "results/unmapped_fastq/{sample}_2_unmapped.fastq" output: - "results/IVA/ERR4082860.trim.good.iva" + "results/IVA/{sample}.trim.good.iva" log: - "workflow/report/IVA/ERR4082860.log" - threads:4 + "workflow/report/IVA/{sample}.log" + threads:20 conda: "../envs/yourenv.yaml" shell: "iva --threads {threads} -f {input[0]} -r {input[1]} {output} 2> {log}" + \ No newline at end of file diff --git a/project/workflow/rules/kraken.smk b/project/workflow/rules/kraken.smk index e01aa28..d6bb7ac 100644 --- a/project/workflow/rules/kraken.smk +++ b/project/workflow/rules/kraken.smk @@ -1,14 +1,13 @@ rule build: input: - "results/fastp/trimmed/ERR4082860.1.fastq" + sample=["results/fastp/trimmed/ERR4082860.1.fastq", "results/fastp/trimmed/ERR4082860.2.fastq"] output: "results/krakendb/db" threads:4 conda: "../envs/yourenv.yaml" shell: - "kraken2-build --standard --threads {threads} --db db" - + "kraken2-build --standard --threads {threads} --db {output}" rule report: input: @@ -19,6 +18,6 @@ rule report: conda: "../envs/yourenv.yaml" log: - "workflow/report/kraken/{sample}.log" + "workflow/report/kraken_report/{sample}.log" shell: "kraken2 --report --db {input.db} {input.sample} > {output} 2> {log}" \ No newline at end of file diff --git a/project/workflow/snakefile b/project/workflow/snakefile index 7e56cb3..9ba3b7d 100644 --- a/project/workflow/snakefile +++ b/project/workflow/snakefile @@ -5,14 +5,13 @@ samples = pd.read_table(config["samples"], index_col="sample") rule all: input: - "results/IVA/ERR4082860.trim.good.iva", - "ERR4082860_report.txt" + expand("results/IVA/{sample}.trim.good.iva", 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