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