push vor branchwechsel

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

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}"
+        "kraken2 --threads {threads} --db {input[0]} --paired {input.sample} --output {output[0]} --report {output[1]} 2> {log}"
\ No newline at end of file

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"