Kraken db, Iva

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

project/workflow/rules/IVA.smk

 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

project/workflow/rules/kraken.smk

 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

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"