IVA produziert contigs für 3/6 samples

project/workflow/rules/IVA.smk

@@ -3,13 +3,13 @@ rule IVA:
         "results/unmapped_fastq/{sample}_1_unmapped.fastq",
         "results/unmapped_fastq/{sample}_2_unmapped.fastq"
     output:
-        "results/IVA/{sample}"
+        "results/IVA/{sample}/"
     log:
         "workflow/report/IVA/{sample}.log"
-    threads:20
+    #threads:20
     conda:
        "../envs/yourenv.yaml"
     shell:
-        "iva --threads {threads} -f {input[0]} -r {input[1]} {output} 2> {log}"
+        "iva -f {input[0]} -r {input[1]} {output} 2> {log}"
         
     
\ No newline at end of file

project/workflow/snakefile

@@ -5,9 +5,10 @@ samples = pd.read_table(config["samples"], index_col="sample")
 
 rule all:
     input:
-        "results/krakendb/db",
-        expand("results/kraken/{sample}_report.txt", sample=samples.index)
-        #expand("results/IVA/{sample}", sample=samples.index)
+        #"results/krakendb/db"
+        #"results/kraken/ERR4181713_report.txt"
+        #expand("results/kraken/{sample}_report.txt", sample=samples.index)
+        expand("results/IVA/{sample}", sample=samples.index)
 
 include: "rules/fastp.smk"
 include: "rules/bowtie2.smk"