kraken kinda working

project/workflow/rules/kraken.smk

@@ -2,30 +2,18 @@ rule build:
     input:
         "results/fastp/trimmed/ERR4082860.1.fastq"
     output:
-        "resources/db/yourdb"
-    conda:
-        "../envs/yourenv.yaml"
-    shell:
-        "kraken-build --standard --db resources/krakendb/db"
-
-
-rule classification:
-    input:
-        "results/fastp/trimmed/ERR4082860.1.fastq",
-        "results/fastp/trimmed/ERR4082860.2.fastq"
-    output:
-        "results/kraken/ERR4082860_kraken_cseqs#.fq"
+        "results/krakendb/db"
     threads:4
     conda:
         "../envs/yourenv.yaml"
     shell:
-        "kraken2 --gzip-compressed --paired --classified-out {output} {input[0]} {input[1]} --db resources/db/yourdb --report ERR4082860_report.txt --threads {threads}"
+        "kraken2-build --standard --threads {threads} --db db"
 
 
 rule report:
     input:
-        db="resources/db/yourdb",
-        sample=["results/fastp/trimmed/{sample}_1.fastq", "results/fastp/trimmed/{sample}_2.fastq"]
+        db="results/krakendb/db",
+        sample=["results/fastp/trimmed/{sample}.1.fastq", "results/fastp/trimmed/{sample}.2.fastq"]
     output:
         "results/kraken/{sample}_report.txt"
     conda:
@@ -33,4 +21,4 @@ rule report:
     log:
         "workflow/report/kraken/{sample}.log"
     shell:
-        "kraken-report --db {input.db} {input.sample} > {output} 2> {log}"
+        "kraken2 --report --db {input.db} {input.sample} > {output} 2> {log}"
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