diff --git a/project/workflow/rules/IVA.smk b/project/workflow/rules/IVA.smk index 15b05e7e6571e26f55618af2933314d8583eb47b..2d299c3b4bbc1fa3206cb0e09dd5a5f3cc649eb1 100644 --- a/project/workflow/rules/IVA.smk +++ b/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 diff --git a/project/workflow/snakefile b/project/workflow/snakefile index 3644c24255caa2d0ca1d8f85f064616702aef1d2..1c2ed9a2b68ba83525679f5d3bdb4579a60d7a1e 100644 --- a/project/workflow/snakefile +++ b/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"