diff --git a/.test/makefile b/.test/makefile index da52f33..83a6e2d 100644 --- a/.test/makefile +++ b/.test/makefile @@ -15,6 +15,7 @@ snakefiles := \ "../workflow/rules/raw_data/genome_variation.smk" \ "../workflow/rules/samtools/faidx.smk" \ "../workflow/rules/common.smk" \ + "../workflow/rules/pyroe/id_to_name.smk" \ "../workflow/Snakefile" python_scripts := \ diff --git a/workflow/Snakefile b/workflow/Snakefile index 09e9865..8e7dd01 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -7,6 +7,7 @@ include: "rules/gatk/picard_dict.smk" include: "rules/samtools/faidx.smk" include: "rules/raw_data/blacklist.smk" include: "rules/bedtools/merge_blacklist.smk" +include: "rules/pyroe/id_to_name.smk" rule target: diff --git a/workflow/rules/pyroe/id_to_name.smk b/workflow/rules/pyroe/id_to_name.smk index 9eccac9..93e933e 100644 --- a/workflow/rules/pyroe/id_to_name.smk +++ b/workflow/rules/pyroe/id_to_name.smk @@ -1,14 +1,14 @@ rule pyroe_id_to_name: input: - "reference/{species}.{build}.{release}.gtf" + "reference/{species}.{build}.{release}.gtf", output: - "resources/{species}.{build}.{release}/tx2gene.tsv" + "resources/{species}.{build}.{release}/tx2gene.tsv", threads: 1 log: "logs/pyroe/id2name/{species}.{build}.{release}.log" benchmark: "benchmark/pyroe/id2name/{species}.{build}.{release}.tsv" params: - extra="type='salmon'" + extra="type='salmon'", wrapper: f"{snakemake_wrappers_version}/bio/pyroe/idtoname" \ No newline at end of file