From 373b4063c2c13d1485de77863b0bb6f5f6296492 Mon Sep 17 00:00:00 2001 From: Kivanc Corut Date: Thu, 16 Mar 2023 16:38:40 -0400 Subject: [PATCH] perf: update to fasterq-dump wrapper v1.23.5 * added fasterq-dump params --- .test/config_ecoli/config.yaml | 10 ++++++++++ config/config.yaml | 10 ++++++++++ workflow/rules/ref.smk | 14 ++++++++------ 3 files changed, 28 insertions(+), 6 deletions(-) diff --git a/.test/config_ecoli/config.yaml b/.test/config_ecoli/config.yaml index 462bf5c..eae0a1b 100644 --- a/.test/config_ecoli/config.yaml +++ b/.test/config_ecoli/config.yaml @@ -101,6 +101,16 @@ resources: params: + # ---------------------------------------------------------------------- + # fasterq-dump Params + # ---------------------------------------------------------------------- + + fasterq_dump: + # Number of threads for fasterq-dump + threads: 6 + # Additional parameters for fasterq-dump + extra: "--skip-technical" + # ---------------------------------------------------------------------- # FastQC Params # ---------------------------------------------------------------------- diff --git a/config/config.yaml b/config/config.yaml index 7d28e92..35eaa1c 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -101,6 +101,16 @@ resources: params: + # ---------------------------------------------------------------------- + # fasterq-dump Params + # ---------------------------------------------------------------------- + + fasterq_dump: + # Number of threads for fasterq-dump + threads: 6 + # Additional parameters for fasterq-dump + extra: "--skip-technical" + # ---------------------------------------------------------------------- # FastQC Params # ---------------------------------------------------------------------- diff --git a/workflow/rules/ref.smk b/workflow/rules/ref.smk index 9d2bc0e..c3247ff 100644 --- a/workflow/rules/ref.smk +++ b/workflow/rules/ref.smk @@ -78,20 +78,22 @@ rule sra_get_fastq_pe: "resources/ref/sra-pe-reads/{accession}_1.fastq", "resources/ref/sra-pe-reads/{accession}_2.fastq" params: - extra="--skip-technical --progress --temp resources/ref/sra-pe-reads" - threads: 6 + extra= config["params"]["fasterq_dump"]["extra"] + threads: + config["params"]["fasterq_dump"]["threads"] log: "logs/ref/sra-pe-reads/{accession}.log" wrapper: - "v1.12.2/bio/sra-tools/fasterq-dump" + "v1.23.5/bio/sra-tools/fasterq-dump" rule sra_get_fastq_se: output: "resources/ref/sra-se-reads/{accession}.fastq" params: - extra="--skip-technical --progress --temp resources/ref/sra-pe-reads" - threads: 6 + extra= config["params"]["fasterq_dump"]["extra"] + threads: + config["params"]["fasterq_dump"]["threads"] log: "logs/ref/sra-pe-reads/{accession}.log" wrapper: - "v1.12.2/bio/sra-tools/fasterq-dump" \ No newline at end of file + "v1.23.5/bio/sra-tools/fasterq-dump" \ No newline at end of file