From 71ed0e74015659782ce6d69eeabebb6f6753777b Mon Sep 17 00:00:00 2001 From: khalid <khalid.belkhir@umontpellier.fr> Date: Tue, 7 Dec 2021 11:21:57 +0100 Subject: [PATCH] change params names --- raw_inputs/raw_fast5_dir.py | 2 +- tools/guppy/guppy.rule.snakefile | 4 ++-- tools/mitoz_annotate/mitoz_annotate.rule.snakefile | 8 ++++---- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/raw_inputs/raw_fast5_dir.py b/raw_inputs/raw_fast5_dir.py index d44e0818..10ca3e19 100755 --- a/raw_inputs/raw_fast5_dir.py +++ b/raw_inputs/raw_fast5_dir.py @@ -8,7 +8,7 @@ def raw_fast5_dir(results_dir, input_dir): out["fast5_dir"] = input_dir out["samples"] = "" - + out["sample_suffix"] = "Minion" return(out) #print(raw_fast5_dir(sys.argv[1],sys.argv[2],sys.argv[3])) \ No newline at end of file diff --git a/tools/guppy/guppy.rule.snakefile b/tools/guppy/guppy.rule.snakefile index 9439fb74..3d0b459e 100644 --- a/tools/guppy/guppy.rule.snakefile +++ b/tools/guppy/guppy.rule.snakefile @@ -21,8 +21,8 @@ rule <step_name>__guppy: "-i {input.fast5_dir} "+ "-s {params.output_dir} "+ "-c /opt/biotools/ont-guppy/data/{params.config_file} " + - "--gpu_num_callers {params.gpu_num_callers} " + - "--guppy_gpu_runners_per_device {params.gpu_runners_per_device} ; " + "--num_callers {params.gpu_num_callers} " + + "--gpu_runners_per_device {params.gpu_runners_per_device} ; " "cat {params.output_dir}/pass/*.fastq.gz > {params.output_dir}/guppy_pass.fq.gz ; " "rm -f {params.output_dir}/pass/*.fastq.gz; " "cat {params.output_dir}/fail/*.fastq.gz > {params.output_dir}/guppy_fail.fastq.gz ; " diff --git a/tools/mitoz_annotate/mitoz_annotate.rule.snakefile b/tools/mitoz_annotate/mitoz_annotate.rule.snakefile index 7637de6e..5c4c0f55 100755 --- a/tools/mitoz_annotate/mitoz_annotate.rule.snakefile +++ b/tools/mitoz_annotate/mitoz_annotate.rule.snakefile @@ -1,5 +1,5 @@ -if config["SeOrPe"] == "SE": - +#if config["SeOrPe"] == "SE": #SeOrPe will not be defined if we are using fast5_dir followed by guppy as the source of reads +if "<step_name>__mitoz_annotate_SE_inputs" in globals(): rule <step_name>__mitoz_annotate_SE: input: **<step_name>__mitoz_annotate_SE_inputs() @@ -55,8 +55,8 @@ if config["SeOrPe"] == "SE": "rm {params.results_dir}/reads_R1{params.sample_suffix} " -elif config["SeOrPe"] == "PE": - +#elif config["SeOrPe"] == "PE": +elif if "<step_name>__mitoz_annotate_PE_inputs" in globals(): rule <step_name>__mitoz_annotate_PE: input: **<step_name>__mitoz_annotate_PE_inputs() -- GitLab