debuh guppy

tools/guppy/guppy.rule.snakefile

@@ -3,11 +3,13 @@ rule <step_name>__guppy:
             **<step_name>__guppy_inputs()
         output:
            sequencing_summary =   config["results_dir"] + "/" + config["<step_name>__guppy_output_dir"]+ "/sequencing_summary.txt" , 
+           readPass = config["results_dir"] + "/" + config["<step_name>__guppy_output_dir"]+ "/guppy_pass.fq.gz",
+           readFail = config["results_dir"] + "/" + config["<step_name>__guppy_output_dir"]+ "/guppy_fail.fq.gz",
         params:
             output_dir = config["results_dir"] + "/" + config["<step_name>__guppy_output_dir"]+ "/",
             command = config["<step_name>__guppy_command"],
-            gpu_num_callers = config["results_dir"] + "/" + config["<step_name>__guppy_gpu_num_callers"],
-            gpu_runners_per_device = = config["results_dir"] + "/" + config["<step_name>__guppy_gpu_runners_per_device"],
+            gpu_num_callers =  config["<step_name>__guppy_gpu_num_callers"],
+            gpu_runners_per_device =  config["<step_name>__guppy_gpu_runners_per_device"],
         log:
             config["results_dir"]+'/logs/' + config["<step_name>__guppy_output_dir"] + '/guppy_log.txt',
         shell:
@@ -16,10 +18,11 @@ rule <step_name>__guppy:
             "--compress_fastq " +
             "-x 'auto' " + # -x "cuda:0"
             "-i {input.fast5_dir} "+
-            "-T {threads} "+
             "-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.guppy_gpu_runners_per_device} ;"
-            "cat {params.output_dir}/pass/*.fastq.gz > {params.output_dir}/guppy_pass.fastq.gz ;"
-            "cat {params.output_dir}/fail/*.fastq.gz > {params.output_dir}/guppy_fail.fastq.gz ;"            
+            "--guppy_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 ; "            
+            "rm -f  {params.output_dir}/fail/*.fastq.gz; "
\ No newline at end of file

tools/guppy/guppy.yaml

@@ -21,13 +21,13 @@
         outputs:
           [
             { name: sequencing_summary, type: "tsv", file: "sequencing_summary.txt", description: "Table containing sequencing summary" },
-            { name: readPass, type: "reads", file: "guppy_pass.fastq.gz", description: "File containing reads with an average quality score > Q7" },
-            { name: readFail, type: "reads", file: "guppy_fail.fastq.gz", description: "File containing reads with an average quality score < Q7" },
+            { name: readPass, type: "reads", file: "guppy_pass.fq.gz", description: "File containing reads with an average quality score > Q7" },
+            { name: readFail, type: "reads", file: "guppy_fail.fq.gz", description: "File containing reads with an average quality score < Q7" },
           ],
         options:
           [
             {
-              name: "gpu_num_callers",
+              name: "guppy_gpu_num_callers",
               prefix: "--num_callers",
               value: 16,
               min: 1,