Merge branch 'work' into 'master'

Work

See merge request susheel.busi/ont_pilot_gitlab!10

Snakefile

@@ -277,7 +277,7 @@ rule guppy_gpu_basecall:
     shell:
         """
         (date &&\
-        {config[guppy_gpu][bin]} --input_path {input} --save_path $(dirname {output}) --config {config[guppy_gpu][config]} --cpu_threads_per_caller {threads} -x "auto" --disable_pings --compress_fastq --records_per_fastq {config[guppy_gpu][records_per_fastq]} && \
+        {config[guppy_gpu][bin]} --input_path {input} --save_path $(dirname {output}) --config {config[guppy_gpu][config]} --cpu_threads_per_caller {threads} -x {config[guppy_gpu][gpu_device]} --disable_pings --compress_fastq --records_per_fastq {config[guppy_gpu][records_per_fastq]} --chunk_size {config[guppy_gpu][chunk_size]} --chunks_per_runner {config[guppy_gpu][chunks_per_runner]} --gpu_runners_per_device {config[guppy_gpu][runners_per_device]} --num_callers {config[guppy_gpu][num_callers]} && \
         touch {output} &&\
         date) 2> >(tee {log}.stderr) > >(tee {log}.stdout)
         """
@@ -290,7 +290,7 @@ rule guppy_gpu_basecall_NO_MOD:
     shell: 
         """
         (date &&\
-        {config[guppy_gpu][bin]} --input_path {input} --save_path $(dirname {output}) --config {config[guppy_gpu][hac_config]} --cpu_threads_per_caller {threads} -x "auto" --disable_pings --compress_fastq --records_per_fastq {config[guppy_gpu][records_per_fastq]} && \
+        {config[guppy_gpu][bin]} --input_path {input} --save_path $(dirname {output}) --config {config[guppy_gpu][hac_config]} --cpu_threads_per_caller {threads} -x {config[guppy_gpu][gpu_device]} --disable_pings --compress_fastq --records_per_fastq {config[guppy_gpu][records_per_fastq]} --chunk_size {config[guppy_gpu][chunk_size]} --chunks_per_runner {config[guppy_gpu][chunks_per_runner]} --gpu_runners_per_device {config[guppy_gpu][runners_per_device]} --num_callers {config[guppy_gpu][num_callers]} && \
         touch {output} &&\
         date) 2> >(tee {log}.stderr) > >(tee {log}.stdout)
         """

config.yaml

@@ -32,6 +32,11 @@ guppy_gpu:
     config: "dna_r9.4.1_450bps_modbases_dam-dcm-cpg_hac.cfg"
     hac_config: "dna_r9.4.1_450bps_hac.cfg"
     records_per_fastq: 8000
+    chunk_size: 1000
+    chunks_per_runner: 1000
+    num_callers: 4
+    runners_per_device: 2
+    gpu_device: "cuda:0"
     cpu_threads: 28
 guppy_barcoder:
     path: "/home/users/sbusi/apps/ont-guppy/bin"