added rocm path

workflow/Snakefile

@@ -30,7 +30,7 @@ rule all:
         #'../data/basecalled_reads/hac.fastq.gz'
         #expand('../data/raw_pod5/PBK98658_853a956f_57f83f46_{batch}.pod5',batch=range(1,config["pod5_dataset_size"]+1,config["pod5_stride"]))
         '../data/aligned_reads/nomiss_hac_to_genome.sorted.bam',
-        '../data/aligned_reads/trap_hac_to_genome.sorted.bam'
+        #'../data/aligned_reads/trap_hac_to_genome.sorted.bam'
         #'../data/ml_inputs/hac_label_store.pq'
         #'../data/ml_inputs/model_layouts/cnn_512_4_100000_11_4.json'
 

workflow/config/main.yaml

@@ -2,6 +2,9 @@ tmp_dir: "/tmp"
 
 seed : 0
 
+#gpu
+gpu_stack : 'cuda' #'cuda' or 'rocm'
+
 # dorado
 dorado_model_dir : "../dorado_models"
 hac_model_name: "dna_r10.4.1_e8.2_400bps_hac@v6.0.0"

workflow/rules/baseline_pipeline.smk

@@ -38,6 +38,8 @@ wildcard_constraints:
     batch=r"(batch)?\d+",
     model=r'hac|fast'
 
+GPU_STACK = config.get('gpu_stack','cuda')
+
 rule download_nomiss_pod5:
     output:
         '../data/raw_pod5/nomiss/PBK98658_853a956f_57f83f46_{batch}.pod5'
@@ -53,7 +55,7 @@ rule download_trap_tar:
         temp(directory('../data/raw_pod5/trap/all'))
     threads: 32
     params:
-        tmp='/tmp/trap_all.tar'
+        tmp='../data/raw_pod5/trap/trap_all.tar'
     shell:
         """
         curl -L --http1.1 -A "Mozilla/5.0" "https://api.figshare.com/v2/file/download/45408628" -o {params.tmp}
@@ -72,24 +74,41 @@ rule extract_trap_pod5:
         """
         mv {params.input_pod5} {output}
         """
-rule basecall_pod5:
+
-    input:
+if GPU_STACK == 'cuda':
-        pod5='../data/raw_pod5/{dataset}/{run}_{batch}.pod5',
+    rule basecall_pod5_dorado:
-        model=get_model_requirement
+        input:
-    output:
+            pod5='../data/raw_pod5/{dataset}/{run}_{batch}.pod5',
-        temp('../data/basecalled_reads/{dataset}/{model}/{run}_{batch}.fastq')
+            model=get_model_requirement
-    threads:
+        output:
-        32
+            temp('../data/basecalled_reads/{dataset}/{model}/{run}_{batch}.fastq')
-    resources:
+        threads:
-        gpu=1
+            32
-    params:
+        resources:
-        benchmarking=get_benchmarking_file,
+            gpu=1
-        min_qscore=get_qscore,
+        params:
-        dorado_model=get_model_name,
+            benchmarking=get_benchmarking_file,
-    shell:
+            min_qscore=get_qscore,
-        """
+            dorado_model=get_model_name,
-        dorado basecaller --models-directory {config[dorado_model_dir]} --emit-fastq {params.benchmarking} {params.min_qscore} {params.dorado_model} {input.pod5} > {output}
+        shell:
-        """
+            """
+            dorado basecaller --models-directory {config[dorado_model_dir]} --emit-fastq {params.benchmarking} {params.min_qscore} {params.dorado_model} {input.pod5} > {output}
+            """
+elif GPU_STACK == 'rocm':
+    rule basecall_pod5_slorado:
+        input:
+            pod5='../data/raw_pod5/{dataset}/{run}_{batch}.pod5',
+            model=get_model_requirement
+        output:
+            temp('../data/basecalled_reads/{dataset}/{model}/{run}_{batch}.fastq')
+        threads:
+            32
+        resources:
+            gpu=1
+        shell:
+            """
+            pod5-slorado basecaller -o {output} -t {threads} --flash=yes {input.model} {input.pod5}
+            """
 
 rule concatenate_basecalled_fastq:
     input: