Separate kmer pair calculation from plotting#

NBISweden · Mar 3, 2021 · 504d34a · 504d34a
1 parent e9e5ee2
commit 504d34a
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Showing 3 changed files with 25 additions and 10 deletions.
diff --git a/workflow/rules/jellyfish.smk b/workflow/rules/jellyfish.smk
@@ -28,21 +28,28 @@ rule jellyfish_histo:
     wrapper: f"{WRAPPER_PREFIX}/bio/jellyfish/histo"
 
 
-rule jellyfish_plot:
+rule jellyfish_kmer_count_pairs:
     output:
-        png = report("{results}/jellyfish/kmer_comparison/{assembly}.{analysis}.{kmer}_jf.png",
-                     caption="../report/kmer_comparison.rst", category="Kmer comparison"),
         tsv = "{results}/jellyfish/kmer_comparison/{assembly}.{analysis}.{kmer}_jf.tsv"
     input:
         assembly = "{results}/jellyfish/assembly/{assembly}.{kmer}mer_counts.jf",
         reads = "{results}/jellyfish/reads/{analysis}.{kmer}mer_counts.jf"
-    params:
-        tmpdir = get_workflow_params("jellyfish", "tmpdir")
     conda:
-        "../envs/jellyfish-python.yaml"
+        "../envs/jellyfish-kmer-utils.yaml"
     resources:
         runtime = lambda wildcards, attempt: resources("jellyfish_plot", "runtime", attempt)
     threads: get_params("jellyfish_plot", "threads")
     log: "logs/{results}/jellyfish/{assembly}.{analysis}.{kmer}_jf.log"
-    script:
+    shell:
+        "kmer_count_pairs {input.assembly} {input.reads} > {output.tsv}"
+
+
+rule jellyfish_kmer_pairs_plot:
+    """Plot kmer assembly and read pairs"""
+    output:
+        png = report("{results}/jellyfish/kmer_comparison/{assembly}.{analysis}.{kmer}_jf.png",
+                     caption="../report/kmer_comparison.rst", category="Kmer pairs plot")
+    input:
+        tsv = "{results}/jellyfish/kmer_comparison/{assembly}.{analysis}.{kmer}_jf.tsv"
+    conda:
         "../scripts/assemblyeval_jellyfish_plot.py"
diff --git a/workflow/schemas/definitions.schema.yaml b/workflow/schemas/definitions.schema.yaml
@@ -255,9 +255,13 @@ definitions:
         default: {}
         $ref: "jellyfish.schema.yaml#/definitions/jellyfish_histo"
 
-      jellyfish_plot:
+      jellyfish_kmer_count_pairs:
         default: {}
-        $ref: "jellyfish.schema.yaml#/definitions/jellyfish_plot"
+        $ref: "jellyfish.schema.yaml#/definitions/jellyfish_kmer_count_pairs"
+
+      jellyfish_kmer_pairs_plot:
+        default: {}
+        $ref: "jellyfish.schema.yaml#/definitions/jellyfish_kmer_pairs_plot"
 
       ##############################
       # busco

diff --git a/workflow/schemas/jellyfish.schema.yaml b/workflow/schemas/jellyfish.schema.yaml
@@ -31,6 +31,10 @@ definitions:
     description: jellyfish histo config
     $ref: "definitions.schema.yaml#/definitions/resources.rule"
 
-  jellyfish_plot:
+  jellyfish_kmer_count_pairs:
+    description: jellyfish kmer count pairs config
+    $ref: "definitions.schema.yaml#/definitions/resources.rule"
+
+  jellyfish_kmer_pairs_plot:
     description: jellyfish plot config
     $ref: "definitions.schema.yaml#/definitions/resources.rule"