Merge pull request #12 from beardymcjohnface/dev

Dev

setup.py

@@ -56,7 +56,7 @@ def get_data_files():
         "snakemake>=7.14.0",
         "pyyaml>=6.0",
         "Click>=8.1.3",
-        "metasnek>=0.0.7",
+        "metasnek>=0.0.8",
     ],
     entry_points={
         "console_scripts": [

tests/test_trimnami.py

@@ -46,15 +46,15 @@ def test_trimnami_cli(tmp_dir):
 def test_trimnami_commands(tmp_dir):
     exec_command("trimnami test --threads 1 -n prinseq fastp roundAB notrim filtlong cutadapt")
     exec_command("trimnami test --threads 1 -n --fastqc")
-    exec_command("trimnami test --threads 1 -n --subsample 1k")
-    exec_command("trimnami test --threads 1 -n --subsample 1k --fastqc")
+    exec_command("trimnami test --threads 1 -n --subsample")
+    exec_command("trimnami test --threads 1 -n --subsample --fastqc")
     exec_command("trimnami testhost --threads 1 -n prinseq fastp roundAB notrim filtlong cutadapt")
     exec_command("trimnami testhost --threads 1 -n --fastqc")
-    exec_command("trimnami testhost --threads 1 -n --subsample 1k")
-    exec_command("trimnami testhost --threads 1 -n --subsample 1k --fastqc")
+    exec_command("trimnami testhost --threads 1 -n --subsample")
+    exec_command("trimnami testhost --threads 1 -n --subsample --fastqc")
     exec_command("trimnami testnp --threads 1 -n")
-    exec_command("trimnami testnp --threads 1 -n --subsample 1k")
+    exec_command("trimnami testnp --threads 1 -n --subsample")
     exec_command("trimnami testnp --threads 1 -n --fastqc")
-    exec_command("trimnami testnp --threads 1 -n --subsample 1k --fastqc")
+    exec_command("trimnami testnp --threads 1 -n --subsample --fastqc")
     exec_command("trimnami config")
     exec_command("trimnami citation")

trimnami/__main__.py

@@ -73,9 +73,9 @@ def common_options(func):
             show_default=True,
         ),
         click.option(
-            "--subsample",
+            "--subsample/--no-subsample",
             default=None,
-            help="Subsample reads to this many bases with rasusa, e.g. 1000, 1m, 1g, 1t",
+            help="Perform subsampling (set in config)",
             show_default=False,
         ),
         click.option(

trimnami/config/config.yaml

@@ -14,6 +14,8 @@ trimnami:
             -F 3584
         cutadapt:
             -m 40
+        subsample:
+            --bases 1g
         fastp:
             --qualified_quality_phred 15
             --length_required 90

trimnami/trimnami.VERSION

@@ -1 +1 @@
-0.1.0
+0.1.1

trimnami/workflow/rules/preflight.smk

@@ -62,7 +62,7 @@ if config["args"]["host"] is not None:
         )[0] + ".idx"
     )
 
-if config["args"]["subsample"] is not None:
+if config["args"]["subsample"]:
     config["args"]["subsampleStr"] = ".subsampled"
 
 if config["args"]["fasta"]:

trimnami/workflow/rules/rasusa.smk

@@ -12,7 +12,7 @@ rule rasusa:
     conda:
         os.path.join(dir["env"], "rasusa.yaml")
     params:
-        bases=lambda wildcards: config["args"]["subsample"] if config["args"]["subsample"] else ""
+        bases=config["qc"]["subsample"]
     benchmark:
         os.path.join(dir["bench"], "rasusa_single.{dir}.{file}.txt")
     log:
@@ -23,7 +23,7 @@ rule rasusa:
                 "-i {input} "
                 "-o {output} "
                 "-O g "
-                "--bases {params.bases} "
+                "{params.bases} "
                 "2> {log}; "
          "else "
             "touch {output}; "