WIP

config/amplicon_cov.yaml

@@ -1,14 +1,15 @@
 #### Parameters
 # The name of the batch to process
-batch: "20240705_AAFH52MM5"
+batch: "20200729"
 
 ###### Inputs
 # where to find the list of samples i.e. samples.tsv
-sample_list_dir: "../../data/amplicon_cov_data/cluster/project/pangolin/work-amplicon-coverage/test_data/"
+sample_list_dir: "workflow/.tests/unit/amplicon_cov/data/subset_vpipe_smkdeploy/test_output_sars-cov-2/samples/"
+
 # where to find the samples from the list
-sample_dir: "../../data/amplicon_cov_data/cluster/project/pangolin/work-amplicon-coverage/test_data/samples"
+sample_dir: "workflow/.tests/unit/amplicon_cov/data/subset_vpipe_smkdeploy/test_output_sars-cov-2/results"
 # bed file with the primers
-primers_fp: "../../data/amplicon_cov_data/resources/amplicon_cov/articV3primers.bed"
+primers_fp: "workflow/.tests/unit/amplicon_cov/data/primer_schemes/articV3primers.bed"
 
 ##### Outputs
 output_dir: "results/"

workflow/.tests/unit/amplicon_cov/amplicon_cov.yaml

@@ -0,0 +1,15 @@
+#### Parameters
+# The name of the batch to process
+batch: "20200729"
+
+###### Inputs
+# where to find the list of samples i.e. samples.tsv
+sample_list_dir: "data/subset_vpipe_smkdeploy/test_output_sars-cov-2/samples/"
+
+# where to find the samples from the list
+sample_dir: "data/subset_vpipe_smkdeploy/test_output_sars-cov-2/results"
+# bed file with the primers
+primers_fp: "data/primer_schemes/articV3primers.bed"
+
+##### Outputs
+output_dir: ""

workflow/.tests/unit/amplicon_cov/data/subset_vpipe_smkdeploy/test_output_sars-cov-2/samples/samples20200729.tsv

@@ -0,0 +1,2 @@
+pos_MN908947_3_1	20200729	250	v3
+pos_MT007544_1_1	20200729	250	v3

workflow/.tests/unit/amplicon_cov/expected/20200729/amplicons_coverages.csv

@@ -0,0 +1,3 @@
+sample,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97
+pos_MN908947_3_1,264.0,10.0,256.0,255.0,255.0,253.0,255.0,256.0,255.0,1.0,256.0,13.0,253.0,484.5,65.0,81.0,0.0,22.0,253.0,254.0,255.0,476.0,15.0,126.0,256.0,255.0,254.0,95.0,255.0,255.0,65.5,255.0,0.0,256.0,256.0,255.0,256.0,327.0,255.0,410.0,161.0,253.0,255.0,256.0,257.0,255.0,255.0,255.0,218.0,0.0,254.0,256.0,255.0,38.0,254.0,253.0,255.0,92.0,255.0,256.0,256.0,256.0,197.0,255.0,254.5,22.0,181.0,256.0,252.0,256.0,254.0,255.0,256.0,220.0,252.0,37.0,256.0,263.0,253.0,256.0,256.0,0.0,18.0,255.0,255.0,254.0,251.0,255.0,256.0,253.0,255.0,254.0,251.0,255.0,73.0,255.0,431.5,74.0
+pos_MT007544_1_1,256.0,10.0,254.0,254.0,254.0,255.0,257.0,255.0,256.0,10.0,255.0,33.0,253.0,506.0,59.0,0.0,0.0,38.0,253.0,251.0,256.0,494.5,39.0,149.0,255.0,256.0,255.0,184.0,256.0,255.0,258.0,253.0,0.0,255.0,255.0,256.0,256.0,315.0,256.0,404.5,163.0,256.0,256.0,256.0,256.0,256.0,255.0,256.0,255.0,0.0,256.0,256.0,256.0,95.0,254.0,254.0,256.0,107.0,256.0,253.0,255.0,255.0,253.0,255.0,253.0,0.0,255.0,255.0,255.0,254.0,253.0,255.0,256.0,300.5,254.0,47.0,258.0,256.0,255.0,255.0,256.0,0.0,0.0,256.0,255.0,255.0,256.0,255.0,256.0,256.0,256.0,256.0,255.0,254.0,73.0,255.5,490.0,9.0

workflow/.tests/unit/amplicon_cov/expected/20200729/amplicons_coverages_norm.csv

@@ -0,0 +1,3 @@
+sample,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97
+pos_MN908947_3_1,0.012546932180029466,0.00047526258257687374,0.012166722113967967,0.01211919585571028,0.01211919585571028,0.012024143339194906,0.01211919585571028,0.012166722113967967,0.01211919585571028,4.752625825768737e-05,0.012166722113967967,0.0006178413573499358,0.012024143339194906,0.02302647212584953,0.003089206786749679,0.0038496269188726773,0.0,0.0010455776816691222,0.012024143339194906,0.012071669597452593,0.01211919585571028,0.02262249893065919,0.0007128938738653106,0.005988308540468609,0.012166722113967967,0.01211919585571028,0.012071669597452593,0.004514994534480301,0.01211919585571028,0.01211919585571028,0.003112969915878523,0.01211919585571028,0.0,0.012166722113967967,0.012166722113967967,0.01211919585571028,0.012166722113967967,0.015541086450263772,0.01211919585571028,0.01948576588565182,0.007651727579487667,0.012024143339194906,0.01211919585571028,0.012166722113967967,0.012214248372225655,0.01211919585571028,0.01211919585571028,0.01211919585571028,0.010360724300175848,0.0,0.012071669597452593,0.012166722113967967,0.01211919585571028,0.0018059978137921202,0.012071669597452593,0.012024143339194906,0.01211919585571028,0.004372415759707238,0.01211919585571028,0.012166722113967967,0.012166722113967967,0.012166722113967967,0.009362672876764412,0.01211919585571028,0.012095432726581437,0.0010455776816691222,0.008602252744641414,0.012166722113967967,0.011976617080937217,0.012166722113967967,0.012071669597452593,0.01211919585571028,0.012166722113967967,0.010455776816691222,0.011976617080937217,0.0017584715555344329,0.012166722113967967,0.012499405921771779,0.012024143339194906,0.012166722113967967,0.012166722113967967,0.0,0.0008554726486383727,0.01211919585571028,0.01211919585571028,0.012071669597452593,0.01192909082267953,0.01211919585571028,0.012166722113967967,0.012024143339194906,0.01211919585571028,0.012071669597452593,0.01192909082267953,0.01211919585571028,0.0034694168528111784,0.01211919585571028,0.0205075804381921,0.0035169431110688657
+pos_MT007544_1_1,0.011828851307642546,0.000462064504204787,0.011736438406801589,0.011736438406801589,0.011736438406801589,0.011782644857222068,0.011875057758063025,0.011782644857222068,0.011828851307642546,0.000462064504204787,0.011782644857222068,0.001524812863875797,0.01169023195638111,0.02338046391276222,0.002726180574808243,0.0,0.0,0.0017558451159781906,0.01169023195638111,0.011597819055540153,0.011828851307642546,0.022849089732926715,0.0018020515663986693,0.006884761112651326,0.011782644857222068,0.011828851307642546,0.011782644857222068,0.00850198687736808,0.011828851307642546,0.011782644857222068,0.011921264208483504,0.01169023195638111,0.0,0.011782644857222068,0.011782644857222068,0.011828851307642546,0.011828851307642546,0.01455503188245079,0.011828851307642546,0.018690509195083634,0.007531651418538028,0.011828851307642546,0.011828851307642546,0.011828851307642546,0.011828851307642546,0.011828851307642546,0.011782644857222068,0.011828851307642546,0.011782644857222068,0.0,0.011828851307642546,0.011828851307642546,0.011828851307642546,0.004389612789945476,0.011736438406801589,0.011736438406801589,0.011828851307642546,0.004944090194991221,0.011828851307642546,0.01169023195638111,0.011782644857222068,0.011782644857222068,0.01169023195638111,0.011782644857222068,0.01169023195638111,0.0,0.011782644857222068,0.011782644857222068,0.011782644857222068,0.011736438406801589,0.01169023195638111,0.011782644857222068,0.011828851307642546,0.01388503835135385,0.011736438406801589,0.002171703169762499,0.011921264208483504,0.011828851307642546,0.011782644857222068,0.011782644857222068,0.011828851307642546,0.0,0.0,0.011828851307642546,0.011782644857222068,0.011782644857222068,0.011828851307642546,0.011782644857222068,0.011828851307642546,0.011828851307642546,0.011828851307642546,0.011828851307642546,0.011782644857222068,0.011736438406801589,0.003373070880694945,0.011805748082432307,0.02264116070603456,0.0004158580537843083

workflow/.tests/unit/test_amplicon_cov.py

@@ -1 +1,94 @@
 """Tests for the `amplicon_cov` rules."""
+
+
+import os
+import subprocess as sp
+from tempfile import TemporaryDirectory
+import shutil
+from pathlib import Path
+
+from common import OutputCheckerV2
+
+
+def print_directory_contents(path):
+    """Prints the contents of the directory at the given path."""
+    try:
+        with os.scandir(path) as entries:
+            for entry in entries:
+                print(entry.name)
+    except FileNotFoundError:
+        print(f"Directory not found: {path}")
+
+
+def test_get_coverage_for_batch():
+    """
+    Test the get_coverage_for_batch rule.
+    using test data from sars-cov-2.
+
+    This version of the test automatically finds the necessary files.
+    """
+    with TemporaryDirectory() as tmpdir:
+        workdir = Path(tmpdir) / "workdir"
+        workdir.mkdir(exist_ok=True)
+
+        # Create necessary subdirectories
+        (workdir / "config").mkdir(exist_ok=True)
+        (workdir / "data").mkdir(exist_ok=True)
+        (workdir / "results").mkdir(exist_ok=True)
+
+        # Define paths
+        mock_data_path = Path("workflow/.tests/unit/amplicon_cov/data")
+        expected_path = Path("workflow/.tests/unit/amplicon_cov/expected")
+        config_path = Path("workflow/.tests/unit/amplicon_cov/amplicon_cov.yaml")
+
+        # Copy config to the temporary workdir
+        wrk_config_path = workdir / "config" / config_path.name
+        shutil.copy(config_path, wrk_config_path)
+
+        # Copy mock data to the temporary workdir
+        wrk_mock_data_path = Path(workdir, "data")
+        shutil.copytree(mock_data_path, wrk_mock_data_path, dirs_exist_ok=True)
+
+        # Print the contents of the workdir
+
+        # Print the contents of the current directory
+        print_directory_contents(workdir)
+        print_directory_contents(wrk_mock_data_path)
+
+        # Run the test job
+
+        sp.check_output(
+            [
+                "snakemake",
+                "--snakefile",
+                "workflow/rules/amplicon_cov.smk",
+                "--configfile",
+                str(wrk_config_path),
+                "--config",
+                "--directory",
+                str(workdir),
+                "--cores",
+                "1",
+                "20200729/cov_heatmap.pdf",
+            ]
+        )
+
+        # Check the output
+        # assert (workdir / "results/").exists()
+
+        # show me the full tree of files in the workdir
+        for root, dirs, files in os.walk(workdir):
+            print(root)
+            for file in files:
+                print(f"  {file}")
+
+        # Compare output with expected result using the OutputChecker
+        checker = OutputCheckerV2(
+            workdir / "data",
+            expected_path,
+            workdir,
+            configdir=workdir / "config",
+            tolerance=1e-4,
+        )
+
+        checker.check()