Develop (#193)

* Refactor HeatmapFiles class to include make_heatmaps property in design.py

* Refactor NonRNAOutput class in design.py to remove computed_field decorator

* fix: correct query function to provide both the ip and control if requested

* Refactor control lambda function in peak_call_chip.smk to allow null control files

* Refactor query function in DesignIP class to return IPExperiment object

* Refactor FastqFile model to handle resolved and absolute paths

* Refactor peak_call_grouped.smk to add runtime and mem resources for lanceotron_no_input_consensus rule

* feat: Refactor pileup_norm.smk to use tile instead of tiles

The commit message suggests refactoring the `pileup_norm.smk` file to use the `tile` parameter instead of `tiles`.

* fix typo design

* fix tests fastq path

* fix merge in design

* fix config

* reinstate snp into design

* revert peaks and design

* fixed typo from merge peak calls

* simplify tests

* update test order

* correct test order

* revert test order

* split tests

* increase cores for tests

* revert single test

* merge

* merge develop to master

---------

Co-authored-by: alsmith <asmith151@outlook.com>

.github/workflows/test_pipelines.yml

@@ -49,11 +49,11 @@ jobs:
     - name: Test design works
       shell: pwsh
       run: |
-        seqnado-design chip tests/data/fastq/CTCF*.fastq.gz
-    - name: Test with pytest
+        seqnado-design chip tests/data/fastq/chip-rx*.fastq.gz
+    - name: Test pipeline
       shell: pwsh
       run: |
-        pytest -vv -s --cov=./ --cov-report=xml --cores 4
+        pytest -vv -s --cov=./ --cov-report=xml --cores 4 
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v4.0.1
       with:

.gitignore

@@ -18,3 +18,4 @@ fastq_class_sandbox.ipynb
 test_rna_size_factors.ipynb
 tests/data/*
 pytestdebug.log
+sps*

tests/test_pipelines.py

@@ -248,7 +248,8 @@ def user_inputs(
         "pileup_method": "deeptools",
         "scale": "no",
         "make_heatmaps": "no",
-        "call_peaks": "no",
+        "call_peaks": "yes",
+        "peak_calling_method": "lanceotron",
     }
 
     defaults_rna = {
@@ -336,15 +337,15 @@ def config_yaml_for_testing(config_yaml, assay):
 
     if assay == "chip":
         config["pileup_method"] = ["deeptools", "homer"]
-        config["peak_calling_method"] = ["lanceotron", "macs", "homer"]
+        config["peak_calling_method"] = ["lanceotron"]
         config["library_complexity"] = False
         config["bowtie2"]["options"] = "--no-mixed --no-discordant"
     elif assay == "chip-rx":
         config["call_peaks"] = True
         config["peak_calling_method"] = ["seacr"]
     elif assay == "atac":
         config["call_peaks"] = True
-        config["peak_calling_method"] = ["macs"]
+        config["peak_calling_method"] = ["lanceotron", "macs", "homer"]
 
     with open(config_yaml, "w") as f:
         yaml.dump(config, f)