Updates to workflow for multiple datasets

.gitignore

@@ -3,3 +3,4 @@
 *.snakemake
 *__pycache__
 *egg-info/
+config/datasets.tsv

MANIFEST.in

@@ -0,0 +1,2 @@
+graft workflow
+graft config

workflow/Snakefile

@@ -1,5 +1,3 @@
-import pandas as pd
-
 configfile: "config/config.yaml"
 
 
@@ -10,23 +8,23 @@ include: "rules/ml.smk"
 
 
 report: "report/workflow.rst"
-#
-#
-#rule all:
-#    input:
-#        all_input,
-#
-#
-#rule all_differentials:
-#    input:
-#        all_diff_files,
-#
-#
-#rule all_ml:
-#    input:
-#        all_ml,
-#
-#
-#rule all_visualizations:
-#    input:
-#        all_viz_files,
+
+
+rule all:
+    input:
+        all_input,
+
+
+rule all_differentials:
+    input:
+        all_differentials,
+
+
+rule all_ml:
+    input:
+        all_ml,
+
+
+rule all_visualizations:
+    input:
+        all_viz_files,

workflow/rules/common.smk

@@ -39,3 +39,42 @@ def get_diffab_tool_columns(wildcards):
         "corncob": "coefs",
     }
     return columns[wildcards.tool]
+
+
+all_differentials = expand(
+    "results/{dataset}/{out}",
+    dataset=names,
+    out=["concatenated_differentials.tsv", "qurro", "differentials_table.html"]
+)
+
+all_ml = expand(
+    "results/{dataset}/ml/{tool}/regression/model_data.pctile_{pctile}.joblib",
+    dataset=names,
+    tool=config["tools"] + ["pca_pc1"],
+    pctile=config["log_ratio_feat_pcts"],
+)
+
+all_viz_files = expand(
+    "figures/{dataset}/{tool}_differentials.svg",
+    dataset=names,
+    tool=config["tools"]
+)
+all_viz_files.extend(expand(
+    "figures/{dataset}/{viz}",
+    dataset=names,
+    viz=["spearman_heatmap.svg", "rank_comparisons.html", "pca.svg"]
+))
+all_viz_files.extend(expand(
+    "figures/{dataset}/upset/upset.pctile_{pctile}.{location}.svg",
+    dataset=names,
+    pctile=config["log_ratio_feat_pcts"],
+    location=["numerator", "denominator"],
+))
+all_viz_files.extend(expand(
+    "figures/{dataset}/{curve}/{curve}.pctile_{pctile}.svg",
+    dataset=names,
+    pctile=config["log_ratio_feat_pcts"],
+    curve=["pr", "roc"],
+))
+
+all_input = all_differentials + all_viz_files + all_ml