Merge pull request #21 from gibsramen/v0.2.0

Update to v0.2.0

Author: gibsramen

README.md

@@ -12,7 +12,7 @@ Importantly, Qadabra focuses on feature *ranks* rather than FDR corrected p-valu
 Qadabra requires both [Snakemake](https://snakemake.readthedocs.io/en/stable/) and [Snakedeploy](https://snakedeploy.readthedocs.io/en/latest/) to be installed.
 
 ```
-snakedeploy deploy-workflow https://github.com/gibsramen/qadabra qadabra_dir --tag v0.1.2
+snakedeploy deploy-workflow https://github.com/gibsramen/qadabra qadabra_dir --tag v0.2.0
 ```
 
 This will download the workflow to your local machine.
@@ -24,12 +24,15 @@ You should also change the model covariate, target, and reference category.
 * `reference`: Reference category for log-fold change calculation
 
 If you have other confounders, you can include them under the `confounders` heading.
-Delete these if you are not including any additional confounders.
-Note you should still leave the `counfounders` entry - just delete the entries in the list.
+Delete these if you are not including any additional confounders as follows:
+
+`confounders: `
 
 Qadabra can also output an [EMPress plot](https://journals.asm.org/doi/10.1128/mSystems.01216-20) of a phylogenetic tree annotated with each tool's differentials.
 Change the `tree` entry to point to this file.
-If you do not have a phylogenetic tree, change this entry to an empty string and EMPress will not be run.
+If you do not have a phylogenetic tree, delete this entry and EMPress will not be run.
+
+`tree: `
 
 Run `snakemake --use-conda <other options>` to start the workflow.
 Please read the [Snakemake documentation](https://snakemake.readthedocs.io/en/stable/executing/cli.html) for how to run Snakemake best on your system.

workflow/Snakefile

@@ -5,7 +5,6 @@ include: "rules/common.smk"
 include: "rules/diffab.smk"
 include: "rules/visualization.smk"
 include: "rules/ml.smk"
-include: "rules/tree.smk"
 
 
 report: "report/workflow.rst"

workflow/rules/tree.smk

@@ -197,25 +197,27 @@ rule create_table:
         "../scripts/create_table.py"
 
 
-rule empress:
-    input:
-        tree=config["tree"],
-        diff="results/concatenated_differentials.tsv",
-    output:
-        report(
-            directory("results/empress"),
-            caption="../report/empress.rst",
-            htmlindex="empress.html",
-            category="Tree",
-        ),
-    log:
-        "log/empress.log",
-    conda:
-        "../envs/qadabra-songbird.yaml"
-    shell:
-        """
-        empress tree-plot \
-            --tree {input.tree} \
-            --feature-metadata {input.diff} \
-            --output-dir {output} > {log} 2>&1
-        """
+if config["tree"]:
+
+    rule empress:
+        input:
+            tree=config["tree"],
+            diff="results/concatenated_differentials.tsv",
+        output:
+            report(
+                directory("results/empress"),
+                caption="../report/empress.rst",
+                htmlindex="empress.html",
+                category="Tree",
+            ),
+        log:
+            "log/empress.log",
+        conda:
+            "../envs/qadabra-songbird.yaml"
+        shell:
+            """
+            empress tree-plot \
+                --tree {input.tree} \
+                --feature-metadata {input.diff} \
+                --output-dir {output} > {log} 2>&1
+            """