add clarification for sample_modifiers and configuring project

docs/defining-a-project.md

@@ -8,7 +8,35 @@ To start, you need a project defined in the [standard Portable Encapsulated Proj
 
 This information generally lives in a `project_config.yaml` file.
 
+Simplest example:
 ```yaml
 pep_version: 2.0.0
 sample_table: sample_annotation.csv
 ```
+
+A more complicated example taken from [PEPATAC](https://pepatac.databio.org/en/latest/):
+
+```yaml
+pep_version: 2.0.0
+sample_table: tutorial.csv
+
+sample_modifiers:
+  derive:
+    attributes: [read1, read2]
+    sources:
+      # Obtain tutorial data from http://big.databio.org/pepatac/ then set
+      # path to your local saved files
+      R1: "${TUTORIAL}/tools/pepatac/examples/data/{sample_name}_r1.fastq.gz"
+      R2: "${TUTORIAL}/tools/pepatac/examples/data/{sample_name}_r2.fastq.gz"
+  imply:
+    - if: 
+        organism: ["human", "Homo sapiens", "Human", "Homo_sapiens"]
+      then: 
+        genome: hg38
+        prealignment_names: ["rCRSd"]
+        deduplicator: samblaster # Default. [options: picard]
+        trimmer: skewer          # Default. [options: pyadapt, trimmomatic]
+        peak_type: fixed         # Default. [options: variable]
+        extend: "250"            # Default. For fixed-width peaks, extend this distance up- and down-stream.
+        frip_ref_peaks: None     # Default. Use an external reference set of peaks instead of the peaks called from this run
+```

docs/pipestat.md

@@ -25,17 +25,6 @@ sample_table: annotation_sheet.csv
 pipeline_interfaces:
   sample:  ./pipeline_interface1_sample_pipestat.yaml
   project: ./pipeline_interface1_project_pipestat.yaml
-looper:
-  all:
-    output_dir: output
-sample_modifiers:
-  append:
-    attr: "val"
-  derive:
-    attributes: [read1, read2]
-    sources:
-      SRA_1: "{SRR}_1.fastq.gz"
-      SRA_2: "{SRR}_2.fastq.gz"
 pipestat:
   project_name: TEST_PROJECT_NAME
   results_file_path: tmp_pipestat_results.yaml