update docs [ci skip]

Author: afrendeiro

docs/source/examples.rst

@@ -8,23 +8,30 @@ Analysis example
 The following is an example of how to use ``ngs_toolkit`` in a ATAC-seq project.
 While straightforward, it still allows considerable customization due to the modularity of the toolkit and the parametrization of most functions (this example uses default values everywhere nonetheless).
 
+.. note::
+    ``ngs_toolkit`` from version 0.25.0 on uses the `PEP 2.0 specification <http://pep.databio.org/en/2.0.0/specification/>`_. If you have a PEP made in an earlier version, you must update it in order to use ``ngs_toolkit``>=0.25.0.
 
-We have the following `PEP project <https://peppy.readthedocs.io>`_ config YAML file:
+
+We have the following `PEP project <http://pep.databio.org/>`_ config YAML file:
 
 .. code-block:: yaml
 
-    project_name: example_project
-    project_description: example_project
+    pep_version: "2.0.0"
+    name: example_project
+    description: example_project
     username: user
-    email: user@cemm.oeaw.ac.at
-    metadata:
-      output_dir: /scratch/lab_bock/shared/projects/example_project
-      results_subdir: data
-      submission_subdir: submission
-      pipeline_interfaces: /home/user/workspace/open_pipelines/pipeline_interface.yaml
-      sample_table: /scratch/lab_bock/shared/projects/example_project/metadata/annotation.csv
-      subsample_table: /scratch/lab_bock/shared/projects/example_project/metadata/sample_subannotation.csv
-      comparison_table: /scratch/lab_bock/shared/projects/example_project/metadata/comparison_table.csv
+    email: user@email.com
+
+    sample_table: annotation.csv
+    subsample_table:
+    comparison_table: comparison_table.csv
+
+    submission_subdir: submission
+    results_subdir: data
+    output_dir: example_project
+
+    pipeline_interfaces: /home/user/workspace/open_pipelines/pipeline_interface.yaml
+
     sample_attributes:
       - sample_name
       - genotype
@@ -41,27 +48,25 @@ We have the following `PEP project <https://peppy.readthedocs.io>`_ config YAML
         derive:
             attributes: [data_source]
             sources:
+                local: data/{sample_name}.bam
                 bsf: /scratch/lab_bsf/samples/{flowcell}/{flowcell}_{lane}_samples/{flowcell}_{lane}#{BSF_name}.bam
-                local: /tmp/tmptd4zmpiw/test_project/data/{sample_name}.bam
-    trackhubs:
-      trackhub_dir: /path/to/public_html/user/example_project/
-      url: http://root-url.com/example_project
 
 
-The following sample annotation CSV file:
+
+The following sample annotation CSV file, 'annotation.csv':
 
 .. csv-table:: Annotation table for example
-   :header: "sample_name", "genotype", "replicate", "organism", flowcell, lane
+   :header: "sample_name", "protocol", "genotype", "replicate", "organism", flowcell, lane
 
-    "ATAC-seq_KOA_r1",  "KO_A",   "1",   "human", "C0RQ31ACXXX",   "1"
-    "ATAC-seq_KOA_r2",  "KO_A",   "2",   "human", "C0RQ31ACXXX",   "1"
-    "ATAC-seq_KOB_r1",  "KO_B",   "1",   "human", "C0RQ31ACXXX",   "1"
-    "ATAC-seq_KOB_r2",  "KO_B",   "2",   "human", "C0RQ31ACXXX",   "1"
-    "ATAC-seq_WT_r1",   "WT",   "1",    "human",    "C0RQ31ACXXX", "1"
-    "ATAC-seq_WT_r2",   "WT",    "2",   "human", "C0RQ31ACXXX",    "1"
+    "ATAC-seq_KOA_r1",  "ATAC-seq", KO_A",   "1",   "human", "C0AXX",   "1"
+    "ATAC-seq_KOA_r2",  "ATAC-seq", KO_A",   "2",   "human", "C0AXX",   "1"
+    "ATAC-seq_KOB_r1",  "ATAC-seq", KO_B",   "1",   "human", "C0AXX",   "1"
+    "ATAC-seq_KOB_r2",  "ATAC-seq", KO_B",   "2",   "human", "C0AXX",   "1"
+    "ATAC-seq_WT_r1",   "ATAC-seq", WT",     "1",   "human", "C0AXX",   "1"
+    "ATAC-seq_WT_r2",   "ATAC-seq", WT",     "2",   "human", "C0AXX",   "1"
 
 
-And the following comparison table:
+And the following comparison table, 'comparison_table.csv':
 
 .. csv-table:: Comparison table for example
    :header: "comparison_name", "comparison_side", "sample_name", "sample_group"
@@ -87,8 +92,7 @@ ATAC-seq analysis example
     from ngs_toolkit.atacseq import ATACSeqAnalysis
 
     # Start project and analysis objects
-    analysis = ATACSeqAnalysis(
-        from_pep=os.path.join("metadata", "project_config.yaml"))
+    analysis = ATACSeqAnalysis(from_pep="project_config.yaml")
 
     # Generate consensus peak set and annotate it
     ## get consensus peak set from all samples
@@ -117,10 +121,6 @@ ATAC-seq analysis example
     # # annotate dataframe with sample metadata
     analysis.accessibility = analysis.annotate_samples()
 
-    # Save analysis object
-    analysis.to_pickle()
-
-
     # UNSUPERVISED ANALYSIS
     # # plot pairwise sample correlations,
     # # perform dimensionality reduction (MDS, PCA)
@@ -132,9 +132,6 @@ ATAC-seq analysis example
     # # differential analysis with DESeq2
     analysis.differential_analysis()
 
-    # # Save analysis object
-    analysis.to_pickle()
-
     # # plot scatter, volcano, MA, heatmaps on the differential regions
     # # by groups and with individual samples, with normalized values
     # # and scalled values (Z-score).

ngs_toolkit/config/default.yaml

@@ -34,7 +34,7 @@ preferences:
       # key:values under parameters are passed to seaborn.set
       parameters:
         context: "paper"
-        style: "white"
+        style: "ticks"
         palette: "colorblind"
         color_codes: True
     figure_saving: