Merge remote-tracking branch 'origin/master' into hotfix

griffithlab · Aug 7, 2023 · af74bab · af74bab
2 parents c3a0153 + ae35f14
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diff --git a/docs/pvacbind/output_files.rst b/docs/pvacbind/output_files.rst
@@ -26,11 +26,11 @@ created):
    * - ``<sample_name>.filtered.tsv``
      - The above file after applying all filters, with cleavage site and stability
        predictions added.
-   * - ``<sample_name>.filtered.tsv.reference_matches`` (optional)
-     - A file outlining details of reference proteome matches
    * - ``<sample_name>.all_epitopes.aggregated.tsv``
      - An aggregated version of the ``all_epitopes.tsv`` file that gives information about
-       the best epitope for each mutation in an easy-to-read format.
+       the best epitope for each mutation in an easy-to-read format. Not generated when running with elution algorithms only.
+   * - ``<sample_name>.all_epitopes.aggregated.tsv.reference_matches`` (optional)
+     - A file outlining details of reference proteome matches
 
 Filters applied to the filtered.tsv file
 ----------------------------------------
@@ -75,6 +75,9 @@ _______________________________________________
 - NetMHCpanEL
 - NetMHCIIpanEL
 
+Please note that when running pVACfuse with only elution algorithms, no
+aggregate report is created.
+
 .. _pvacbind_all_ep_and_filtered:
 
 all_epitopes.tsv and filtered.tsv Report Columns
@@ -243,8 +246,8 @@ Criteria Details
 
 .. _pvacbind_reference_matches:
 
-filtered.tsv.reference_matches Report Columns
----------------------------------------------
+aggregated.tsv.reference_matches Report Columns
+-----------------------------------------------
 
 This file is only generated when the ``--run-reference-proteome-similarity``
 option is chosen.

diff --git a/docs/pvacfuse/output_files.rst b/docs/pvacfuse/output_files.rst
@@ -37,11 +37,11 @@ created):
    * - ``<sample_name>.filtered.tsv``
      - The above file after applying all filters, with cleavage site and stability
        predictions added.
-   * - ``<sample_name>.filtered.tsv.reference_matches`` (optional)
-     - A file outlining details of reference proteome matches
    * - ``<sample_name>.all_epitopes.aggregated.tsv``
      - An aggregated version of the ``all_epitopes.tsv`` file that gives information about
-       the best epitope for each mutation in an easy-to-read format.
+       the best epitope for each mutation in an easy-to-read format. Not generated when running with elution algorithms only.
+   * - ``<sample_name>.all_epitopes.aggregated.tsv.reference_matches`` (optional)
+     - A file outlining details of reference proteome matches
 
 Filters applied to the filtered.tsv file
 ----------------------------------------
@@ -89,6 +89,9 @@ _______________________________________________
 - NetMHCpanEL
 - NetMHCIIpanEL
 
+Please note that when running pVACfuse with only elution algorithms, no
+aggregate report is created.
+
 all_epitopes.tsv and filtered.tsv Report Columns
 ------------------------------------------------
 

diff --git a/docs/pvacseq/getting_started.rst b/docs/pvacseq/getting_started.rst
@@ -12,7 +12,7 @@ The example data output can be reproduced by running the following command:
 .. code-block:: none
 
    pvacseq run \
-   <example_data_dir>/input.vcf \
+   <example_data_dir>/annotated.expression.vcf.gz \
    HCC1395_TUMOR_DNA \
    HLA-A*29:02,HLA-B*45:01,DRB1*04:05 \
    all \

diff --git a/docs/pvacseq/output_files.rst b/docs/pvacseq/output_files.rst
@@ -41,20 +41,22 @@ created):
    * - ``<sample_name>.filtered.tsv``
      - The above file after applying all filters, with (optionally) cleavage site, stability
        predictions, and reference proteome similarity metrics added.
-   * - ``<sample_name>.filtered.tsv.reference_matches`` (optional)
-     - A file outlining details of reference proteome matches
    * - ``<sample_name>.all_epitopes.aggregated.tsv``
      - An aggregated version of the ``all_epitopes.tsv`` file that gives information about
-       the best epitope for each mutation in an easy-to-read format.
+       the best epitope for each mutation in an easy-to-read format. Not
+       generated when running with elution algorithms only.
+   * - ``<sample_name>.all_epitopes.aggregated.tsv.reference_matches`` (optional)
+     - A file outlining details of reference proteome matches
    * - ``<sample_name>.all_epitopes.aggregated.metrics.json``
      - A JSON file with detailed information about the predicted epitopes,
        formatted for pVACview. This file, in combination with the
        aggregated.tsv file, is required to visualize your results
-       in pVACview.
+       in pVACview. Not generated when running with elution algorithms only.
    * - ``ui.R``, ``app.R``, ``server.R``, ``styling.R``, ``anchor_and_helper_functions.R``
-     - pVACview R Shiny application files
+     - pVACview R Shiny application files. Not generated when running with elution algorithms only.
    * - ``www`` (directory)
-     - Directory containing image files for pVACview
+     - Directory containing image files for pVACview. Not generated when running with elution algorithms only.
+
 
 Filters applied to the filtered.tsv file
 ----------------------------------------
@@ -101,6 +103,9 @@ _______________________________________________
 - NetMHCpanEL
 - NetMHCIIpanEL
 
+Please note that when running pVACseq with only elution algorithms, no
+aggregate report and pVACview files are created.
+
 .. _all_ep_and_filtered:
 
 all_epitopes.tsv and filtered.tsv Report Columns