Clean up documentation and associated links

Makefile

@@ -93,6 +93,6 @@ wdl-run-lipid :
 
 convert_lipid_rst_to_md:
     # convert the lipid documentation from rst to md
-	pandoc -f rst -t markdown -o docs/README_LCMS_LIPID.md docs/index_lipid.rst
+	pandoc -f rst -t markdown -o docs/lcms_lipidomics/README_LCMS_LIPID.md docs/lcms_lipidomics/index.rst
 	# render the lipid documentation into html from the rst file
-	pandoc -f rst -t html -o docs/index_lipid.html docs/index_lipid.rst
+	pandoc -f rst -t html -o docs/lcms_lipidomics/index.html docs/lcms_lipidomics/index.rst

README.md

@@ -14,8 +14,8 @@
 
 ## Available Workflows
 
-- [GC/MS metabolomics workflow](docs/README_GCMS.md)
-- [LC/MS lipidomics workflow](docs/README_LCMS_LIPID.md)
+- [GC/MS metabolomics workflow](docs/gcms_metabolomics/README_GCMS.md)
+- [LC/MS lipidomics workflow](docs/lcms_lipidomics/README_LCMS_LIPID.md)
 
 For information about data input, output, and execution for the individual workflows, follow the linked readmes above.
 

docs/lcms_lipidomics/README_LCMS_LIPID.md

@@ -29,8 +29,7 @@ acquisition for MS2 is supported at this time.
 ## Workflow Availability
 
 The workflow is available in GitHub:
-<https://github.com/microbiomedata/metaMS> #TODO KRH: update with direct
-link to lipidomics wdl
+<https://github.com/microbiomedata/metaMS/wdl/metaMS_lcmslipidomics.wdl>
 
 The container is available at Docker Hub (microbiomedata/metaMS):
 <https://hub.docker.com/r/microbiomedata/metams>
@@ -58,14 +57,15 @@ with the required workflow dependencies.*
 
 ### Database
 
--   PNNL Metabref Database (<https://metabref.emsl.pnnl.gov/>)
+-   A local copy of the in silico lipid spectra. See PNNL Metabref
+    Database (<https://metabref.emsl.pnnl.gov/>).
 
 The in-silico lipid spectra in PNNL\'s Metaref database are generated
 from the LipidBlast database (v68), found at
 <https://systemsomicslab.github.io/compms/msdial/main.html>. Note that
 there is no retention time in the PNNL version of the database and the
 workflow does not use retention time scoring. Currently the workflow
-uses a local copy of the database, but the database is available by
+uses a local copy of the database, and the database is available by
 request.
 
 ## Sample datasets
@@ -109,18 +109,17 @@ The following inputs are required (declared in the input json file):
 
 -   Lipidomics data
     -   Peak data table with annotated lipids (.csv)
-    -   HDF: CoreMS HDF5 format of CoreMS LCMS object for further
-        analysis
+    -   CoreMS HDF5 format of CoreMS LCMS object for further analysis
+        and exploration (.hdf5)
 -   Workflow Metadata
-    -   CoreMS Parameter file (.toml), the full set of parameters used
-        in the workflow, some of which are set dynamically within the
-        workflow.
+    -   The full set of CoreMS parameters used in the workflow, some of
+        which are set dynamically within the workflow (.toml)
 
 ## Version History
 
 -   v1.0.0: Initial release of the lipidomics workflow #TODO KRH: update
-    wtih release date when available
+    with release date when available
 
 ## Point of contact
 
-Package maintainer: Katherine R. Heal \<<[email protected]>\>
+Workflow maintainer: Katherine R. Heal \<<[email protected]>\>

docs/lcms_lipidomics/index_lipid.html → docs/lcms_lipidomics/index.html

@@ -28,8 +28,7 @@ <h2 id="workflow-overview">Workflow Overview</h2>
 data-dependent acquisition for MS2 is supported at this time.</p>
 <h2 id="workflow-availability">Workflow Availability</h2>
 <p>The workflow is available in GitHub: <a
-href="https://github.com/microbiomedata/metaMS">https://github.com/microbiomedata/metaMS</a>
-#TODO KRH: update with direct link to lipidomics wdl</p>
+href="https://github.com/microbiomedata/metaMS/wdl/metaMS_lcmslipidomics.wdl">https://github.com/microbiomedata/metaMS/wdl/metaMS_lcmslipidomics.wdl</a></p>
 <p>The container is available at Docker Hub (microbiomedata/metaMS): <a
 href="https://hub.docker.com/r/microbiomedata/metams">https://hub.docker.com/r/microbiomedata/metams</a></p>
 <p>The database is available by request. Please contact NMDC (<a
@@ -51,15 +50,16 @@ <h3 id="software-requirements">Software Requirements</h3>
 docker with the required workflow dependencies.</em></p>
 <h3 id="database">Database</h3>
 <ul>
-<li>PNNL Metabref Database (<a
-href="https://metabref.emsl.pnnl.gov/">https://metabref.emsl.pnnl.gov/</a>)</li>
+<li>A local copy of the in silico lipid spectra. See PNNL Metabref
+Database (<a
+href="https://metabref.emsl.pnnl.gov/">https://metabref.emsl.pnnl.gov/</a>).</li>
 </ul>
 <p>The in-silico lipid spectra in PNNL's Metaref database are generated
 from the LipidBlast database (v68), found at <a
 href="https://systemsomicslab.github.io/compms/msdial/main.html">https://systemsomicslab.github.io/compms/msdial/main.html</a>.
 Note that there is no retention time in the PNNL version of the database
 and the workflow does not use retention time scoring. Currently the
-workflow uses a local copy of the database, but the database is
+workflow uses a local copy of the database, and the database is
 available by request.</p>
 <h2 id="sample-datasets">Sample datasets</h2>
 <ul>
@@ -103,21 +103,20 @@ <h3 id="outputs">Outputs</h3>
 <li>Lipidomics data
 <ul>
 <li>Peak data table with annotated lipids (.csv)</li>
-<li>HDF: CoreMS HDF5 format of CoreMS LCMS object for further
-analysis</li>
+<li>CoreMS HDF5 format of CoreMS LCMS object for further analysis and
+exploration (.hdf5)</li>
 </ul></li>
 <li>Workflow Metadata
 <ul>
-<li>CoreMS Parameter file (.toml), the full set of parameters used in
-the workflow, some of which are set dynamically within the
-workflow.</li>
+<li>The full set of CoreMS parameters used in the workflow, some of
+which are set dynamically within the workflow (.toml)</li>
 </ul></li>
 </ul>
 <h2 id="version-history">Version History</h2>
 <ul>
 <li>v1.0.0: Initial release of the lipidomics workflow #TODO KRH: update
-wtih release date when available</li>
+with release date when available</li>
 </ul>
 <h2 id="point-of-contact">Point of contact</h2>
-<p>Package maintainer: Katherine R. Heal &lt;<a
+<p>Workflow maintainer: Katherine R. Heal &lt;<a
 href="mailto:[email protected]">[email protected]</a>&gt;</p>

docs/lcms_lipidomics/index_lipid.rst → docs/lcms_lipidomics/index.rst

@@ -37,7 +37,7 @@ Workflow Availability
 ---------------------
 
 The workflow is available in GitHub:
-https://github.com/microbiomedata/metaMS #TODO KRH: update with direct link to lipidomics wdl
+https://github.com/microbiomedata/metaMS/wdl/metaMS_lcmslipidomics.wdl
 
 The container is available at Docker Hub (microbiomedata/metaMS):
 https://hub.docker.com/r/microbiomedata/metams
@@ -64,12 +64,12 @@ Software Requirements
 Database
 ~~~~~~~~
 
--  PNNL Metabref Database
-   (https://metabref.emsl.pnnl.gov/)
+-  A local copy of the in silico lipid spectra.  See PNNL Metabref Database
+   (https://metabref.emsl.pnnl.gov/).
 
 The in-silico lipid spectra in PNNL's Metaref database are generated from the LipidBlast database (v68), found at https://systemsomicslab.github.io/compms/msdial/main.html.
 Note that there is no retention time in the PNNL version of the database and the workflow does not use retention time scoring.  
-Currently the workflow uses a local copy of the database, but the database is available by request.
+Currently the workflow uses a local copy of the database, and the database is available by request.
 
 Sample datasets
 ---------------
@@ -113,16 +113,16 @@ Outputs
 
 -  Lipidomics data
    -  Peak data table with annotated lipids (.csv)
-   -  HDF: CoreMS HDF5 format of CoreMS LCMS object for further analysis
+   -  CoreMS HDF5 format of CoreMS LCMS object for further analysis and exploration (.hdf5)
 -  Workflow Metadata
-   -  CoreMS Parameter file (.toml), the full set of parameters used in the workflow, some of which are set dynamically within the workflow.
+   -  The full set of CoreMS parameters used in the workflow, some of which are set dynamically within the workflow (.toml)
 
 Version History
 ---------------
 
-- v1.0.0: Initial release of the lipidomics workflow #TODO KRH: update wtih release date when available
+- v1.0.0: Initial release of the lipidomics workflow #TODO KRH: update with release date when available
 
 Point of contact
 ----------------
 
-Package maintainer: Katherine R. Heal <[email protected]>
+Workflow maintainer: Katherine R. Heal <[email protected]>