Add lipid workflow diagrams

docs/README_LCMS_LIPID.md

@@ -1,10 +1,8 @@
 # Lipidomics Workflow (v1.0.0)
 
-![](metamsworkflow.png)
+![](lipid_workflow_v1.png)
 
-#TODO KRH: replace with lipid diagram when available
-
-## Overview
+## Workflow Overview
 
 The liquid chromatography-mass spectrometry (LC-MS)-based lipidomics
 workflow (part of MetaMS) is built using PNNL's CoreMS software
@@ -27,14 +25,12 @@ acquisition for MS2 is supported at this time.
 ## Workflow Availability
 
 The workflow is available in GitHub:
-<https://github.com/microbiomedata/metaMS>
+<https://github.com/microbiomedata/metaMS> #TODO KRH: update with direct
+link to lipidomics wdl
 
 The container is available at Docker Hub (microbiomedata/metaMS):
 <https://hub.docker.com/r/microbiomedata/metams>
 
-The python package is available on PyPi:
-<https://pypi.org/project/metaMS/>
-
 The database is available by request. Please contact NMDC
 (<[email protected]>) for access.
 
@@ -54,7 +50,7 @@ speed, 8GB of RAM, 10GB of free hard disk space.
 -   miniwdl (v1, <https://pypi.org/project/miniwdl/>)
 
 *Note that the wdl file will automatically pull the necessary docker
-with the required software dependencies.*
+with the required workflow dependencies.*
 
 ### Database
 
@@ -67,7 +63,7 @@ LipidBlast database (v68), found at
 there is no retention time in the PNNL version of the database and the
 workflow does not use retention time scoring.
 
-## Test datasets
+## Sample datasets
 
 -   An example dataset can be downloaded from here:
     <https://nmdcdemo.emsl.pnnl.gov/lipidomics/blanchard_11_8ws97026/Blanch_Nat_Lip_H_32_AB_O_19_NEG_25Jan18_Brandi-WCSH5801.raw>

docs/index_lipid.html

@@ -1,9 +1,8 @@
 <h1 id="lipidomics-workflow-v1.0.0">Lipidomics Workflow (v1.0.0)</h1>
 <figure>
-<img src="metamsworkflow.png" alt="metamsworkflow.png" />
+<img src="lipid_workflow_v1.png" alt="lipid_workflow_v1.png" />
 </figure>
-<p>#TODO KRH: replace with lipid diagram when available</p>
-<h2 id="overview">Overview</h2>
+<h2 id="workflow-overview">Workflow Overview</h2>
 <p>The liquid chromatography-mass spectrometry (LC-MS)-based lipidomics
 workflow (part of MetaMS) is built using PNNL’s CoreMS software
 framework. The workflow leverages many features of CoreMS as well as
@@ -22,11 +21,10 @@ <h2 id="overview">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></p>
+href="https://github.com/microbiomedata/metaMS">https://github.com/microbiomedata/metaMS</a>
+#TODO KRH: update with direct link to lipidomics wdl</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 python package is available on PyPi: <a
-href="https://pypi.org/project/metaMS/">https://pypi.org/project/metaMS/</a></p>
 <p>The database is available by request. Please contact NMDC (<a
 href="mailto:[email protected]">[email protected]</a>)
 for access.</p>
@@ -43,7 +41,7 @@ <h3 id="software-requirements">Software Requirements</h3>
 href="https://pypi.org/project/miniwdl/">https://pypi.org/project/miniwdl/</a>)</li>
 </ul>
 <p><em>Note that the wdl file will automatically pull the necessary
-docker with the required software dependencies.</em></p>
+docker with the required workflow dependencies.</em></p>
 <h3 id="database">Database</h3>
 <ul>
 <li>PNNL Metabolomics LC-MS <em>in silico</em> Spectral Database (<a
@@ -54,7 +52,7 @@ <h3 id="database">Database</h3>
 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.</p>
-<h2 id="test-datasets">Test datasets</h2>
+<h2 id="sample-datasets">Sample datasets</h2>
 <ul>
 <li>An example dataset can be downloaded from here: <a
 href="https://nmdcdemo.emsl.pnnl.gov/lipidomics/blanchard_11_8ws97026/Blanch_Nat_Lip_H_32_AB_O_19_NEG_25Jan18_Brandi-WCSH5801.raw">https://nmdcdemo.emsl.pnnl.gov/lipidomics/blanchard_11_8ws97026/Blanch_Nat_Lip_H_32_AB_O_19_NEG_25Jan18_Brandi-WCSH5801.raw</a></li>

docs/index_lipid.rst

@@ -1,13 +1,11 @@
 Lipidomics Workflow (v1.0.0)
 ============================
 
-.. figure:: metamsworkflow.png
+.. figure:: lipid_workflow_v1.png
    :alt: diagram of lipid workflow
 
-#TODO KRH: replace with lipid diagram when available
-
-Overview
---------
+Workflow Overview
+-----------------
 
 The liquid chromatography-mass spectrometry (LC-MS)-based lipidomics
 workflow (part of MetaMS) is built using PNNL’s CoreMS software
@@ -31,14 +29,11 @@ Workflow Availability
 ---------------------
 
 The workflow is available in GitHub:
-https://github.com/microbiomedata/metaMS
+https://github.com/microbiomedata/metaMS #TODO KRH: update with direct link to lipidomics wdl
 
 The container is available at Docker Hub (microbiomedata/metaMS):
 https://hub.docker.com/r/microbiomedata/metams
 
-The python package is available on PyPi:
-https://pypi.org/project/metaMS/
-
 The database is available by request. Please contact NMDC
 ([email protected]) for access.
 
@@ -56,7 +51,7 @@ Software Requirements
 -  Docker Container Runtime
 -  miniwdl (v1, https://pypi.org/project/miniwdl/)
 
-*Note that the wdl file will automatically pull the necessary docker with the required software dependencies.*
+*Note that the wdl file will automatically pull the necessary docker with the required workflow dependencies.*
 
 Database
 ~~~~~~~~
@@ -67,8 +62,8 @@ Database
 The in-silico lipid spectra in the 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.
 
-Test datasets
--------------
+Sample datasets
+---------------
 
 - An example dataset can be downloaded from here: https://nmdcdemo.emsl.pnnl.gov/lipidomics/blanchard_11_8ws97026/Blanch_Nat_Lip_H_32_AB_O_19_NEG_25Jan18_Brandi-WCSH5801.raw
 - Example CoreMS Parameter file (applicable to the example dataset): https://nmdcdemo.emsl.pnnl.gov/lipidomics/parameter_files/emsl_lipidomics_corems_params.toml
@@ -110,8 +105,6 @@ Outputs
 -  Lipidomics data
    -  Peak data table with annotated lipids (.csv)
    -  HDF: CoreMS HDF5 format of CoreMS LCMS object for further analysis
-
-
 -  Workflow Metadata
    -  CoreMS Parameter file (.toml), the full set of parameters used in the workflow, some of which are set dynamically within the workflow.