diff --git a/Makefile b/Makefile index 9dea2ed..e1a5af7 100644 --- a/Makefile +++ b/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 \ No newline at end of file + pandoc -f rst -t html -o docs/lcms_lipidomics/index.html docs/lcms_lipidomics/index.rst \ No newline at end of file diff --git a/README.md b/README.md index 5567226..bf402e6 100644 --- a/README.md +++ b/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. diff --git a/docs/gcms_metabolomics/index.html b/docs/index.html similarity index 100% rename from docs/gcms_metabolomics/index.html rename to docs/index.html diff --git a/docs/lcms_lipidomics/README_LCMS_LIPID.md b/docs/lcms_lipidomics/README_LCMS_LIPID.md index 04f7922..bc98795 100644 --- a/docs/lcms_lipidomics/README_LCMS_LIPID.md +++ b/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: - #TODO KRH: update with direct -link to lipidomics wdl + The container is available at Docker Hub (microbiomedata/metaMS): @@ -58,14 +57,15 @@ with the required workflow dependencies.* ### Database -- PNNL Metabref Database () +- A local copy of the in silico lipid spectra. See PNNL Metabref + Database (). The in-silico lipid spectra in PNNL\'s Metaref database are generated from the LipidBlast database (v68), found at . 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 \<\> +Workflow maintainer: Katherine R. Heal \<\> diff --git a/docs/lcms_lipidomics/index_lipid.html b/docs/lcms_lipidomics/index.html similarity index 89% rename from docs/lcms_lipidomics/index_lipid.html rename to docs/lcms_lipidomics/index.html index de9741d..0d57b2d 100644 --- a/docs/lcms_lipidomics/index_lipid.html +++ b/docs/lcms_lipidomics/index.html @@ -28,8 +28,7 @@

Workflow Overview

data-dependent 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

+href="https://github.com/microbiomedata/metaMS/wdl/metaMS_lcmslipidomics.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

The database is available by request. Please contact NMDC (Software Requirements docker with the required workflow dependencies.

Database

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 +workflow uses a local copy of the database, and the database is available by request.

Sample datasets

    @@ -103,21 +103,20 @@

    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
    • +with release date when available

Point of contact

-

Package maintainer: Katherine R. Heal <Workflow maintainer: Katherine R. Heal <katherine.heal@pnnl.gov>

diff --git a/docs/lcms_lipidomics/index_lipid.rst b/docs/lcms_lipidomics/index.rst similarity index 89% rename from docs/lcms_lipidomics/index_lipid.rst rename to docs/lcms_lipidomics/index.rst index f5ac25f..39459c9 100644 --- a/docs/lcms_lipidomics/index_lipid.rst +++ b/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 +Workflow maintainer: Katherine R. Heal