Documentation updates for 0.10.1

Author: cflerin

README.rst

@@ -17,6 +17,14 @@ in no time. The latter is achieved via the dask_ framework for distributed compu
 News
 ----
 
+2020-05-17
+^^^^^^^^^^
+
+**0.10.1 release**
+
+* CLI: file compression (optionally) enabled for intermediate files for the major steps: grn (adjacencies matrix), ctx (regulons), and aucell (auc matrix). Compression is used when the file name argument has a .gz ending.
+
+
 2020-02-27
 ^^^^^^^^^^
 
@@ -47,10 +55,15 @@ All the functionality of the original R implementation is available and in addit
 3. Regulons, i.e. the regulatory network that connects a TF with its target genes, with targets that are repressed are now also derived and used for cell enrichment analysis.
 
 
-Website
--------
+Additional resources
+--------------------
+
+For more information, please visit LCB_, or SCENIC_ (R version).
+The CLI to pySCENIC has also been streamlined into a pipeline that can be run with a single command, using the Nextflow workflow manager.
+There are two Nextflow implementations available:
 
-For more information, please visit LCB_, SCENIC_ (R version), or SCENICprotocol_ (for a Nextflow implementation).
+* `SCENICprotocol`_: A Nextflow DSL1 implementation of pySCENIC alongside a basic "best practices" expression analysis. Includes details on pySCENIC installation, usage, and downstream analysis, along with detailed tutorials.
+* `VSNPipelines`_: A Nextflow DSL2 implementation of pySCENIC with a comprehensive and customizable pipeline for expression analysis. Includes additional pySCENIC features (multi-runs, integrated motif- and track-based regulon pruning, loom file generation).
 
 
 Acknowledgments
@@ -82,6 +95,7 @@ References
 .. _arboreto: https://arboreto.readthedocs.io
 .. _LCB: https://aertslab.org
 .. _`SCENICprotocol`: https://github.com/aertslab/SCENICprotocol
+.. _`VSNPipelines`: https://github.com/vib-singlecell-nf/vsn-pipelines
 .. _notebooks: https://github.com/aertslab/pySCENIC/tree/master/notebooks
 .. _issue: https://github.com/aertslab/pySCENIC/issues/new
 .. _PyPI: https://pypi.python.org/pypi/pyscenic

docs/installation.rst

@@ -115,31 +115,31 @@ A mount point (or more than one) needs to be specified, which contains the input
 .. code-block:: bash
 
     docker run -it --rm \
-        -v /path/to/data:/scenicdata \
-        aertslab/pyscenic:[version] pyscenic grn \
+        -v /data:/data \
+        aertslab/pyscenic:0.10.0 pyscenic grn \
             --num_workers 6 \
-            -o /scenicdata/expr_mat.adjacencies.tsv \
-            /scenicdata/expr_mat.tsv \
-            /scenicdata/allTFs_hg38.txt
+            -o /data/expr_mat.adjacencies.tsv \
+            /data/expr_mat.tsv \
+            /data/allTFs_hg38.txt
 
     docker run -it --rm \
-        -v /path/to/data:/scenicdata \
-        aertslab/pyscenic:[version] pyscenic ctx \
-            /scenicdata/expr_mat.adjacencies.tsv \
-            /scenicdata/hg19-tss-centered-5kb-7species.mc9nr.feather \
-            /scenicdata/hg19-tss-centered-10kb-7species.mc9nr.feather \
-            --annotations_fname /scenicdata/motifs-v9-nr.hgnc-m0.001-o0.0.tbl \
-            --expression_mtx_fname /scenicdata/expr_mat.tsv \
+        -v /data:/data \
+        aertslab/pyscenic:0.10.0 pyscenic ctx \
+            /data/expr_mat.adjacencies.tsv \
+            /data/hg19-tss-centered-5kb-7species.mc9nr.feather \
+            /data/hg19-tss-centered-10kb-7species.mc9nr.feather \
+            --annotations_fname /data/motifs-v9-nr.hgnc-m0.001-o0.0.tbl \
+            --expression_mtx_fname /data/expr_mat.tsv \
             --mode "dask_multiprocessing" \
-            --output /scenicdata/regulons.csv \
+            --output /data/regulons.csv \
             --num_workers 6
 
     docker run -it --rm \
-        -v /path/to/data:/scenicdata \
-        aertslab/pyscenic:[version] pyscenic aucell \
-            /scenicdata/expr_mat.tsv \
-            /scenicdata/regulons.csv \
-            -o /scenicdata/auc_mtx.csv \
+        -v /data:/data \
+        aertslab/pyscenic:0.10.0 pyscenic aucell \
+            /data/expr_mat.tsv \
+            /data/regulons.csv \
+            -o /data/auc_mtx.csv \
             --num_workers 6
 
 Singularity
@@ -169,7 +169,7 @@ The first step (GRN inference) is shown as an example:
 Using the Docker or Singularity images with Jupyter notebook
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-As of version 0.9.7, the pySCENIC containers have the `ipykernel` package installed, and can also be used interactively in a notebook.
+As of version 0.9.7, the pySCENIC containers have the ``ipykernel`` package installed, and can also be used interactively in a notebook.
 This can be achieved using a kernel command similar to the following (for singularity).
 Note that in this case, a bind needs to be specified.
 
@@ -181,12 +181,15 @@ Note that in this case, a bind needs to be specified.
 Nextflow
 --------
 
-The CLI to pySCENIC has also been streamlined into a pipeline that can be run with a single command, using the Nextflow workflow manager.
-For details on this usage, along with more detailed pySCENIC tutorials, see the `SCENICprotocol`_ repository.
+There are two Nextflow implementations available:
+
+* `SCENICprotocol`_: A Nextflow DSL1 implementation.
+* `VSNPipelines`_: A Nextflow DSL2 implementation.
 
 
 .. _`Singularity Hub`: https://www.singularity-hub.org/collections/2033
 .. _`SCENICprotocol`: https://github.com/aertslab/SCENICprotocol
+.. _`VSNPipelines`: https://github.com/vib-singlecell-nf/vsn-pipelines
 .. _dask: https://dask.pydata.org/en/latest/
 .. _distributed: https://distributed.readthedocs.io/en/latest/
 .. _`Docker Hub`: https://hub.docker.com/r/aertslab/pyscenic