Merge pull request #21 from drneavin/v2.0.2

V2.0.2

Singularity.Demuxafy

@@ -332,4 +332,3 @@ From: continuumio/miniconda3
 
     conda clean --all 
 
-    export PATH=/opt:/usr/games:/opt/samtools-1.16.1/samtools:/opt/bcftools-1.16:/opt/conda/envs/py37/bin:/opt/conda/bin:/opt/Demultiplexing_Doublet_Detecting_Docs/scripts:opt/Demultiplexing_Doublet_Detecting_Docs/mods:/opt/bedtools2/bin:opt/vcflib/bin:/opt/vcflib/scripts:/opt/souporcell:/opt/souporcell/troublet/target/release:/opt/minimap2-2.7:/root/.cargo/bin:/opt/freebayes/scripts:/opt/popscle/bin/:/opt/conda/envs/py37/lib/python3.7/site-packages/scSplit/:$PATH

Singularity.Demuxafy_update

@@ -0,0 +1,53 @@
+Bootstrap: docker
+From: drneavin/demuxafy:v2.0.1
+
+%labels
+    Author = Drew Neavin
+    Image_version = 2.1.0
+
+%environment
+    export PATH=/opt:/usr/games:/opt/samtools-1.16.1:/opt/bcftools-1.16:/opt/conda/envs/py37/bin:/opt/conda/bin:/opt/Demultiplexing_Doublet_Detecting_Docs/scripts:opt/Demultiplexing_Doublet_Detecting_Docs/mods:/opt/bedtools2/bin:opt/vcflib/bin:/opt/vcflib/scripts:/opt/souporcell:/opt/souporcell/troublet/target/release:/opt/minimap2-2.7:/root/.cargo/bin:/opt/freebayes/scripts:/opt/popscle/bin/:/opt/conda/envs/py37/lib/python3.7/site-packages/scSplit/:/opt/Drop-seq_tools-2.5.4/:$PATH
+    export PYTHONPATH=/opt/conda/envs/py37/lib/python3.7/site-packages/
+    export LC_ALL=C 
+
+
+%post 
+### Add in demuxalot and dropulation tools 
+## demuxalot
+/opt/conda/envs/py37/bin/pip install demuxalot
+
+
+## dropulation
+cd opt
+wget https://github.com/broadinstitute/Drop-seq/releases/download/v2.5.4/Drop-seq_tools-2.5.4.zip
+unzip Drop-seq_tools-2.5.4.zip
+
+
+## Install java (for dropulation)
+# apt-get install libc6-i386 libc6-x32 libxi6 libxtst6 -y
+# wget https://download.oracle.com/java/20/latest/jdk-20_linux-x64_bin.deb
+# dpkg -i jdk-20_linux-x64_bin.deb
+
+# apt-get update
+# apt-get install -y openjdk-11-jdk
+## dependency: libasound2
+apt-get install -y libasound2
+wget https://download.bell-sw.com/java/11.0.20+8/bellsoft-jdk11.0.20+8-linux-amd64.deb
+dpkg -i bellsoft-jdk11.0.20+8-linux-amd64.deb
+
+
+### Remove and reisntall Demuxafy
+rm -rf /opt/Demultiplexing_Doublet_Detecting_Docs
+
+### Get the github repo with scripts for workflow ###
+cd /opt
+    git clone  --branch v2.1.0 https://github.com/drneavin/Demultiplexing_Doublet_Detecting_Docs.git
+#    git clone  --branch main https://github.com/drneavin/Demultiplexing_Doublet_Detecting_Docs.git
+        cd Demultiplexing_Doublet_Detecting_Docs
+        rm -rf references ## Only hosting on  github for people to download if they want, no need to take up extra space in the image
+        rm -rf docs ## doc files, dont need in image
+
+
+### Make scripts executable ###
+chmod 777 -R /opt/Demultiplexing_Doublet_Detecting_Docs/scripts
+

docs/source/CombineResults.rst

@@ -200,6 +200,26 @@ Providing the possible parameter options:
 
 An example command that combines :ref:`Demuxlet <Demuxlet-docs>` results, :ref:`Souporcell <Souporcell-docs>` results, :ref:`Solo <Solo-docs>` results and :ref:`Scds <scds-docs>` results would look like this:
 There are a two different options for using this script:
+1. Combining the results **and** calling the droplet type through the combination of the softwares.
+1. Combining the results without any joint droplet calling. You  might choose this if you just want to see how the different softwares perform on your data before deciding which to move forward with for final joint droplet calling.
+
+First, let's assign the variables that will be used to execute each step.
+
+.. admonition:: Example Variable Settings
+  :class: grey
+
+    Below is an example of the variables that we can set up to be used in the command below.
+    These are files provided as a :ref:`test dataset <TestData>` available in the :ref:`Data Preparation Documentation <DataPrep-docs>`
+    Please replace paths with the full path to data on your system.
+
+    .. code-block:: bash
+
+      OUTDIR=/path/to/output/combined
+      DEMUXLET_OUTDIR=/path/to/output/demuxlet
+      SOUPORCELL_OUTDIR=/path/to/output/souporcell
+      SOLO_OUTDIR=/path/to/output/solo
+      SCDS_OUTDIR=/path/to/output/scds
+
 
 .. tabs::
 
@@ -215,7 +235,7 @@ There are a two different options for using this script:
         --souporcell $SOUPORCELL_OUTDIR \
         --solo $SOLO_OUTDIR \
         --scds $SCDS_OUTDIR \
-        --method "MajoritySinglet"
+        --method "MajoritySinglet" ## there are other methods that can also be used, please see the help message above for the other options
 
   .. tab:: Combine Results
 
@@ -244,7 +264,7 @@ Here, we show the results for the above example that also provides combined call
 
 .. code-block:: bash
 
-  .
+  /path/to/output/combined
   ├── combined_results_demultiplexing_summary.tsv
   ├── combined_resultsSinglets_upset.pdf
   ├── combined_results_summary.tsv

docs/source/DataPrep.rst

@@ -1,3 +1,5 @@
+.. _DataPrep-docs:
+
 Data Preparation
 ================
 
@@ -115,9 +117,12 @@ Next, filter for the SNPs that overlap exons.
 
 
 
+.. _TestData:
+
 Test Dataset
 ------------
 In addition, we have provided a test dataset that you can use.
+Find the data that can be downloaded below along with some information about the data.
 
 .. admonition:: Information
   :class: important
@@ -169,9 +174,7 @@ You can download the dataset with one of the following commands:
     .. code-block:: bash
 
       TestData4PipelineFull
-      ├── donor_list.txt
-      ├── individuals_list_dir
-      │   └── test_dataset.txt
+      ├── donor_list.txt 
       ├── samplesheet.txt
       ├── test_dataset
       │   ├── outs
@@ -221,7 +224,6 @@ You can download the dataset with one of the following commands:
       ├── donor_list.txt
       ├── individuals_list_dir
       │   └── test_dataset.txt
-      ├── ls
       ├── samplesheet.txt
       ├── test_dataset
       │   └── outs