coming soon docs

docs/index.rst

@@ -125,6 +125,7 @@ Iliad Workflow Schematics
 
    projectinfo/citing
    projectinfo/more_resources
+   projectinfo/comingsoon
    projectinfo/container_images
    projectinfo/faq
    projectinfo/contributing

docs/projectinfo/comingsoon.rst

@@ -0,0 +1,115 @@
+.. _projectinfo/comingsoon:
+
+===========
+Coming Soon
+===========
+
+
+Sequence Read Archive retrieval
+===============================
+
+This feature will give users an option to automatically perform data downloads using the SRAtoolkit and access data from the NCBI Sequence Read Archive (SRA).
+
+
+CRAM remapping
+==============
+
+Genomic data is commonly stored in CRAM format. Of course, these data files have already been mapped to a reference genome. 
+To our knowledge, there is not a direct option for remapping a CRAM file, however, reverting a CRAM sample to a FASTQ or FASTA file is possible via samtools. 
+This feature will include that step and steps thereafter for re-alignment to a reference genome of the user's choice. 
+
+
+Variant discovery
+=================
+
+The current format of Iliad Sequence processing entails the use of variant genotyping using annotation files from the NYGC. We understand the importance of variant discovery 
+and aim to streamline this option in a future release. Currently, you can manually (and quite easily) set this up by commenting out three lines of code and adding one new line
+of code to ``./Iliad/workflow/Snakefile`` (for raw sequence reads) or ``./Iliad/workflow/cram_Snakefile`` (for cram sequence data) while we develop this method further. 
+See the code blocks and images below to manually perform this.
+
+**Raw sequence reads**
+
+.. image:: img/coming-soon-Seq.png
+   :align: center
+   :width: 800
+
+Raw sequence reads - file found in ``./Iliad/workflow/Snakefile``
+
+You can delete the contents of ``./Iliad/workflow/Snakefile`` and copy/paste below to replace it:
+.. code-block:: console
+
+    singularity: "library://ncherric/iliad/igdp-container:v1.16"
+
+    include: "rules/common.smk"
+    #splits=config['NYGC']['numberOfSplitRegionsFiles']
+
+    ##### Target rules #####
+    rule all:
+        input: 
+            expand("results/vcf/Merged-chr{chroms}-allSamples-with-rsIDs.vcf.gz.tbi", chroms=CHROMS),
+            expand("results/vcf/{sample}/chrStrCheck/alignmentFileHeader.out", sample=samples["sample"]),
+
+    ##### Modules #####
+
+
+    include: "rules/fq.smk"
+
+    include: "rules/fastQC.smk"
+
+    include: "rules/concatRawReads.smk"
+
+    include: "rules/ref.smk"
+
+    include: "rules/mapping.smk"
+
+    #include: "rules/nygcAnnotations-bam.smk"
+
+    #include: "rules/variantCalling.smk"
+    include: "rules/variantCalling-Discovery.smk"
+
+    include: "rules/dbsnpAnnotation.smk"
+
+    include: "rules/dbsnpsSeq.smk"
+
+
+**Stored sequence reads**
+
+.. image:: img/coming-soon-storedSeq.png
+   :align: center
+   :width: 800
+
+CRAM stored sequence reads - file found in ``./Iliad/workflow/cram_Snakefile``
+
+You can delete the contents of ``./Iliad/workflow/cram_Snakefile`` and copy/paste below to replace it:
+.. code-block:: console
+
+    singularity: "library://ncherric/iliad/igdp-container:v1.16"
+
+    include: "rules/common.smk"
+    #splits=config['NYGC']['numberOfSplitRegionsFiles']
+
+    ##### Target rules #####
+    rule all:
+        input: 
+            expand("results/vcf/Merged-chr{chroms}-allSamples-with-rsIDs.vcf.gz.tbi", chroms=CHROMS),
+            expand("results/vcf/{sample}/chrStrCheck/alignmentFileHeader.out", sample=cramSamples["cramSample"]),
+
+    ##### Modules #####
+
+    include: "rules/cram.smk"
+
+    include: "rules/ref.smk"
+
+    #include: "rules/nygcAnnotations-cram.smk"
+
+    #include: "rules/cram_variantCalling.smk"
+    include: "rules/cram_variantCalling-Discovery.smk"
+
+    include: "rules/dbsnpsSeq.smk"
+
+    include: "rules/dbsnpAnnotation.smk"
+
+
+Model organism genome processing
+================================
+