diff --git a/docs/index.rst b/docs/index.rst index 6ad506d..874897a 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -125,6 +125,7 @@ Iliad Workflow Schematics projectinfo/citing projectinfo/more_resources + projectinfo/comingsoon projectinfo/container_images projectinfo/faq projectinfo/contributing diff --git a/docs/projectinfo/comingsoon.rst b/docs/projectinfo/comingsoon.rst new file mode 100644 index 0000000..9032c56 --- /dev/null +++ b/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 +================================ + diff --git a/docs/projectinfo/img/coming-soon-Seq.png b/docs/projectinfo/img/coming-soon-Seq.png new file mode 100644 index 0000000..4bbb074 Binary files /dev/null and b/docs/projectinfo/img/coming-soon-Seq.png differ diff --git a/docs/projectinfo/img/coming-soon-storedSeq.png b/docs/projectinfo/img/coming-soon-storedSeq.png new file mode 100644 index 0000000..11ed518 Binary files /dev/null and b/docs/projectinfo/img/coming-soon-storedSeq.png differ