docs: added some pages

docs/alignment.md

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+# Alignment
+
+rulegraph

docs/cnv_sv.md

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+# CNV SV
+hello

docs/includes/abbreviations.md

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-*[DNA]: Deoxyribonucleic acid
+*[DNA]: Deoxyribonucleic acid
+*[GMS]: Genome Medicin Sweden

docs/index.md

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 <img src="static/poppy_light.svg" style="height: 200px;" />
 
-Poppy is a Snakemake pipeline used for analysing hybrid capture short-read sequencing data from the [Genomic Medicine Sweden](https://genomicmedicine.se/en/) myeloid gene panels.
+[Poppy](https://github.com/genomic-medicine-sweden/Twist_DNA_Hematology) is a Snakemake pipeline used for analysing hybrid capture short-read sequencing data from the [Genomic Medicine Sweden](https://genomicmedicine.se/en/) myeloid gene panels.
 
 # Hydra-genetics
 

docs/intro.md

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 # Introduction
 
-Poppy is a Snakemake pipeline used for analysing hybrid capture short-read sequencing data from the [Genomic Medicine Sweden](https://genomicmedicine.se/en/) myeloid gene panels.
+[Poppy](https://github.com/genomic-medicine-sweden/Twist_DNA_Hematology) is a Snakemake pipeline used for analyzing hybrid capture short-read sequencing data from the [Genomic Medicine Sweden](https://genomicmedicine.se/en/)  (GMS) myeloid gene panels. It uses the [Hydra-Genetics](https://github.com/hydra-genetics) framework.
+
+![rule graph](images/rulegraph.png){: style="height:90%;width:90%"} 

docs/overview.md

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+# Overview of the pipeline
+Here is a brief overview of the entire tumor pipeline. For details see subsections and the [hydra-genetics](https://github.com/hydra-genetics/hydra-genetics) documentation.
+
+## Prealignment and Alignment
+- Input files: fastq
+- Trimming: fastp_pe
+- Alignment: bwa mem
+
+## SNV_indels
+Serveral variant callers are used and then normalized and decomponated with vt, then merged with bcbios ensemble into one vcf. That vcf is then annotated using vep.
+
+SNV callers: 
+- GATK mutect2
+- Vardict
+- Freebayes
+
+
+## CNV_SV
+
+## QC
+The following qc tools are used and then merged into a single report using MultiQC.
+

docs/prealignment.md

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+# Prealignment
+
+I like this https://twist-solid.readthedocs.io/en/stable/dna_prealignment/

docs/qc.md

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+# QC
+hello

docs/reference_overview.md

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+# Reference pipeline
+Pipeline used to produce reference files such as CNV pools of normals

docs/reference_setup.md

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+# Reference pipeline set-up
+
+Set upo and running the reference pipeline instructions

docs/results_file.md

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+# Results files
+The following files are produced by the pipeline..

docs/snv_indels.md

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+# SNV indels
+rulegraph
+
+annotation and filtering here as well

mkdocs.yaml

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 site_name: Poppy
 nav:
-  - Introduction: intro.md
-  - Software: software.md
+  - Overview:
+    - Introduction: intro.md
+    - Overview: overview.md
+    - Results files: results_file.md
+  - Pipeline:
+    - Prealignment: prealignment.md 
+    - Alignment: alignment.md
+    - SNV_indels: snv_indels.md
+    - CNV_SV: cnv_sv.md
+    - QC: qc.md
+  - Pipeline specific rules:
+    - Software: software.md
+  - Reference Pipeline:
+    - Overview: reference_overview.md
+    - Set up and running: reference_setup.md
 
 theme: readthedocs
 extra_css: [extra.css]