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Commit a172279a authored by van den Berg's avatar van den Berg
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Add github link to readme, and remove graph 

Since external users cannot submit issues or pull requests without an
account for the LUMC gitlab instance, we should refer them to the public
github instance of HAMLET.

The pipeline graph doesn't add a lot of information, and it doesn't
render on github, so it was removed.
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README.md
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# Hamlet
Hamlet is a pipeline for analysis of human acute myeloid leukemia RNA-seq samples. It is based on the
[Snakemake workflow management system](https://snakemake.readthedocs.io/en/stable/). Four distinct analysis modules
comprise Hamlet:
Hamlet is a pipeline for analysis of human acute myeloid leukemia RNA-seq samples. Please use the
[public github repository](https://github.com/LUMC/HAMLET) to open issues or pull requests.
Four distinct analysis modules comprise Hamlet, which can be run independently:
1. `snv-indels`, for small variant detection
2. `fusion`, for fusion gene detection
......@@ -25,191 +27,6 @@ environment is also defined by an `environment.yml` file.
In addition to the raw output files, Hamlet also generates a PDF report containing an overview of the essential results
and a zipped file containing this report and the essential result files.
The following diagram shows an overview of the Snakemake rules that are executed by Hamlet:
```plantuml
digraph snakemake_dag {
graph[bgcolor=white, margin=0];
node[shape=box, style=rounded, fontname=sans, fontsize=10, penwidth=2];
edge[penwidth=2, color=grey];
0[label = "all", color = "0.38 0.6 0.85", style="rounded"];
1[label = "merge_fastqs_r2", color = "0.01 0.6 0.85", style="rounded"];
2[label = "merge_fastqs_r1", color = "0.11 0.6 0.85", style="rounded"];
3[label = "create_summary", color = "0.28 0.6 0.85", style="rounded"];
4[label = "generate_report", color = "0.14 0.6 0.85", style="rounded"];
5[label = "package_results", color = "0.57 0.6 0.85", style="rounded"];
6[label = "reorder_aln_header", color = "0.36 0.6 0.85", style="rounded"];
7[label = "annotate_vars", color = "0.60 0.6 0.85", style="rounded"];
8[label = "table_vars_all", color = "0.29 0.6 0.85", style="rounded"];
9[label = "table_vars_hi", color = "0.45 0.6 0.85", style="rounded"];
10[label = "plot_vars", color = "0.55 0.6 0.85", style="rounded"];
11[label = "star_fusion_cp", color = "0.46 0.6 0.85", style="rounded"];
12[label = "plot_cp\next: star-fusion", color = "0.16 0.6 0.85", style="rounded"];
13[label = "combine_plots", color = "0.33 0.6 0.85", style="rounded"];
14[label = "fusioncatcher_cp", color = "0.06 0.6 0.85", style="rounded"];
15[label = "plot_cp\next: fusioncatcher", color = "0.16 0.6 0.85", style="rounded"];
16[label = "intersect_fusions", color = "0.30 0.6 0.85", style="rounded"];
17[label = "plot_cp\next: sf-isect", color = "0.16 0.6 0.85", style="rounded"];
18[label = "subset_sf", color = "0.63 0.6 0.85", style="rounded"];
19[label = "count_fragments", color = "0.31 0.6 0.85", style="rounded"];
20[label = "count_bases_gene", color = "0.07 0.6 0.85", style="rounded"];
21[label = "count_bases_exon", color = "0.23 0.6 0.85", style="rounded"];
22[label = "calc_exon_ratios", color = "0.47 0.6 0.85", style="rounded"];
23[label = "sample_stats", color = "0.18 0.6 0.85", style="rounded"];
24[label = "aln_stats", color = "0.17 0.6 0.85", style="rounded"];
25[label = "rna_stats", color = "0.21 0.6 0.85", style="rounded"];
26[label = "insert_stats", color = "0.39 0.6 0.85", style="rounded"];
27[label = "exon_cov", color = "0.37 0.6 0.85", style="rounded"];
28[label = "align_flt3", color = "0.48 0.6 0.85", style="rounded"];
29[label = "detect_flt3", color = "0.56 0.6 0.85", style="rounded"];
30[label = "plot_itd_flt3", color = "0.03 0.6 0.85", style="rounded"];
31[label = "align_kmt2a", color = "0.54 0.6 0.85", style="rounded"];
32[label = "detect_kmt2a", color = "0.44 0.6 0.85", style="rounded"];
33[label = "plot_itd_kmt2a", color = "0.34 0.6 0.85", style="rounded"];
34[label = "cutadapt\nread_group: rg_1\nsample: Sample1", color = "0.62 0.6 0.85", style="rounded"];
35[label = "sort_bamfile", color = "0.22 0.6 0.85", style="rounded"];
36[label = "call_vars", color = "0.52 0.6 0.85", style="rounded"];
37[label = "extract_vars", color = "0.25 0.6 0.85", style="rounded"];
38[label = "star_fusion", color = "0.10 0.6 0.85", style="rounded"];
39[label = "plot_sf", color = "0.64 0.6 0.85", style="rounded"];
40[label = "fusioncatcher", color = "0.43 0.6 0.85", style="rounded"];
41[label = "plot_fc", color = "0.02 0.6 0.85", style="rounded"];
42[label = "plot_isect", color = "0.13 0.6 0.85", style="rounded"];
43[label = "idsort_aln", color = "0.05 0.6 0.85", style="rounded"];
44[label = "count_raw_bases", color = "0.61 0.6 0.85", style="rounded"];
45[label = "rg_stats", color = "0.08 0.6 0.85", style="rounded"];
46[label = "exon_cov_ref", color = "0.24 0.6 0.85", style="rounded"];
47[label = "genome_txt", color = "0.59 0.6 0.85", style="rounded"];
48[label = "align_vars", color = "0.41 0.6 0.85", style="rounded"];
49[label = "merge_fastqs_raw_r1\nsample: Sample1", color = "0.66 0.6 0.85", style="rounded"];
50[label = "merge_fastqs_raw_r2\nsample: Sample1", color = "0.00 0.6 0.85", style="rounded"];
51[label = "fastqc_raw\npair: R1\nread_group: rg_1\nsample: Sample1", color = "0.49 0.6 0.85", style="rounded"];
52[label = "fastqc_raw\npair: R2\nread_group: rg_1\nsample: Sample1", color = "0.49 0.6 0.85", style="rounded"];
53[label = "fastqc_processed\npair: R1", color = "0.09 0.6 0.85", style="rounded"];
54[label = "fastqc_processed\npair: R2", color = "0.09 0.6 0.85", style="rounded"];
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}
```
# Installation
The dependencies required for running the pipeline are listed in the provided `environment.yml` file. To use it, first
......@@ -227,12 +44,12 @@ conda activate HAMLET
Additionally, `singularity` version 3 or greater should be installed on the system.
# Data files
## Data files
HAMLET requires around 100GB of reference files to run. You can download the data files [here](https://barmsijs.lumc.nl/HAMLET/deps.tar.gz),
the md5sum for the archive is `5541718e8bc17bcd00ec90ff23ebcfae`.
Please contact the author or open an issue if the link is not working.
# Testing
## Testing
The following commands can be used to test different aspects of HAMLET. First, activate the HAMLET conda environment
which was created in the previous step.
```bash
......
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