Commit 00bca9c4 authored by van den Berg's avatar van den Berg
Browse files

Add tests data of targeted RNA-Seq

HAMLET has been developed using whole RNA sequencing. When it is used to
analyse targeted RNA-Seq data, various tools find no results, which can
lead to crashes in various parts of the pipeline.

The targeted RNA-Seq files were added were kindly provided by the
Radboudumc
parents 04e3d2c7 cd589779
Pipeline #6702 failed with stages
......@@ -13,9 +13,9 @@ include: "includes/itd/Snakefile"
localrules: create_summary, generate_report, package_results
containers = {
"fsnviz": "docker://quay.io/biocontainers/fsnviz:0.3.0--py_3",
"hamlet-scripts": "docker://quay.io/redmar_van_den_berg/hamlet-scripts:0.3",
"debian": "docker://debian:buster-slim",
"fsnviz": "docker://quay.io/biocontainers/fsnviz:0.3.0--pyhdfd78af_5",
"hamlet-scripts": "docker://quay.io/redmar_van_den_berg/hamlet-scripts:0.3",
"zip": "docker://quay.io/redmar_van_den_berg/zip:3.0"
}
......
......@@ -8,8 +8,8 @@ localrules: combine_plots, fusioncatcher_cp, intersect_fusions, plot_cp, plot_is
containers = {
"debian": "docker://debian:buster-slim",
"fsnviz": "docker://quay.io/biocontainers/fsnviz:0.3.0--py_3",
"fuma": "docker://quay.io/biocontainers/fuma:3.0.5--py27h24bf2e0_1",
"fsnviz": "docker://quay.io/biocontainers/fsnviz:0.3.0--py_4",
"fuma": "docker://quay.io/biocontainers/fuma:4.0.0--pyhb7b1952_0",
"fusioncatcher": "docker://quay.io/biocontainers/fusioncatcher:1.20--2",
"star-fusion": "docker://quay.io/biocontainers/star-fusion:1.6.0--1",
"hamlet-scripts": "docker://quay.io/redmar_van_den_berg/hamlet-scripts:0.2"
......
{
"settings": {
"flt3_bwa_index": "/exports/sasc-testing/fixtures/HAMLET/deps/data/bwa-flt3-index/flt3-001.fa",
"kmt2a_fasta": "/exports/sasc-testing/fixtures/HAMLET/deps/data/bwa-kmt2a-index/kmt2a-213.fa",
"genome_star_fusion_lib": "/exports/sasc-testing/fixtures/HAMLET/deps/data/GRCh38_gencode_v31_CTAT_lib_Aug152019.plug-n-play/ctat_genome_lib_build_dir",
"flt3_start": 1787,
"relative_gene_name": "HMBS",
"expression_gtf": "/exports/sasc-testing/fixtures/HAMLET/deps/data/ucsc_gencode.gtf",
"expression_bed": "/exports/sasc-testing/fixtures/HAMLET/deps/data/ucsc_gencode.flat.bed",
"vcf_gonl": "/exports/sasc-testing/fixtures/HAMLET/deps/data/gonl.grch38.sorted.filtered.snps_indels.r5.vcf.gz",
"kmt2a_start": 406,
"annotation_refflat": "/exports/sasc-testing/fixtures/HAMLET/deps/data/ucsc_gencode.refFlat",
"kmt2a_end": 4769,
"kmt2a_name": "KMT2A-213",
"bed_variant_hotspots": "/exports/sasc-testing/fixtures/HAMLET/deps/data/hotspots_genome.bed",
"exon_names": [
"MECOM:169146722-169147734"
],
"exon_min_ratio": 0.1,
"ref_annot_goi": "/exports/sasc-testing/fixtures/HAMLET/deps/data/Homo_sapiens.GRCh38.77.goi-extended.gtf",
"flt3_end": 2024,
"genome_fasta": "/exports/sasc-testing/fixtures/HAMLET/deps/data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa",
"fasta_vep": "/exports/sasc-testing/fixtures/HAMLET/deps/vep/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz",
"flt3_name": "FLT3-001",
"cache_vep": "/exports/sasc-testing/fixtures/HAMLET/deps/vep/ensembl-vep/cache_dir/",
"ref_id_mapping": "/exports/sasc-testing/fixtures/HAMLET/deps/data/id_mappings.tsv",
"kmt2a_bwa_index": "/exports/sasc-testing/fixtures/HAMLET/deps/data/bwa-kmt2a-index/kmt2a-213.fa",
"flt3_fasta": "/exports/sasc-testing/fixtures/HAMLET/deps/data/bwa-flt3-index/flt3-001.fa",
"rrna_refflat": "/exports/sasc-testing/fixtures/HAMLET/deps/data/ucsc_rrna.refFlat",
"ref_amplicons": "/exports/sasc-testing/fixtures/HAMLET/deps/data/amplicons.bed",
"genome_gmap_index": "/exports/sasc-testing/fixtures/HAMLET/deps/data/gmap-genome-index/GCA_000001405.15_GRCh38_no_alt_analysis_set",
"run_name": "hamlet-hiseq2500",
"vcf_1kg": "/exports/sasc-testing/fixtures/HAMLET/deps/data/1KG.phase3.GRCh38.with_chr.vcf.gz",
"transcripts_bed": "/exports/sasc-testing/fixtures/HAMLET/deps/data/transcripts.bed",
"fusioncatcher_data": "/exports/sasc-testing/fixtures/HAMLET/deps/fusioncatcher/human_v98/",
},
"samples": {
"NOMO1-RNAseq-1-16714": {
"read_groups": {
"rg_1": {
"R1": "test/data/fastq/NOMO1-RNAseq-1-16714_R1.fastq.gz",
"R2": "test/data/fastq/NOMO1-RNAseq-1-16714_R2.fastq.gz"
}
}
}
}
}
......@@ -64,3 +64,13 @@
- path: "Frankenstein/hamlet_results.Frankenstein.zip"
- path: "Frankenstein/Frankenstein.summary.json"
- path: "Frankenstein/hamlet_report.Frankenstein.pdf"
- name: test-hamlet-NOMO
tags:
- integration
command: >
snakemake -rp
--snakefile Snakefile
--configfile test/data/config/test-NOMO.config
--verbose
--use-singularity
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