Commit 8a1acd6b authored by van den Berg's avatar van den Berg
Browse files

Merge branch 'issue-13' into devel

parents a172279a 8c133f10
Pipeline #3992 failed with stages
in 31 minutes and 48 seconds
......@@ -8,7 +8,7 @@ localrules: table_vars_all, table_vars_hi
containers = {
"bedtools-2.27-grep-2.14-gawk-5.0-click-7-python-3.7": "docker://quay.io/biocontainers/mulled-v2-a4b89e0b16b1d7db92e5a069e5c40405b3b53aab:98c4ac2f0e27869be58f6a4d8bb7ae3bc02a3a70-0",
"debian": "docker://debian:buster-slim",
"gsnap": "docker://quay.io/biocontainers/gmap:2014.12.23--pl5.22.0_4",
"gsnap": "docker://quay.io/biocontainers/gmap:2020.06.30--pl526h2f06484_0",
"hamlet-scripts": "docker://lumc/hamlet-scripts:0.2",
"picard": "docker://quay.io/biocontainers/picard:2.20.5--0",
"python3": "docker://python:3.7.4-slim-stretch",
......
{
"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": {
"7075-04-001-006": {
"read_groups": {
"rg_1": {
"R1": "test/data/fastq/7075-04-001-006-TET2_R1.fastq.gz",
"R2": "test/data/fastq/7075-04-001-006-TET2_R2.fastq.gz",
}
}
}
}
}
......@@ -161,3 +161,18 @@
- path: "7075-04-001-002/snv-indels/7075-04-001-002.raw.vcf.gz"
contains:
- "chr21\t34792223\t.\tA\tACGTCGCTCTGGTT"
- name: test-TET2-false-positive-mutation
tags:
- integration
command: >
snakemake -rp
--snakefile includes/snv-indels/Snakefile
--configfile test/data/config/test-TET2-mutation.config
--verbose
--use-singularity
"7075-04-001-006/snv-indels/7075-04-001-006.raw.vcf.gz"
files:
- path: "7075-04-001-006/snv-indels/7075-04-001-006.raw.vcf.gz"
must_not_contain:
- "chr4\t105243576\t.\tC\tA"
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