/
rd_dna_initiation_map.yaml
97 lines (97 loc) · 2.34 KB
/
rd_dna_initiation_map.yaml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
---
CHAIN_ALL:
- CHAIN_MAIN:
- gzip_fastq
# Parallel chain (branch)
- CHAIN_SPLITFASTQ:
- split_fastq_file
- CHAIN_FASTQ:
- fastqc_ar
- CHAIN_MAIN:
- bwa_mem
- bwa_mem2
- samtools_merge
- markduplicates
- gatk_baserecalibration
# Parallel chains (branches), which inherit from MAIN in initiation
- CHAIN_CHSEX:
- chanjo_sexcheck
- CHAIN_STSUBSMT:
- samtools_subsample_mt
- CHAIN_TCOV:
- tiddit_coverage
- chromograph_cov
- CHAIN_SBCOV:
- sambamba_depth
- CHAIN_SMN:
- smncopynumbercaller
- CHAIN_CYRIUS:
- star_caller
- CHAIN_TEL:
- telomerecat_ar
- CHAIN_PTMME:
- picardtools_collectmultiplemetrics
- CHAIN_PTCHSM:
- picardtools_collecthsmetrics
- CHAIN_SV:
# PARALLEL chains, which inherit from MAIN in initiation, but are merged back to CHAIN_SV after execution
- PARALLEL:
- cnvnator_ar
- expansionhunter
- manta
- tiddit
- DELLY_CALL:
- delly_call
- delly_reformat
- sv_combinevariantcallsets
- sv_annotate
- sv_varianteffectpredictor
- sv_vcfparser
- sv_rankvariant
- sv_reformat
- vcf2cytosure_ar
- CHAIN_MAIN:
# PARALLEL chains, which inherit from MAIN in initiation, but are merged back to CHAIN_MAIN after execution
- PARALLEL:
- CHAIN_DEEPVAR:
- deepvariant
- glnexus_merge
- GATK_HAPLOTYPECALLER:
- gatk_haplotypecaller
- gatk_genotypegvcfs
- gatk_gathervcfs
- gatk_variantrecalibration
- gatk_combinevariantcallsets
# Parallel chains (branches), which inherit from MAIN in initiation
- CHAIN_PEDDY:
- peddy_ar
- CHAIN_PLINK:
- plink
- CHAIN_RTEVAL:
- rtg_vcfeval
- CHAIN_GATKEVALALL:
- gatk_variantevalall
- CHAIN_MAIN:
- prepareforvariantannotationblock
- rhocall_ar
- vt_ar
- variant_annotation
- CHAIN_RHOCALL_VIZ:
- rhocall_viz
- CHAIN_UPD:
- upd_ar
- chromograph_upd
- frequency_filter
- cadd_ar
- varianteffectpredictor
- vcfparser_ar
- rankvariant
- endvariantannotationblock
- CHAIN_GATKEVALEXO:
- gatk_variantevalexome
- qccollect_ar
- version_collect_ar
- multiqc_ar
- varg_ar
- analysisrunstatus
- sacct