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Merge pull request #169 from hydra-genetics/develop
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chore: dev to master
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padraicc authored Mar 28, 2024
2 parents 6523a5a + c55a89e commit 475482d
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33 changes: 33 additions & 0 deletions .github/workflows/test-build-mkdocs.yaml
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name: build mkdocs

on:
push:
branches:
- develop
- master
pull_request:
branches:
- develop
- master
workflow_dispatch:

jobs:
build-mkdocs:
name: build mkdocs
runs-on: ubuntu-22.04
steps:
- uses: actions/checkout@v3
- name: Set up Python 3.8
uses: actions/setup-python@v3
with:
python-version: 3.8
- name: Install requirements.txt
run: |
pip install -r requirements.txt
- name: Install requirements.test.txt
run: |
pip install -r requirements.test.txt
pip install -r docs/requirements.txt
- name: build mkdocs
run: |
mkdocs build
20 changes: 20 additions & 0 deletions .readthedocs.yaml
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# .readthedocs.yaml
# Read the Docs configuration file
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details

# Required
version: 2

# Set the version of Python and other tools you might need
build:
os: ubuntu-22.04
tools:
python: "3.11"

mkdocs:
configuration: mkdocs.yml

# Optionally declare the Python requirements required to build your docs
python:
install:
- requirements: docs/requirements.txt
4 changes: 2 additions & 2 deletions .tests/compatibility/config.yaml
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Expand Up @@ -102,8 +102,8 @@ manta_run_workflow_tn:
manta_run_workflow_n:
container: "docker://hydragenetics/manta:1.6.0"

pindel_update_vcf_sequence_dictionary:
container: "docker://hydragenetics/picard:2.25.0"
pindel_update_vcf:
container: "docker://hydragenetics/picard:2.25.4"

pindel_call:
include_bed: "reference/twist_DNA_solid.chr1.annotated.bed"
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15 changes: 10 additions & 5 deletions .tests/integration/config.yaml
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Expand Up @@ -30,20 +30,22 @@ cnvkit_scatter:

cnvkit_vcf:
container: "docker://hydragenetics/cnvkit:0.9.9"
hom_del_limit: 0.5

cnvkit_seg:
container: "docker://hydragenetics/cnvkit:0.9.9"

cnvpytor_readdepth:
container: "docker://hydragenetics/cnvpytor:1.2.1"
container: "docker://hydragenetics/cnvpytor:1.3.1"
length_list: "10000"

cnvpytor_filter:
container: "docker://hydragenetics/cnvpytor:1.2.1"
container: "docker://hydragenetics/cnvpytor:1.3.1"
calling_model: "rd_mean_shift"
dG_range: "100000 inf"
p_range: "0 0.01"
pN_range: "0 0.5"
Q0_range: "0 0.05"
Q0_range: "0 0.5"
view: "10000"

exomedepth_call:
Expand Down Expand Up @@ -94,8 +96,8 @@ manta_run_workflow_tn:
manta_run_workflow_n:
container: "docker://hydragenetics/manta:1.6.0"

pindel_update_vcf_sequence_dictionary:
container: "docker://hydragenetics/picard:2.25.0"
pindel_update_vcf:
container: "docker://hydragenetics/picard:2.25.4"

pindel_call:
include_bed: "reference/twist_DNA_solid.chr1.annotated.bed"
Expand Down Expand Up @@ -131,13 +133,16 @@ svdb_merge:
cnv_caller:
- cnvkit
- gatk
priority: "cnvkit,gatk"
- name: pathology
cnv_caller:
- cnvkit
- gatk
priority: "cnvkit,gatk"
- name: no_tc
cnv_caller:
- pindel
priority: "pindel"
container: "docker://hydragenetics/svdb:2.6.0"

svdb_query:
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Original file line number Diff line number Diff line change
Expand Up @@ -226,7 +226,7 @@
##INFO=<ID=PanelMedian,Number=1,Type=Float,Description="Background median MAF in panel">
##INFO=<ID=PositionNrSD,Number=1,Type=Float,Description="Number of Standard Deviations from background panel median">
##INFO=<ID=AA,Number=1,Type=String,Description="Amino acid change">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT VAL-01
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HD832.HES45_T
chr1 934487 . C T . PASS PositionNrSD=1000;PanelMedian=0;Artifact=0|0|0|0;AF=0.34;AS_FilterStatus=SITE;AS_SB_TABLE=594,514|358,237;CALLERS=mutect2,vardict,varscan,freebayes;DP=1740;ECNT=2;GERMQ=93;MBQ=32,20;MFRL=236,241;MMQ=60,60;MPOS=34;POPAF=7.3;ROQ=93;TLOD=1209.3;CSQ=T|synonymous_variant|LOW|HES4|57801|Transcript|NM_001142467.1|protein_coding|3/3||NM_001142467.1:c.696G>A|NP_001135939.1:p.Arg232%3D|895|696|232|R|agG/agA|rs777633362||-1||SNV|EntrezGene||YES||||NP_001135939.1|||||C|C|OK||||||||||||0.000221|0|0|0|0|0|0.0003425|0|0|0.0003425|gnomAD_NFE|||||||| GT:AD:AF:DP:F1R2:F2R1:SB_mutect2 0/1:1108,595:0.34:1703:512,237:552,214:594,514,358,237
chr1 935222 . C A . Artifact PositionNrSD=30.29;PanelMedian=0.0015;Artifact=21|20|20|21;AF=0.487;AS_FilterStatus=SITE;AS_SB_TABLE=420,516|392,518;CALLERS=mutect2,vardict,varscan,freebayes;DP=1883;ECNT=1;GERMQ=24;MBQ=32,20;MFRL=230,235;MMQ=60,60;MPOS=33;POPAF=7.3;ROQ=93;TLOD=1953.14;CSQ=A|missense_variant|MODERATE|HES4|57801|Transcript|NM_001142467.1|protein_coding|1/3||NM_001142467.1:c.132G>T|NP_001135939.1:p.Arg44Ser|331|132|44|R/S|agG/agT|rs2298214||-1||SNV|EntrezGene||YES||||NP_001135939.1|||||C|C|OK||tolerated_low_confidence(0.72)|benign(0)|||0.4938|0.0356|0.6268|0.7718|0.5895|0.6339|0.6136|0.1208|0.7139|0.6344|0.786|0.5555|0.595|0.5882|0.6625|0.786|gnomAD_EAS|||||||| GT:AD:AF:DP:F1R2:F2R1:SB_mutect2 0/1:936,910:0.487:1846:429,320:464,353:420,516,392,518
chr1 935339 . C T . PASS PositionNrSD=38.31;PanelMedian=0.0004;Artifact=0|0|0|0;AF=0.084;AS_FilterStatus=SITE;AS_SB_TABLE=537,764|48,79;CALLERS=mutect2,vardict,varscan;DP=1495;ECNT=1;GERMQ=93;MBQ=36,21;MFRL=238,230;MMQ=60,60;MPOS=39;POPAF=7.3;ROQ=93;TLOD=233.15;CSQ=T|synonymous_variant|LOW|HES4|57801|Transcript|NM_001142467.1|protein_coding|1/3||NM_001142467.1:c.15G>A|NP_001135939.1:p.Thr5%3D|214|15|5|T|acG/acA|||-1||SNV|EntrezGene||YES||||NP_001135939.1|||||C|C|OK|||||||||||||||||||||||||||||| GT:AD:AF:DP:F1R2:F2R1:SB_mutect2 0/1:1301,127:0.084:1428:594,60:671,52:537,764,48,79
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4 changes: 4 additions & 0 deletions README.md
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@@ -1,3 +1,7 @@
<p align="center">
<a href="https://hydra-genetics-cnv-sv.readthedocs.io">https://hydra-genetics-cnv-sv.readthedocs.io</a>
</p>

# <img src="images/hydragenetics.png" width=40 /> hydra-genetics/cnv_sv

Snakemake module containing steps to call copy number variants and structural variants
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8 changes: 6 additions & 2 deletions config/config.yaml
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Expand Up @@ -11,12 +11,16 @@ automap:
build: "hg38"
extra: "--DP 10 --minsize 3 --chrX"

cnvkit_export_seg:
extra: "--enumerate-chroms"

cnvpytor_readdepth:
container: "docker://hydragenetics/cnvpytor:1.2.1"
length_list: ""

cnvpytor_filter:
container: "docker://hydragenetics/cnvpytor:1.2.1"
calling_model: "rd_mean_shift"
dG_range: ""
p_range: ""
pN_range: ""
Expand All @@ -41,8 +45,8 @@ manta_config_n:
manta_run_workflow_n:
container: "docker://hydragenetics/manta:1.6.0"

pindel_update_vcf_sequence_dictionary:
container: "docker://hydragenetics/picard:2.25.0"
pindel_update_vcf:
container: "docker://hydragenetics/picard:2.25.4"

smn_caller:
container: "docker://hydragenetics/smncopynumbercaller:1.1.2"
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50 changes: 50 additions & 0 deletions docs/extra.css
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.wy-nav-content {
max-width: 1600px !important;
}
h1,h2 {
margin-top: 50px;
margin-bottom: 10px !important;
}
h3 {
font-size: 18px;
margin-top: 30px;
margin-bottom: 10px !important;
}
h4 {
font-size: 17px;
font-style: italic;
margin-top: 30px;
margin-bottom: 10px !important;

}
h5 {
font-size: 16px;
font-style: italic;
margin-top: 30px;
margin-bottom: 10px !important;

}
p {
margin-top: 5px !important;
}
* {
margin-bottom: 0px !important;
}

table td {
min-width: 10px;
max-width: 600px;
}
table td:last-child {
width: 100%;
}

hr {
margin-top: 50px;
border: 1px solid black;
}

.twemoji {
width: 20px;
color: black;
}
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