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Merge pull request #379 from genomic-medicine-sweden/develop
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chore: dev to master
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jonca79 authored Dec 1, 2023
2 parents c2ba7b1 + a845431 commit 2b8d6de
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Showing 73 changed files with 10,780 additions and 762 deletions.
10 changes: 10 additions & 0 deletions .gitignore
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Expand Up @@ -12,4 +12,14 @@ venv

docs/changelog.md
docs/license.md
docs/includes/config.yaml
docs/includes/resources.yaml

site/

*.sif
ref_dat

*.gz
*.sif
ref_data
27 changes: 22 additions & 5 deletions .tests/integration/config/config.yaml
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@@ -1,4 +1,5 @@
output: "../../config/output_files.yaml"
singularity_schema: "../../config/singularity.schema.yaml"

annotate_cnv:
cnv_amp_genes: "reference/cnv_amp_genes.bed"
Expand Down Expand Up @@ -49,7 +50,7 @@ cnvkit_batch_hrd:
normal_reference_hrd: "DATA/design.PoN.cnn"

cnv_html_report:
template_dir: "../../config/cnv_report_template"
template_dir: "../../config/reports/cnv_report_template"


exon_skipping:
Expand Down Expand Up @@ -95,12 +96,28 @@ gene_fuse:

hotspot_annotation:
hotspots: "DATA/Hotspots_combined.csv"
chr_translation_file: "../../config/hotspot_report.chr.translation.hg19"
chr_translation_file: "../../config/reports/hotspot_report.chr.translation.hg19"

hotspot_info:
hotspot_mutations: "DATA/Hotspots_combined.csv"

hotspot_report:
hotspot_mutations: "DATA/Hotspots_combined.csv"
report_config: "../../config/config/hotspot_report.yaml"
chr_translation_file: "../../config/hotspot_report.chr.translation.hg19"
report_config: "../../config/reports/config/reports/hotspot_report.yaml"
chr_translation_file: "../../reports/config/reports/hotspot_report.chr.translation.hg19"
levels:
- [300, "ok", "yes"]
- [30, "low", "yes"]
- [0, "low", "not analyzable"]

manta_config_t:
container: "docker://hydragenetics/manta:1.6.0"

manta_run_workflow_t:
container: "docker://hydragenetics/manta:1.6.0"

mosdepth_bed:
container: "docker://hydragenetics/mosdepth:0.3.2"

msisensor_pro:
PoN: "DATA/msisensor_pro_reference_26_normal.list_baseline"
Expand Down Expand Up @@ -160,4 +177,4 @@ star_fusion:

vep:
vep_cache: "DATA/VEP/homo_sapiens/"


3 changes: 3 additions & 0 deletions .tests/integration/config/config_reference.yaml
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@@ -1 +1,4 @@
output: "../../config/output_reference_files.yaml"

reference:
mappability: "DATA/access-5k-mappable.bed"
32 changes: 16 additions & 16 deletions .tests/jenkins/Jenkinsfile
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Expand Up @@ -11,7 +11,7 @@ pipeline {
sh 'printenv'
}
}
stage('VAL2022') {
stage('develop') {
when {
anyOf {
expression { isPullRequest == false && env.BRANCH_NAME == 'develop' }
Expand All @@ -23,16 +23,16 @@ pipeline {
virtualenv venv -p python3.8
source venv/bin/activate
pip install -r requirements.txt
mkdir -p VAL2022/slurm_out
cp -r config VAL2022/
cp .tests/jenkins/units_VAL2022.tsv VAL2022/units.tsv
cp .tests/jenkins/samples_VAL2022.tsv VAL2022/samples.tsv
cp .tests/jenkins/resources.yaml VAL2022/config/resources.yaml
cp .tests/jenkins/test_input_VAL2022.tsv VAL2022/test_input.tsv
mkdir -p develop/slurm_out
cp -r config develop/
cp .tests/jenkins/units_develop.tsv develop/units.tsv
cp .tests/jenkins/samples_develop.tsv develop/samples.tsv
cp .tests/jenkins/resources.yaml develop/config/resources.yaml
cp .tests/jenkins/test_input_develop.tsv develop/test_input.tsv
module load singularity
module load slurm-drmaa
cd VAL2022
cd develop
snakemake -s ../workflow/Snakefile --profile ../.tests/jenkins/profile --configfile config/config.yaml -w 60 --notemp --keep-incomplete
git clone https://github.com/clinical-genomics-uppsala/validation_workflow.git
module load nextflow
Expand All @@ -41,7 +41,7 @@ pipeline {
}
}
}
stage('ALL') {
stage('main') {
when {
anyOf {
expression { isPullRequest == false && env.BRANCH_NAME == 'master' }
Expand All @@ -53,16 +53,16 @@ pipeline {
virtualenv venv -p python3.8
source venv/bin/activate
pip install -r requirements.txt
mkdir -p ALL/slurm_out
cp -r config ALL/
cp .tests/jenkins/units_all.tsv ALL/units.tsv
cp .tests/jenkins/samples_all.tsv ALL/samples.tsv
cp .tests/jenkins/resources.yaml ALL/config/resources.yaml
cp .tests/jenkins/test_input_all.tsv ALL/test_input.tsv
mkdir -p main/slurm_out
cp -r config main/
cp .tests/jenkins/units_main.tsv main/units.tsv
cp .tests/jenkins/samples_main.tsv main/samples.tsv
cp .tests/jenkins/resources.yaml main/config/resources.yaml
cp .tests/jenkins/test_input_main.tsv main/test_input.tsv
module load singularity
module load slurm-drmaa
cd ALL
cd main
snakemake -s ../workflow/Snakefile --profile ../.tests/jenkins/profile --configfile config/config.yaml -w 60 --notemp --keep-incomplete
git clone https://github.com/clinical-genomics-uppsala/validation_workflow.git
module load nextflow
Expand Down
2 changes: 1 addition & 1 deletion .tests/jenkins/profile/config.yaml
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Expand Up @@ -7,5 +7,5 @@ singularity-args: "-e --cleanenv -B /home/jenkins -B /projects -B /data -B /beeg
singularity-prefix: "/projects/wp1/nobackup/singularity_cache"
drmaa: " -A wp1 -N 1-1 -t {resources.time} -n {resources.threads} --mem={resources.mem_mb} --mem-per-cpu={resources.mem_per_cpu} --mem-per-cpu={resources.mem_per_cpu} --partition={resources.partition} -J {rule} -e slurm_out/{rule}_%j.err -o slurm_out/{rule}_%j.out"
drmaa-log-dir: "slurm_out"
configfile: config/config.yaml
configfiles: ["config/config.yaml", "config/config.data.hg19.yaml"]
default-resources: "tmpdir='/projects/wp1/temp'"
2 changes: 0 additions & 2 deletions .tests/jenkins/samples_VAL2022.tsv

This file was deleted.

3 changes: 3 additions & 0 deletions .tests/jenkins/samples_develop.tsv
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@@ -0,0 +1,3 @@
sample tumor_content
VAL2022-2-5M 0.25
SeraSeq-NTRK-FFPE-2-5M 1.0
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Expand Up @@ -3,3 +3,4 @@ HD827 0.5
HD832 0.5
NA12878 0.5
VAL2022 0.25
SeraSeq-NTRK-FFPE 1.0
36 changes: 0 additions & 36 deletions .tests/jenkins/test_input_VAL2022.tsv

This file was deleted.

43 changes: 43 additions & 0 deletions .tests/jenkins/test_input_develop.tsv
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@@ -0,0 +1,43 @@
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