If you usenf-core/sarekfor your analysis, please cite theSarekarticle as follows: You can cite the sarek zenodo record for a specific version using the followingdoi: 10.5281/zenodo.3476425 An extensive list of references for the tools used by the pipeline can be found in theCITATIONS.mdfile...
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing - sarek/tests at master · nf-core/sarek
Sarek can also handle tumour / normal pairs and could include additional relapses. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly...
https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz Command used and terminal output Command:nextflow run nf-core/sarek -r dev -profile ...
files_exist - File found: assets/nf-core-sarek_logo_light.png files_exist - File found: conf/test.config files_exist - File found: conf/test_full.config files_exist - File found: docs/images/nf-core-sarek_logo_light.png files_exist - File found: docs/images/nf-core-sarek_logo_dark....
nf-core / sarek Public Notifications Fork 417 Star 411 Commit Permalink bump module version Browse files master (#1613) 3.5.0 FriederikeHanssen committed Dec 10, 2024 1 parent 532902a commit a172fbe Showing 6 changed files with 260 additions and 294 deletions. Whitespace ...
run:docker build --no-cache . -t nfcore/sarek:dev run:docker build --no-cache . -t nfcore/sarek:2.7 -name:Pull docker image if:${{ !env.MATCHED_FILES }} run:| docker pull nfcore/sarek:dev docker tag nfcore/sarek:dev nfcore/sarek:dev ...
nf-core-sarek_logo_light.png samplesheet.csv schema_input.json sendmail_template.txt slackreport.json conf docs lib modules subworkflows tests workflows .editorconfig .gitattributes .gitignore .gitpod.yml .nf-core.yml .pre-commit-config.yaml .prettierignore .prettierrc.yml CHANGELOG.md CITATIONS....
files_exist - File found: assets/nf-core-sarek_logo_light.png files_exist - File found: conf/test.config files_exist - File found: conf/test_full.config files_exist - File found: docs/images/nf-core-sarek_logo_light.png files_exist - File found: docs/images/nf-core-sarek_logo_dark....
Open Description of the bug q Command used and terminal output nextflow run nf-core/sarek -r 3.4.2 -latest -profile docker --input data/markduplicates_no_table_local.csv --outdir ./test_single_sample --igenomes_base ../data/references --step variant_calling --tools cnvkit,strelka,deepvari...