nf-core/sarek is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse, it can work on any species with a reference genome. Sarek can also handle tumour / normal pairs and could include additional relapses. The pipeline is...
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
方法:JHUBiobank从人类NF1肿瘤样本中生成的原始全外显子组测序(WES) 和RNA测序(RNA‑seq) 数据在NF数据门户上共享。NF‑OSI使用来自nf‑core社区(nf‑core/sarekv2.7和nf‑core/rnaseqv3.7)的Nextflow工作流程将数据与最新的人类参考基因组(GRCh38)...
log.warn "[nf-core/sarek] in ${params.input} directory, all fastqs are assuming to be from the same sample, which is assumed to be a germline one" inputSample = extractFastqFromDir(params.input) (inputSample, fastqTMP) = inputSample.into(2) ...
Kulbe H, Hagemann T, Szlosarek PW, Balkwill FR, Wilson JL: The inflammatory cytokine tumor necrosis factor-alpha regulates chemokine receptor expression on ovarian cancer cells. Cancer Res 2005, 65: 10355–10362. 10.1158/0008-5472.CAN-05-0957 Article CAS PubMed Google Scholar Coussens LM, We...
if ('mutect2' in tools && !(params.pon)) log.warn "[nf-core/sarek] Mutect2 was requested, but as no panel of normals were given, results will not be optimal" if (params.sentieon) log.warn "[nf-core/sarek] Sentieon will be used, only works if Sentieon is available where nf-...
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....
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing - bump module version · nf-core/sarek@a172fbe
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...