CNV_pipeline
Visit source
Download RO-CrateStructuralVariants Workflow
Click and drag the diagram to pan, double click or use the controls to zoom.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| fastq1 | n/a | FASTQ 1 list of files |
|
| fastq2 | n/a | FASTQ 2 list of files |
|
| generate_bwa_indexes | n/a | enable generation of reference genome indexes |
|
| reference_fasta | n/a | reference genome |
|
| reference_fai | n/a | fai index for reference genome |
|
| reference_amb | n/a | amb index for reference genome |
|
| reference_ann | n/a | ann index for reference genome |
|
| reference_bwt | n/a | bwt index for reference genome |
|
| reference_pac | n/a | pac index reference genome |
|
| reference_sa | n/a | sa index reference genome |
|
| bed | n/a | capture kit |
|
| samples | n/a | TXT file mapping cases ID, samples ID and batch |
|
| threads_fastqc | n/a | number of threads for fastqc |
|
| threads_fastp | n/a | number of threads for fastp |
|
| threads_bwa_mem | n/a | number of threads for bwa-mem |
|
| threads_samtools | n/a | number of threads for samtools |
|
| threads_gridss | n/a | number of threads for GRIDSS |
|
| bwt_algorithm | n/a | BWT construction algorithm: bwtsw or is (Default: auto) |
|
| read_group | n/a | FASTA read group (used to fix BAM files) |
|
| min_mapping_quality | n/a | skip alignments with MAPQ smaller than this minimum |
|
| bits_set | n/a | skip output alignments with this bits set |
|
| manta_exome | n/a | provide appropriate settings for WES |
|
| manta_min_len | n/a | minimum CNV lenght for MANTA |
|
| manta_max_len | n/a | maximum CNV lenght for MANTA |
|
| manta_min_q | n/a | minimum CNV quality for MANTA |
|
| blacklist | n/a | BED file containing regions to ignore |
|
| gridss_min_len | n/a | minimum CNV lenght for GRIDSS |
|
| gridss_max_len | n/a | maximum CNV lenght for GRIDSS |
|
| gridss_min_q | n/a | minimum CNV quality for GRIDSS |
|
| exomeDepth_min_len | n/a | minimum CNV lenght for EXOME_DEPTH |
|
| exomeDepth_max_len | n/a | maximum CNV lenght for EXOME_DEPTH |
|
| exomeDepth_min_bf | n/a | minimum CNV Bayes factor for EXOME_DEPTH |
|
| chromosome | n/a | chromosome for targeted sequencing for CODEX |
|
| codex_min_len | n/a | minimum CNV lenght for CODEX |
|
| codex_max_len | n/a | maximum CNV lenght for CODEX |
|
| codex_min_lratio | n/a | minimum CNV lratio for CODEX |
|
| enable_manta | n/a | execute MANTA predictions |
|
| enable_gridss | n/a | execute GRIDSS predictions |
|
| enable_exomeDepth | n/a | execute EXOME_DEPTH predictions |
|
| enable_codex | n/a | execute CODEX predictions |
|
Steps
| ID | Name | Description |
|---|---|---|
| bwa_index | n/a | n/a |
| trimmed_fastq | n/a | n/a |
| bwa_mem | n/a | n/a |
| samtools_view_sam2bam | n/a | n/a |
| samtools_sort | n/a | n/a |
| samtools_merge | n/a | n/a |
| samtools_index | n/a | n/a |
| picard_markduplicates | n/a | n/a |
| bam_filtering | n/a | n/a |
| cnv_manta | n/a | n/a |
| cnv_gridss | n/a | n/a |
| cnv_exomedepth | n/a | n/a |
| cnv_codex | n/a | n/a |
| final_filtering | n/a | n/a |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| fastqc_raw_zip | n/a | n/a |
|
| fastqc_raw_html | n/a | n/a |
|
| html_report | n/a | n/a |
|
| json_report | n/a | n/a |
|
| fastqc_paired_zip | n/a | n/a |
|
| fastqc_paired_html | n/a | n/a |
|
| output_bam_filtering | n/a | n/a |
|
| output_manta | n/a | n/a |
|
| output_gridss | n/a | n/a |
|
| output_exomedepth | n/a | n/a |
|
| output_codex | n/a | n/a |
|
| output_all | n/a | n/a |
|
Version History
1.1.3 (latest) Created 11th Oct 2022 at 12:04 by Laura Rodriguez-Navas
deleted cnvChr channel
Frozen
1.1.393fbc4e
1.1.0 Created 9th Sep 2022 at 11:27 by Laura Rodriguez-Navas
minor changes in main.nf
Frozen
1.1.0
6f16906
1.0.9 Created 30th Jun 2022 at 14:07 by Laura Rodriguez-Navas
minor change in main of CWL workflow
Frozen
1.0.9
b62c7bf
1.0.8 Created 30th Jun 2022 at 13:00 by Laura Rodriguez-Navas
add support for input BED to exomeDepth (CWL)
Frozen
1.0.8
a478446
1.0.7 Created 1st Jun 2022 at 18:26 by Laura Rodriguez-Navas
add gunzip in bwa-index subworkflow
Frozen
1.0.7
94bcf49
1.0.6 Created 11th May 2022 at 15:27 by Laura Rodriguez-Navas
update r-base container
Frozen
1.0.6
32a040f
1.0.5 Created 10th May 2022 at 10:04 by Laura Rodriguez-Navas
added new steps to control optionality for reference fasta input
Frozen
1.0.5
a4a3547
1.0.4 Created 25th Apr 2022 at 08:30 by Laura Rodriguez-Navas
read group param as default
Frozen
1.0.4
9ac2d15
1.0.3 Created 23rd Mar 2022 at 14:19 by Laura Rodriguez-Navas
update algoType parameter on bwa index process (CWL), updating abstract too
Frozen
1.0.3
26ae491
1.0.2 Created 14th Mar 2022 at 15:00 by Laura Rodriguez-Navas
rename json and html reports of fastp CWL tool
Frozen
1.0.2
13e8e65
1.0.1 (earliest) Created 14th Mar 2022 at 12:07 by Laura Rodriguez-Navas
Merge branch 'master' into 'master'
Updated abstracts
See merge request lrodrig1/structuralvariants_poc!3
Frozen
1.0.1
27011e8
Creators and Submitter
Views: 7204 Downloads: 1705
Created: 14th Mar 2022 at 12:07
Last updated: 30th Jun 2022 at 13:00
AttributionsNone
Related items
Teams: GalaxyProject SARS-CoV-2, nf-core viralrecon, EOSC-Life - Demonstrator 7: Rare Diseases, iPC: individualizedPaediatricCure, EJPRD WP13 case-studies workflows, TransBioNet, OpenEBench, ELIXIR Proteomics
Organizations: Barcelona Supercomputing Center (BSC-CNS), ELIXIR
https://orcid.org/0000-0003-4929-1219
Computer Engineer in Barcelona Supercomputing Center (BSC)
A space managed by WorkflowHub administrators for teams that don't want/need to manage their own space.
Teams: IBISBA Workflows, NMR Workflow, UNLOCK, NanoGalaxy, Galaxy Climate, PNDB, IMBforge, COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource, LBI-RUD, Nick-test-team, usegalaxy-eu, Italy-Covid-data-Portal, UX trial team, Integrated and Urban Plant Pathology Laboratory, SARS-CoV-2 Data Hubs, lmjxteam2, virAnnot pipeline, Ay Lab, iPC: individualizedPaediatricCure, Harkany Lab, MOLGENIS, EJPRD WP13 case-studies workflows, Common Workflow Language (CWL) community, Testing, SeBiMER, IAA-CSIC, MAB - ATGC, Probabilistic graphical models, GenX, Snakemake-Workflows, ODA, IPK BIT, CO2MICS Lab, FAME, CHU Limoges - UF9481 Bioinformatique / CNR Herpesvirus, Quadram Institute Bioscience - Bioinformatics, HecatombDevelopment, Institute of Human Genetics, Testing RO Crates, Test Team, Applied Computational Biology at IEG/HMGU, INFRAFRONTIER workflows, OME, TransBioNet, OpenEBench, Bioinformatics and Biostatistics (BIO2 ) Core, VIB Bioinformatics Core, CRC Cohort, ICAN, MustafaVoh, Single Cell Unit, CO-Graph, emo-bon, TestEMBL-EBIOntology, CINECA, Toxicology community, Pitagora-Network, Workflows Australia, Medizinisches Proteom-Center, Medical Bioinformatics, AGRF BIO, EU-Openscreen, X-omics, ELIXIR Belgium, URGI, Size Inc, GA-VirReport Team, The Boucher Lab, Air Quality Prediction, pyiron, CAPSID, Edinburgh Genomics, Defragmentation TS, NBIS, Phytoplankton Analysis, Seq4AMR, Workflow registry test, Read2Map, SKM3, ParslRNA-Seq: an efficient and scalable RNAseq analysis workflow for studies of differentiated gene expression, de.NBI Cloud, Meta-NanoSim, ILVO Plant Health, EMERGEN-BIOINFO, KircherLab, Apis-wings, BCCM_ULC, Dessimoz Lab, TRON gGmbH, GEMS at MLZ, Computational Science at HZDR, Big data in biomedicine, TRE-FX, MISTIC, Guigó lab, Statistical genetics, Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation, WES, Bioinformatics Unit @ CRG, Bioinformatics Innovation Lab, BSC-CES, ELIXIR Proteomics, Black Ochre Data Labs, Zavolan Lab, Metabolomics-Reproducibility, Team Cardio, NGFF Tools, Bioinformatics workflows for life science, Workflows for geographic science, Pacific-deep-sea-sponges-microbiome, CSFG, SNAKE, Katdetectr, INFRAFRONTIER GmbH, PerMedCoE, Euro-BioImaging, EOSC-Life WP3 OC Team, cross RI project, ANSES-Ploufragan, SANBI Pathogen Bioinformatics, Biodata Analysis Group, DeSci Labs, Erasmus MC - Viroscience Bioinformatics, ARA-dev, Mendel Centre for Plant Genomics and Proteomics, Metagenomic tools, WorkflowEng, Polygenic Score Catalog, bpm, scNTImpute, Systems Biotechnology laboratory, Cimorgh IT solutions, MLme: Machine Learning Made Easy, Hurwitz Lab, Dioscuri TDA, Scipion CNB, System Biotechnology laboratory, yPublish - Bioinfo tools, NIH CFDE Playbook Workflow Partnership, MMV-Lab, EMBL-CBA, EBP-Nor, Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data, Bioinformatics Laboratory for Genomics and Biodiversity (LBGB), multi-analysis dFC, CholGen, RNA group, Plant Genomes Pipelines in Galaxy, Pathogen Genomic Laboratory, Chemical Data Lab, JiangLab, Pangenome database project, HP2NET - Framework for construction of phylogenetic networks on High Performance Computing (HPC) environment, Center for Open Bioimage Analysis, Generalized Open-Source Workflows for Atomistic Molecular Dynamics Simulations of Viral Helicases, Historical DNA genome skimming, QCDIS, Peter Menzel's Team, NHM Clark group, ESRF Workflow System (Ewoks), Kalbe Bioinformatics, Nextflow4Metabolomics, GBCS, CEMCOF, Jackson Laboratory NGS-Ops, Schwartz Lab, BRAIN - Biomedical Research on Adult Intracranial Neoplasms, Cancer Therapeutics and Drug Safety, Deepdefense, Mid-Ohio Regional Planning Commission, MGSSB, Institute for Human Genetics and Genomic Medicine Aachen, FengTaoSMU, EGA, Plant-Food-Research-Open, KrauthammerLab, Geo Workflows, grassland pDT, FunGIALab, CRIM - Computer Research Institute of Montréal, Medvedeva Lab, Metagenlab, FAIR-EASE, Protein-protein and protein-nucleic acid binding site prediction research, Culhane Lab, IDUN - Drug Delivery and Sensing, Edge Computing DAG Task Scheduling Research Group, Stratum corneum nanotexture feature detection using deep learning and spatial analysis: a non-invasive tool for skin barrier assessment, COPO, Taudière group, ErasmusMC Clinical Bioinformatics, interTwin, fluid flow modeling, EnrichDO, WorkflowResearch, Application Security - Test Crypt4GH solutions
Web page: Not specified
TransBioNet is the Translational Bioinformatics Network impulsed and coordinated by the Spanish National Bioinformatics Institute (INB) as a reference network of 35+ bioinformatics support units working at health care settings including Health Research Institutes (IIS) certified by the Carlos III Health Institute (ISCIII), and bioinformatics core facilities from biomedical research institutions. TransBioNet is an Excellence Thematic Network (Red de Excelencia Temática) recognized by the Spanish ...
Space: Independent Teams
Public web page: https://inb-elixir.es/transbionet
