Kallisto RNAseq Workflow Version 1
Visit source
Download RO CrateWorkflow Kallisto RNAseq
(pseudoalignment on transcripts)
- Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1
- kallisto
All tool CWL files and other workflows can be found here:
Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl
Workflows: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows
How to setup and use an UNLOCK workflow:
https://m-unlock.gitlab.io/docs/setup/setup.html
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| identifier | Identifier | Identifier for this dataset used in this workflow |
|
| threads | Threads | Number of threads to use for computational processes |
|
| memory | Maximum memory in MB | Maximum memory usage in megabytes |
|
| filter_rrna | Filter rRNA | Optionally remove rRNA sequences from the reads. |
|
| forward_reads | Forward reads | Forward sequence file locally |
|
| reverse_reads | Reverse reads | Reverse sequence file locally |
|
| kallisto_index | kallisto index file | kallisto index file location |
|
| contamination_references | Reference filters files | Reference fasta file(s) for filtering (optional) |
|
| destination | Output Destination | Optional Output destination used for cwl-prov reporting. |
|
Steps
| ID | Name | Description |
|---|---|---|
| workflow_quality | Quality and filtering workflow | Quality assessment of illumina reads with rRNA filtering option |
| kallisto | kallisto | Calculates transcript abundances |
| kallisto_files_to_folder | kallisto output | Preparation of kallisto output files to a specific output folder |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| illumina_quality_stats | Filtered statistics | Statistics on quality and preprocessing of the reads |
|
| kallisto_output | kallisto output | kallisto results folder. Contains transcript abundances, run info and summary. |
|
Version History
Version 1 (earliest) Created 20th May 2022 at 11:10 by Bart Nijsse
Initial commit
Open
masterc7adcde
Creators and Submitter
Views: 626
Created: 20th May 2022 at 11:10
Last updated: 2nd Nov 2022 at 15:26
TagsThis item has not yet been tagged.
AttributionsNone
Related items
https://orcid.org/0000-0001-8172-8981
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, Genomics Coordination Center, 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, Galaxycompchem, 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, Cluster Emergent del Cervell Humà, 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, DLSW, 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, EuroScienceGateway
Web page: Not specified
An open infrastructure for exploring new horizons for research on microbial communities.
