NonSpliced RNAseq workflow Version 1
Visit source
Download RO-CrateWorkflow for NonSpliced RNAseq data with multiple aligners.
Steps:
- workflowquality.cwl:
- FastQC (control)
- fastp (trimming)
- bowtie2 (read mapping)
- samto_sorted-bam
- featurecounts (transcript read counts)
- kallisto (transcript [pseudo]counts)
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| threads | number of threads | number of threads to use for computational processes | int? |
| memory | Max memory | maximum memory usage in megabytes | int? |
| filter_rrna | Filer rRNA | Filter rRNA from reads if true | boolean |
| prefix_id | Filename prefix | Prefix of the output filenames. | string |
| forward_reads | forward reads | forward sequence file locally | File |
| reverse_reads | reverse reads | reverse sequence file locally | File |
| bowtie2-indexfolder | bowtie2 index | Folder location of the bowtie2 index files. | Directory |
| kallisto-indexfolder | kallisto index | Folder location of the kallisto index file. | Directory? |
| gtf | GTF file | GTF file location | File? |
Steps
| ID | Name | Description |
|---|---|---|
| quality | Quality and filtering workflow | Quality assessment of illumina reads with rRNA filtering option |
| bowtie2 | bowtie2 | runs bowtie2 alignment on the genome with the quality filtered reads. |
| sam_to_sorted-bam | sam to sorted bam | Converts a SAM file to a sorted BAM file |
| featurecounts | FeatureCounts | Calculates gene counts with bowtie2 mapped data and input GTF file with FeatureCounts. |
| kallisto | kallisto | Calculates transcript abundances |
| bowtie2_files_to_folder | bowtie2 output | Preparation of bowtie2 output files to a specific output folder |
| featurecounts_files_to_folder | FeatureCounts output | Preparation of FeatureCounts output files to a specific output folder |
| kallisto_files_to_folder | FeatureCounts output | Preparation of kallisto output files to a specific output folder |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| files_to_folder_fastqc | FASTQC | Quality reporting by FASTQC | Directory |
| files_to_folder_filtered | Filtered reads folder | Output folder with filtered reads. | Directory |
| files_to_folder_bowtie2 | bowtie2 output | bowtie2 mapping results folder. Contains sorted bam file, metrics file and mapping statistics (stdout). | Directory |
| files_to_folder_featurecounts | FeatureCounts output | FeatureCounts results folder. Contains readcounts, summary and mapping statistics (stdout). | Directory |
| files_to_folder_kallisto | kallisto output | kallisto results folder. Contains transcript abundances, run info and summary. | Directory |
Creators and Submitter
Views: 598 Downloads: 29
Created: 24th Nov 2020 at 11:05
Last updated: 8th Jun 2021 at 08:32
Last used: 16th Oct 2021 at 14:52
AttributionsNone
Version History
Version 1 Created 24th Nov 2020 at 11:05 by Bart Nijsse
No revision comments
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
Web page: Not specified
An open infrastructure for exploring new horizons for research on microbial communities.
