Workflow Type: Common Workflow Language
Open
Work-in-progress
Workflow for Spliced RNAseq data Steps:
- workflow_quality.cwl:
- FastQC (Read Quality Control)
- fastp (Read Trimming)
- STAR (Read mapping)
- featurecounts (transcript read counts)
- kallisto (transcript [pseudo]counts)
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Inputs
ID | Name | Description | Type |
---|---|---|---|
threads | number of threads | number of threads to use for computational processes |
|
memory | maximum memory usage in megabytes | maximum memory usage in megabytes |
|
filter_rrna | n/a | n/a |
|
prefix_id | n/a | prefix of the filename outputs |
|
forward_reads | forward reads | forward sequence file locally |
|
reverse_reads | reverse reads | reverse sequence file locally |
|
STAR-indexfolder | folder where the STAR indices are | n/a |
|
kallisto-indexfolder | folder where the kallisto indices are | n/a |
|
gtf | n/a | gtf file |
|
quantMode | n/a | Run with get gene quantification |
|
Steps
ID | Name | Description |
---|---|---|
quality | Quality and filtering workflow | Quality assessment of illumina reads with rRNA filtering option |
STAR | STAR | runs STAR alignment on the genome with the quality filtered reads. |
featurecounts | FeatureCounts | Calculates gene counts with bowtie2 mapped data and input GTF file with FeatureCounts. |
kallisto | kallisto | Calculates transcript abundances |
STAR_files_to_folder | STAR output | Preparation of STAR 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 | kallisto 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 |
|
files_to_folder_filtered | Filtered reads folder | Output folder with filtered reads. |
|
files_to_folder_STAR | STAR output folder | STAR results folder. Contains logs, bam file, readcounts per gene and splice_junctions. |
|
files_to_folder_featurecounts | FeatureCounts output | FeatureCounts results folder. Contains readcounts, summary and mapping statistics (stdout). |
|
files_to_folder_kallisto | kallisto output | kallisto results folder. Contains transcript abundances, run info and summary. |
|
Version History
Version 1 (earliest) Created 22nd Dec 2020 at 15:53 by Bart Nijsse
Added/updated 1 files
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Views: 2627 Downloads: 334
Created: 22nd Dec 2020 at 15:53
Last updated: 8th Jun 2021 at 13:31
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