Workflow Type: Common Workflow Language
Open
Work-in-progress
Workflow for NonSpliced RNAseq data with multiple aligners.
Steps:
- workflow_quality.cwl:
- FastQC (control)
- fastp (trimming)
- bowtie2 (read mapping)
- sam_to_sorted-bam
- featurecounts (transcript read counts)
- kallisto (transcript [pseudo]counts)
Click and drag the diagram to pan, double click or use the controls to zoom.
Inputs
ID | Name | Description | Type |
---|---|---|---|
threads | number of threads | number of threads to use for computational processes |
|
memory | Max memory | maximum memory usage in megabytes |
|
filter_rrna | Filer rRNA | Filter rRNA from reads if true |
|
prefix_id | Filename prefix | Prefix of the output filenames. |
|
forward_reads | forward reads | forward sequence file locally |
|
reverse_reads | reverse reads | reverse sequence file locally |
|
bowtie2-indexfolder | bowtie2 index | Folder location of the bowtie2 index files. |
|
kallisto-indexfolder | kallisto index | Folder location of the kallisto index file. |
|
gtf | GTF file | GTF file location |
|
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 |
|
files_to_folder_filtered | Filtered reads folder | Output folder with filtered reads. |
|
files_to_folder_bowtie2 | bowtie2 output | bowtie2 mapping results folder. Contains sorted bam file, metrics file and mapping statistics (stdout). |
|
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 24th Nov 2020 at 11:05 by Bart Nijsse
Added/updated 1 files
Open
master
533f564
Creators and Submitter
Creators
Submitter
Discussion Channel
Activity
Views: 2750 Downloads: 337
Created: 24th Nov 2020 at 11:05
Last updated: 8th Jun 2021 at 08:32
Attributions
None