Explore Workflows

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **paired-end** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 3. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. Calculate isoform expression level for the sorted BAM file and GTF/TAB annotation file using GEEP reads-counting utility; export results to file

https://github.com/datirium/workflows.git

Path: workflows/rnaseq-pe-dutp.cwl

Branch/Commit ID: e238d1756f1db35571e84d72e1699e5d1540f10c

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf1.cwl

Branch/Commit ID: 526f36f93655bfb098f766ff020708b5a707513a

local

https://github.com/aplbrain/saber.git

Path: demos/em_pipelines/workflow_i2g.cwl

Branch/Commit ID: 051b9506fd7356113be013ac3c435a101fd95123

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/count-lines2-wf.cwl

Branch/Commit ID: a0f2d38e37ff51721fdeaf993bb2ab474b17246b

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/downsampled_alignment.cwl

Branch/Commit ID: 789267ce0e3fed674ea5212a562315218fcf1bfc

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/align_sort_markdup.cwl

Branch/Commit ID: 789267ce0e3fed674ea5212a562315218fcf1bfc

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/panel_of_normals.cwl

Branch/Commit ID: 27dcb1ae121be6a23057b74332b8c752ea425735

https://github.com/hubmapconsortium/azimuth-annotate.git

Path: pipeline.cwl

Branch/Commit ID: f1215df5ee3c680ef18b98f1a1934874326d8d9c

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/gatk_haplotypecaller_iterator.cwl

Branch/Commit ID: ad65dc1dfff9afa5077f498b85e699716c47f6cb

https://github.com/common-workflow-language/cwl-utils.git

Path: testdata/count-lines7-wf_v1_0.cwl

Branch/Commit ID: 77669d4dd1d1ebd2bdd9810f911608146d9b8e51