Explore Workflows

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Graph Name Retrieved From View
workflow graph chipseq-se.cwl

Runs ChIP-Seq BioWardrobe basic analysis with single-end data file.

https://github.com/Barski-lab/workflows.git

Path: workflows/chipseq-se.cwl

Branch/Commit ID: 812b0ff40dda18ab7a9a872ff13a577be8531ba6
workflow graph ValidateCameraTimeResponse

Validate camera time response.

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

Path: workflows/ValidateCameraTimeResponse.cwl

Branch/Commit ID: 789752af87eb190387ff2acb4c95c7a5cdb961e7
workflow graph Trim Galore SMARTer RNA-Seq pipeline paired-end strand specific

https://chipster.csc.fi/manual/library-type-summary.html Modified original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **pair-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 single-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 4. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 5. Generate BigWig file on the base of sorted BAM file 6. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 7. 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/trim-rnaseq-pe-smarter-dutp.cwl

Branch/Commit ID: 12e5256de1b680c551c87fd5db6f3bc65428af67
workflow graph HBA_calibrator.cwl

https://git.astron.nl/RD/LINC.git

Path: workflows/HBA_calibrator.cwl

Branch/Commit ID: efd84bf3c56117c6a05852b3b47aaf4ad8de11bd
workflow graph xenbase-fastq-bowtie-bigwig-se-pe.cwl

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

Path: subworkflows/xenbase-fastq-bowtie-bigwig-se-pe.cwl

Branch/Commit ID: dda9e6e06a656b7b3fa7504156474b962fe3953c
workflow graph revsort.cwl

https://github.com/ResearchObject/runcrate.git

Path: cwl/revsortlcase/revsort.cwl

Branch/Commit ID: 9e40a51a9e48239bbd5fb5d3b6c4a8ef32e8169b
workflow graph mut2.cwl

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

Path: tests/wf/mut2.cwl

Branch/Commit ID: 65aedc5e7e1f3ccace7f9022f8a54b3f0d5c9a8c
workflow graph mut2.cwl

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

Path: tests/wf/mut2.cwl

Branch/Commit ID: 048eb55aefd8d71d161fbc89ec0e888b8bfa0aa1
workflow graph count-lines13-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines13-wf.cwl

Branch/Commit ID: 814bd0405a7701efc7d63e8f0179df394c7766f7
workflow graph bam_readcount workflow

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

Path: definitions/subworkflows/bam_readcount.cwl

Branch/Commit ID: 3f3b186da9bf82a5e2ae74ba27aef35a46174ebe