Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph record-in-secondaryFiles-missing-wf.cwl

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

Path: tests/record-in-secondaryFiles-missing-wf.cwl

Branch/Commit ID: a0f2d38e37ff51721fdeaf993bb2ab474b17246b
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: 92f1a6da9c4f85fb51340b01b32373a50fde0891
workflow graph module-1.cwl

https://github.com/mskcc/ACCESS-Pipeline.git

Path: workflows/module-1.cwl

Branch/Commit ID: 09ddd9711fb550f56d52f1806cdefd4a8cd943b0
workflow graph qiime2 rarefaction visualization

Alpha rarefaction plotting from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/

 https://github.com/bespin-workflows/16s-qiime2.git

Path: subworkflows/qiime2-07-alpha-rarefaction.cwl

Branch/Commit ID: b4c07a7e07ba9ce862a2be057a905d300f3c8882
workflow graph call_variants.cwl

https://github.com/mskcc/ACCESS-Pipeline.git

Path: workflows/subworkflows/call_variants.cwl

Branch/Commit ID: 5bf88423593441e4bf6b432111160446cd8dcf13
workflow graph qc_workflow.cwl

https://github.com/andurill/ACCESS-Pipeline.git

Path: workflows/QC/qc_workflow.cwl

Branch/Commit ID: f8b57834ad0ce78e4d5bdd90ed0991923685d87f
workflow graph workflow.cwl

https://github.com/nal-i5k/organism_onboarding.git

Path: flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl

Branch/Commit ID: f452184daca189341f65e09a0d5ab878dd312dfd
workflow graph Apply filters to VCF file

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

Path: definitions/subworkflows/filter_vcf.cwl

Branch/Commit ID: 31a179d7a2f2ac86bfd7fcc4dc79832c3739ae76
workflow graph waltz-workflow.cwl

https://github.com/andurill/ACCESS-Pipeline.git

Path: workflows/waltz/waltz-workflow.cwl

Branch/Commit ID: f8b57834ad0ce78e4d5bdd90ed0991923685d87f
workflow graph Add snv and indel bam-readcount files to a vcf

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

Path: definitions/subworkflows/vcf_readcount_annotator.cwl

Branch/Commit ID: 5be54bf09092c53e6c7797a875f64a360d511d7f