Explore Workflows

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

Graph Name Retrieved From View
workflow graph cram_to_bam workflow

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

Path: definitions/subworkflows/cram_to_bam_and_index.cwl

Branch/Commit ID: d297528e53b6c1ecb69b1ab27b8e03323b4463ad
workflow graph taxonomy_check_16S

https://github.com/ncbi/pgap.git

Path: task_types/tt_taxonomy_check_16S.cwl

Branch/Commit ID: 686b570a9fa46f3ace3f8e9935490b75df86a1fc
workflow graph Trim Galore RNA-Seq pipeline single-read

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **single-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 file 2. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 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 file 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-se.cwl

Branch/Commit ID: 4106b7dc96e968db291b7a61ecd1641aa3b3dd6d
workflow graph count-lines12-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines12-wf.cwl

Branch/Commit ID: 665141f319e6b23bd9924b14844f2e979f141944
workflow graph cram_to_bam workflow

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

Path: definitions/subworkflows/cram_to_bam_and_index.cwl

Branch/Commit ID: 258bd4353ad1ca7790b3ae626bf42ab8194e7561
workflow graph wgs alignment with qc

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

Path: definitions/pipelines/alignment_wgs.cwl

Branch/Commit ID: d57c2af01a3cb6016e5a264f60641eafd2e5aa05
workflow graph allele-process-reference.cwl

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

Path: subworkflows/allele-process-reference.cwl

Branch/Commit ID: cb5e5b8563be4977e9f2babc14fe084faa234847
workflow graph mut.cwl

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

Path: tests/wf/mut.cwl

Branch/Commit ID: 814bd0405a7701efc7d63e8f0179df394c7766f7
workflow graph gaps_or_not.cwl

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

Path: gaps_or_not.cwl

Branch/Commit ID: add45db6f08de518e224bdc3c04094fd69cad2d2
workflow graph workflow.cwl

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

Path: flow_download/workflow.cwl

Branch/Commit ID: add45db6f08de518e224bdc3c04094fd69cad2d2