Explore Workflows

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

Graph Name Retrieved From View
workflow graph cond-wf-011_nojs.cwl

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

Path: tests/conditionals/cond-wf-011_nojs.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733
workflow graph RNA-Seq pipeline paired-end stranded mitochondrial

Slightly changed original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific pair-end** experiment. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with the pair-end strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `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/rnaseq-pe-dutp-mitochondrial.cwl

Branch/Commit ID: e238d1756f1db35571e84d72e1699e5d1540f10c
workflow graph scatter2.cwl

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

Path: tests/wf/scatter2.cwl

Branch/Commit ID: 55ccde7c2fe3e7899136ce8606a341e292d7050a
workflow graph Exome QC workflow

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

Path: definitions/subworkflows/qc_exome.cwl

Branch/Commit ID: d297528e53b6c1ecb69b1ab27b8e03323b4463ad
workflow graph Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs

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

Path: definitions/subworkflows/pvacseq.cwl

Branch/Commit ID: ae57b60e9b01e3f0f02f4e828042748409dff5a3
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: e0b3c76e38630fb6234414b5adebfb6a4fb23117
workflow graph Single-cell Multiome ATAC and RNA-Seq Filtering Analysis

Single-cell Multiome ATAC and RNA-Seq Filtering Analysis Filters single-cell multiome ATAC and RNA-Seq datasets based on the common QC metrics.

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

Path: workflows/sc-multiome-filter.cwl

Branch/Commit ID: 12e5256de1b680c551c87fd5db6f3bc65428af67
workflow graph Merge, annotate, and generate a TSV for SVs

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

Path: definitions/subworkflows/merge_svs.cwl

Branch/Commit ID: dc2c019c1aa24cc01b451a0f048cf94a35f163c4
workflow graph scatterfail.cwl

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

Path: tests/wf/scatterfail.cwl

Branch/Commit ID: 55ccde7c2fe3e7899136ce8606a341e292d7050a
workflow graph io-int-default-tool-and-wf.cwl

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

Path: tests/io-int-default-tool-and-wf.cwl

Branch/Commit ID: a0f2d38e37ff51721fdeaf993bb2ab474b17246b