Explore Workflows

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

Graph Name Retrieved From View
workflow graph Align reference proteins plane complete workflow, with miniprot

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

Path: protein_alignment/wf_protein_alignment_miniprot.cwl

Branch/Commit ID: 8ea3637b0f11eac1ea5599c41d74e00d85fb778d
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: a68821bf3a9ceadc3b2ffbb535d601d9a645b377
workflow graph Bisulfite QC tools

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

Path: definitions/subworkflows/bisulfite_qc.cwl

Branch/Commit ID: a9133c999502acf94b433af8d39897e6c2cdf65f
workflow graph scatter-wf3_v1_0.cwl#main

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

Path: testdata/scatter-wf3_v1_0.cwl

Branch/Commit ID: e78db9870cb744fe36674f43b3223c688e9989e1

Packed ID: main
workflow graph Align reference proteins plane complete workflow

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

Path: protein_alignment/wf_protein_alignment.cwl

Branch/Commit ID: 8ea3637b0f11eac1ea5599c41d74e00d85fb778d
workflow graph count-lines11-wf-noET.cwl

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

Path: tests/count-lines11-wf-noET.cwl

Branch/Commit ID: 1f3ef888d9ef2306c828065c460c1800604f0de4
workflow graph spurious_annot pass2

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

Path: spurious_annot/wf_spurious_annot_pass2.cwl

Branch/Commit ID: 8ea3637b0f11eac1ea5599c41d74e00d85fb778d
workflow graph workflow_input_sf_expr.cwl

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

Path: testdata/workflow_input_sf_expr.cwl

Branch/Commit ID: 0ad6983898f0d9001fe0f416f97c4d8b940e384a
workflow graph wgs alignment and germline variant detection

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

Path: definitions/pipelines/germline_wgs.cwl

Branch/Commit ID: 8438316338e66823e1c9aca9f675b2bf33f2aa59
workflow graph gatk4.2.4.1_mutect2_workflow.cwl

GATK4.2.4.1 Mutect2 workflow

https://github.com/nci-gdc/gatk4_mutect2_cwl.git

Path: subworkflows/gatk4.2.4.1_mutect2_workflow.cwl

Branch/Commit ID: cc7d31c9b8e5a0d0be41203513007df2cb341f73