Explore Workflows

The BD Rhapsody™ assays are used to create sequencing libraries from single cell transcriptomes. After sequencing, the analysis pipeline takes the FASTQ files and a reference file for gene alignment. The pipeline generates molecular counts per cell, read counts per cell, metrics, and an alignment file.

https://github.com/longbow0/cwl.git

Path: v1.8/rhapsody_targeted_1.8.cwl

Branch/Commit ID: master

Packed ID: main

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

Path: bacterial_orthology/wf_bacterial_orthology.cwl

Branch/Commit ID: master

Runs RNA-Seq dUTP BioWardrobe basic analysis with strand specific single-end data file.

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

Path: workflows/rnaseq-se-dutp.cwl

Branch/Commit ID: master

https://github.com/nci-gdc/htseq-cwl.git

Path: workflows/htseq_count_workflow.cwl

Branch/Commit ID: master

https://github.com/ddbj/human-reseq.git

Path: Workflows/fastqSE2bam.cwl

Branch/Commit ID: master

Reverse the lines in a document, then sort those lines.

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

Path: tests/wf/revsort.cwl

Branch/Commit ID: main

Run metrics workflow

https://github.com/Sentieon/Sentieon-cwl.git

Path: stage/metrics-flow.cwl

Branch/Commit ID: master

STARR-seq pipeline - reads: PE

https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/STARR-seq_pipeline/pipeline-pe.cwl

Branch/Commit ID: master

PGAP pipeline for external usage, powered via containers, simple user input: (FASTA + yaml only, no template)

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

Path: pgap.cwl

Branch/Commit ID: 546742b523ce12f6246a52c838a51920a08dad4b

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/harmonization/harmonization_bwa_mem_no_trim.cwl

Branch/Commit ID: master