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Graph Name Retrieved From View
workflow graph Kallisto index pipeline

This workflow indexes the input reference FASTA with kallisto, and generates a kallisto index file (.kdx). This index sample can then be used as input into the kallisto transcript-level quantification workflow (kallisto-quant-pe.cwl), or others that may include this workflow as an upstream source. ### __Inputs__ - FASTA file of the reference genome that will be indexed - number of threads to use for multithreading processes ### __Outputs__ - kallisto index file (.kdx). - stdout log file (output in Overview tab as well) - stderr log file ### __Data Analysis Steps__ 1. cwl calls dockercontainer robertplayer/scidap-kallisto to index reference FASTA with `kallisto index`, generating a kallisto index file. ### __References__ - Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification, Nature Biotechnology 34, 525-527(2016), doi:10.1038/nbt.3519

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

Path: workflows/kallisto-index.cwl

Branch/Commit ID: 30031ca5e69cec603c4733681de54dc7bffa20a3
workflow graph extract_gencoll_ids

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

Path: task_types/tt_extract_gencoll_ids.cwl

Branch/Commit ID: 42df0c0f9a4e5697abadd9cb52440691fafc8f5d
workflow graph rnaseq-se-dutp.cwl

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: 144eee15187c1a1145ce1ee0239da69059fd2752
workflow graph taxonomy_check_16S

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

Path: task_types/tt_taxonomy_check_16S.cwl

Branch/Commit ID: 72c3091012f5c2dce38ad9213cda617d2c7a61ac
workflow graph Single-Cell ATAC-Seq Cluster Analysis

Single-Cell ATAC-Seq Cluster Analysis Clusters cells by similarity of chromatin accessibility data from the outputs of the “Single-Cell ATAC-Seq Dimensionality Reduction Analysis” pipeline. The results of this workflow are used in the “Single-Cell Manual Cell Type Assignment”, “Single-Cell ATAC-Seq Differential Accessibility Analysis”, and “Single-Cell ATAC-Seq Genome Coverage” pipelines.

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

Path: workflows/sc-atac-cluster.cwl

Branch/Commit ID: 30031ca5e69cec603c4733681de54dc7bffa20a3
workflow graph env-wf3.cwl

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

Path: cwltool/schemas/v1.0/v1.0/env-wf3.cwl

Branch/Commit ID: 2256a30d0c1365b30e0a7338fb883c74674fcd25
workflow graph step-valuefrom3-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/step-valuefrom3-wf.cwl

Branch/Commit ID: 8010fd2bf1e7090ba6df6ca8c84bbb96e2272d32
workflow graph HBA_calibrator.cwl

https://git.astron.nl/RD/LINC.git

Path: workflows/HBA_calibrator.cwl

Branch/Commit ID: 0c5bd78e3f2d08564f5c9a563bcc8bb7704e6202
workflow graph dynresreq-workflow-tooldefault.cwl

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

Path: tests/dynresreq-workflow-tooldefault.cwl

Branch/Commit ID: 1f3ef888d9ef2306c828065c460c1800604f0de4
workflow graph heatmap-prepare.cwl

Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs - bam_file - fragment_size - total_reads `dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job: 1) bam_file[0] fragment_size[0] total_reads[0] 2) bam_file[1] fragment_size[1] total_reads[1] ... N) bam_file[N] fragment_size[N] total_reads[N] `bam_file`, `fragment_size` and `total_reads` arrays should have the identical order.

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

Path: tools/heatmap-prepare.cwl

Branch/Commit ID: 30031ca5e69cec603c4733681de54dc7bffa20a3