Explore Workflows

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

Graph Name Retrieved From View
workflow graph qiime2 explore sample taxonomic composition

Taxonomic analysis from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/

 https://github.com/Duke-GCB/bespin-cwl.git

Path: packed/qiime2-step2-dada2.cwl

Branch/Commit ID: ef08cb00bd55b4c712645d171dbc691e01ed6165

Packed ID: qiime2-08-taxonomic-analysis.cwl
workflow graph qiime2 DADA2 detect/correct sequence data

Option 1: DADA2 from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/

 https://github.com/Duke-GCB/bespin-cwl.git

Path: packed/qiime2-step2-dada2.cwl

Branch/Commit ID: ef08cb00bd55b4c712645d171dbc691e01ed6165

Packed ID: qiime2-03-dada2.cwl
workflow graph hmmsearch_wnode and gpx_qdump combined workflow to apply scatter/gather

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

Path: task_types/tt_hmmsearch_wnode_plus_qdump.cwl

Branch/Commit ID: be465ad19b07378f3f863f2c4e0019b420c859f2
workflow graph Filter single sample sv vcf from depth callers(cnvkit/cnvnator)

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

Path: definitions/subworkflows/sv_depth_caller_filter.cwl

Branch/Commit ID: 3a822294da63b4e19446a285e2fef075e23cf3d0
workflow graph GSEApy - Gene Set Enrichment Analysis in Python

GSEAPY: Gene Set Enrichment Analysis in Python ============================================== Gene Set Enrichment Analysis is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes). GSEA requires as input an expression dataset, which contains expression profiles for multiple samples. While the software supports multiple input file formats for these datasets, the tab-delimited GCT format is the most common. The first column of the GCT file contains feature identifiers (gene ids or symbols in the case of data derived from RNA-Seq experiments). The second column contains a description of the feature; this column is ignored by GSEA and may be filled with “NA”s. Subsequent columns contain the expression values for each feature, with one sample's expression value per column. It is important to note that there are no hard and fast rules regarding how a GCT file's expression values are derived. The important point is that they are comparable to one another across features within a sample and comparable to one another across samples. Tools such as DESeq2 can be made to produce properly normalized data (normalized counts) which are compatible with GSEA.

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

Path: workflows/gseapy.cwl

Branch/Commit ID: 1f03ff02ef829bdb9d582825bcd4ca239e84ca2e
workflow graph BAM to BEDPE

Comvert BAM to BEDPE and compress the output

 https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/File-formats/bamtobedpe-gzip.cwl

Branch/Commit ID: 00d21c7c7b35e4da3d272540f7356e9a63798442
workflow graph Subworkflow to allow calling different SV callers which require bam files as inputs

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

Path: definitions/subworkflows/single_sample_sv_callers.cwl

Branch/Commit ID: e56f1024306aeb427d8aae2fff715ed2e8b8f86f
workflow graph bam_readcount workflow

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

Path: definitions/subworkflows/bam_readcount.cwl

Branch/Commit ID: 35e6b3ef71b4a2a9caba1dbd5dc424a8809bcc0a
workflow graph umi molecular alignment workflow

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

Path: definitions/subworkflows/molecular_alignment.cwl

Branch/Commit ID: 35e6b3ef71b4a2a9caba1dbd5dc424a8809bcc0a
workflow graph phase VCF

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

Path: definitions/subworkflows/phase_vcf.cwl

Branch/Commit ID: e8b7759826df40b8bb821b40b15aea960a4951c4