Explore Workflows

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

Graph Name Retrieved From View
workflow graph sequence (bam or fastqs) to trimmed fastqs and HISAT alignments

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

Path: definitions/subworkflows/sequence_to_trimmed_fastq_and_hisat_alignments.cwl

Branch/Commit ID: b8000c793d6e7ce4d690406c4f914c5c62acd51f
workflow graph PGAP Pipeline

PGAP pipeline for external usage, powered via containers

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

Path: wf_common.cwl

Branch/Commit ID: b38b0070edf910984f29a4a495b5dfa525b8b305
workflow graph Motif Finding with HOMER with custom background regions

Motif Finding with HOMER with custom background regions --------------------------------------------------- HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. For more information please refer to: ------------------------------------- [Official documentation](http://homer.ucsd.edu/homer/motif/)

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

Path: workflows/homer-motif-analysis-bg.cwl

Branch/Commit ID: 10ce6e113f749c7bd725e426445220c3bdc5ddf1
workflow graph transform_pack.cwl#fastq_clean_se.cwl

https://github.com/NCI-GDC/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/transform_pack.cwl

Branch/Commit ID: 3cb464a3a5c39cc060cd23d9c60918bc9ffb169b

Packed ID: fastq_clean_se.cwl
workflow graph Get Proteins

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

Path: wf_bacterial_prot_src.cwl

Branch/Commit ID: b38b0070edf910984f29a4a495b5dfa525b8b305
workflow graph Run genomic CMsearch (Rfam rRNA)

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

Path: bacterial_ncrna/wf_gcmsearch.cwl

Branch/Commit ID: b38b0070edf910984f29a4a495b5dfa525b8b305
workflow graph Bacterial Annotation, pass 3, structural annotation, functional annotation: ab initio GeneMark, by WP, by HMM (second pass)

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

Path: bacterial_annot/wf_bacterial_annot_pass3.cwl

Branch/Commit ID: b38b0070edf910984f29a4a495b5dfa525b8b305
workflow graph Execute CRISPR

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

Path: bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl

Branch/Commit ID: b38b0070edf910984f29a4a495b5dfa525b8b305
workflow graph Bacterial Annotation, pass 4, blastp-based functional annotation (second pass)

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

Path: bacterial_annot/wf_bacterial_annot_pass4.cwl

Branch/Commit ID: b38b0070edf910984f29a4a495b5dfa525b8b305
workflow graph bacterial_orthology_cond

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

Path: bacterial_orthology/wf_bacterial_orthology_conditional.cwl

Branch/Commit ID: b38b0070edf910984f29a4a495b5dfa525b8b305