Explore Workflows

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

Graph Name Retrieved From View
workflow graph simple_magicblast.cwl

https://github.com/NCBI-Hackathons/BLAST-Pipelines-and-FAIR.git

Path: blast-pipelines/simple_magicblast.cwl

Branch/Commit ID: b7fbc09ae6579b08fa30b43bb7c8ac7ea5b519e0
workflow graph EMG pipeline v3.0 (single end version)

https://github.com/proteinswebteam/ebi-metagenomics-cwl.git

Path: workflows/emg-pipeline-v3.cwl

Branch/Commit ID: 5e8217435bcdd597b2ad236f3e847d13d4c21824
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: 609aead9804a8f31fa9b3dbc7e52105aec487f31
workflow graph mut3.cwl

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

Path: tests/wf/mut3.cwl

Branch/Commit ID: 75271e2a0887d47cca4077b60dd51ac763c09b63
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: 669166450aba26f3560c15960eeebdd0313a7f84
workflow graph schemadef-wf.cwl

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

Path: tests/schemadef-wf.cwl

Branch/Commit ID: a0f2d38e37ff51721fdeaf993bb2ab474b17246b
workflow graph cache_asnb_entries

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

Path: task_types/tt_cache_asnb_entries.cwl

Branch/Commit ID: 205f4ceb47ba7537a6923d2dfb03668317c2fd89
workflow graph portal-workflow.cwl

https://github.com/mskcc/pluto-cwl.git

Path: cwl/portal-workflow.cwl

Branch/Commit ID: 462f6015c9268a4205b6e81de018a470b8a4a153
workflow graph Tag enrichment heatmap and density profile around regions of interest

Generates tag density heatmap and histogram for the centered list of features in a headerless regions file. - If provided regions file is a gene list with the following columns `chrom start end name score strand` set `Gene TSS` as a re-centering criteria. - If provided regions file is a peak list with the following columns `chrom start end name` set `Peak Center` as a re-centering criteria. `score` column is always ignored.

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

Path: workflows/heatmap.cwl

Branch/Commit ID: fa4f172486288a1a9d23864f1d6962d85a453e16
workflow graph Trim Galore RNA-Seq pipeline single-read strand specific

Note: should be updated 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-dutp.cwl

Branch/Commit ID: b5e16e359007150647b14dc6e038f4eb8dccda79