Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
|---|---|---|---|
|
|
count-lines2-wf.cwl
|
https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/count-lines2-wf.cwl Branch/Commit ID: bbe20f54deea92d9c9cd38cb1f23c4423133d3de |
|
|
|
exome alignment and germline variant detection
|
https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/germline_exome.cwl Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370 |
|
|
|
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: 29bf638904709cfbf10908adcd51ba4886ace94a |
|
|
|
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: be9d12a3f8e1924183a1dc6a0bda6ada4195ca71 |
|
|
|
SoupX (workflow) - an R package for the estimation and removal of cell free mRNA contamination
Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs. |
https://github.com/datirium/workflows.git
Path: tools/soupx-subworkflow.cwl Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f |
|
|
|
varscan somatic workflow
|
https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/varscan.cwl Branch/Commit ID: 5cb188131f786ed33156e2f0e3dd63ab9c04245d |
|
|
|
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: c0543fc3f552a521aa498b6597b9a972599de056 |
|
|
|
count-lines1-wf.cwl
|
https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/count-lines1-wf.cwl Branch/Commit ID: 1eb6bfe3c77aebaf69453a669d21ae7a5a78056f |
|
|
|
Single-cell ATAC-Seq Differential Binding Analysis
Single-cell ATAC-Seq Differential Binding Analysis Identifies differential bound sites between two groups of cells |
https://github.com/datirium/workflows.git
Path: workflows/sc-atac-dbinding.cwl Branch/Commit ID: 22880e0f41d0420a17d643e8a6e8ee18165bbfbf |
|
|
|
Apply filters to VCF file
|
https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/filter_vcf.cwl Branch/Commit ID: 44ada20f3eeb59005d5bd999d2435102e9bae991 |
