Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
|---|---|---|---|
|
|
bgzip and index VCF
|
https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/bgzip_and_index.cwl Branch/Commit ID: 6d03a918639a69ddf6a7b93fe9f72128ef37edc3 |
|
|
|
wffail.cwl
|
https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/wffail.cwl Branch/Commit ID: 819c81af5449ec912bbbbead042ad66b8d3fd8d4 |
|
|
|
env-wf2.cwl
|
https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/env-wf2.cwl Branch/Commit ID: 0e98de8f692bb7b9626ed44af835051750ac20cd |
|
|
|
env-wf1.cwl
|
https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/env-wf1.cwl Branch/Commit ID: 09323506da219ba3ddb5313bd83022b52cac9adc |
|
|
|
harmonization_bwa_mem.cwl
|
https://github.com/uc-cdis/genomel_pipelines.git
Path: genomel/cwl/workflows/harmonization/harmonization_bwa_mem.cwl Branch/Commit ID: 7f01768479e6a77a5caf6b3382174aa038ba05fc |
|
|
|
QuantSeq 3' FWD, FWD-UMI or REV for single-read mRNA-Seq data
### Devel version of QuantSeq 3' FWD, FWD-UMI or REV for single-read mRNA-Seq data |
https://github.com/datirium/workflows.git
Path: workflows/trim-quantseq-mrnaseq-se-strand-specific.cwl Branch/Commit ID: 22880e0f41d0420a17d643e8a6e8ee18165bbfbf |
|
|
|
wffail.cwl
|
https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/wffail.cwl Branch/Commit ID: d5f7fa162611243f0c66dd3e933c16a4964a09ca |
|
|
|
RNA-Seq pipeline single-read stranded mitochondrial
Slightly changed original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific single-read** experiment. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with single-read strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `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/rnaseq-se-dutp-mitochondrial.cwl Branch/Commit ID: 46a077b51619c6a14f85e0aa5260ae8a04426fab |
|
|
|
Filter single sample sv vcf from paired read callers(Manta/Smoove)
|
https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/sv_paired_read_caller_filter.cwl Branch/Commit ID: 7b4b489474473c3d2d992a838b89632c2b97dc2c |
|
|
|
Trim Galore RNA-Seq pipeline single-read
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.cwl Branch/Commit ID: ddc35c559d1ac6aab4972fe1a2b63300c4373f54 |
