Explore Workflows

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

Path: tests/scatter-valuefrom-wf1.cwl

Branch/Commit ID: 31ec48a8d81ef7c1b2c5e9c0a19e7623efe4a1e2

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

Path: tests/timelimit-wf.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3

https://github.com/d3b-center/canine-dev.git

Path: subworkflows/canine_deepvariant_module.cwl

Branch/Commit ID: 7da5645975f5712362cce7908d2ab138e05876fb

Quality Control and Raw Data trimming

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/subworkflows/trimmed_fastq.cwl

Branch/Commit ID: 70eec658fd1b92c4d0e3b24146820010b5983d41

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 pair-end** 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 the pair-end 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-pe-dutp-mitochondrial.cwl

Branch/Commit ID: 00ea05e22788029370898fd4c17798b11edf0e57

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/count-lines8-wf.cwl

Branch/Commit ID: 3e90671b25f7840ef2926ad2bacbf447772dda94

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/subworkflows/indexing_bed.cwl

Branch/Commit ID: c494fa4f60d9215842c4d2c75ed7d89757435b0f

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

Path: tests/step-valuefrom2-wf.cwl

Branch/Commit ID: 31ec48a8d81ef7c1b2c5e9c0a19e7623efe4a1e2

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

Path: definitions/subworkflows/single_cell_rnaseq.cwl

Branch/Commit ID: 4bc0a4577d626b65a4b44683e5a1ab2f7d7faf4c

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

Path: testdata/record-output-wf_v1_0.cwl

Branch/Commit ID: 6a46105708870aa3cf97c8ba91884272b2857975