Explore Workflows

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

Path: tests/wf/secret_wf.cwl

Branch/Commit ID: 67aa64a089cfc50e9999ccdf550dfdae631a946e

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 **strand specific single-read** 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-read RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 3. 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/rnaseq-se-dutp.cwl

Branch/Commit ID: a1f6ca50fcb0881781b3ba0306dd61ebf555eaba

https://github.com/ddbj/imputation-server-wf.git

Path: Workflows/beagle-imputation-scatter-region.cwl

Branch/Commit ID: c3524050ec2f6e6a43a93a3ac6734ccb8799eac2

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

Path: tests/io-int-default-tool-and-wf.cwl

Branch/Commit ID: b1d4a69df86350059bd49aa127c02be0c349f7de

Workflow without outputs.

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

Path: tests/no-outputs-wf.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733

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

Path: tests/timelimit-wf.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733

https://github.com/reanahub/reana-demo-worldpopulation.git

Path: workflow/cwl/worldpopulation-slurmcern.cwl

Branch/Commit ID: 7d08708a8deff739a2b9bc0a7b2d4e50105f21d8

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: d6ec0dee61ef65a110e10141bde1a79332a64ab0

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

Path: subworkflows/main/gdc_dnaseq_main_workflow.cwl

Branch/Commit ID: e0f19eb6da82b643ce891f81a8a127dee48ba97a

https://github.com/FAIR-tools/workflow-description.git

Path: cwl/workflow.cwl

Branch/Commit ID: f701312fc2a6066aab39c516a0a37ff95cd1ec4b