Explore Workflows

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

Path: cwltool/schemas/v1.0/v1.0/count-lines10-wf.cwl

Branch/Commit ID: f997d13af87216e9b5048c732a511053c7ba714c

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/variant_calling/unifiedgenotyper.cwl

Branch/Commit ID: 342c8a39d5823bbcf298d2f807ec235910e5f412

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

Path: tests/wf/default-dir5.cwl

Branch/Commit ID: 1441c285e8a5afe399f5d52ca9059cb8bb513edb

Inspect provided directory and return filenames. Generate a new directory and return it (including content).

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

Path: tests/wf/directory.cwl

Branch/Commit ID: 6003cbb94f16103241b562f2133e7c4acac6c621

Workflow for genome annotation from EMBL format

https://git.wur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_sapp_others.cwl

Branch/Commit ID: d944d61ddc34a5b24ebac6e1701efd6f8fdf54ae

Assemble a set of reads using SKESA

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

Path: assemble.cwl

Branch/Commit ID: f5d70f3ad365a2c017fab1c9654c88bc1caf41aa

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-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.cwl

Branch/Commit ID: 7fb8a1ebf8145791440bc2fed9c5f2d78a19d04c

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

Path: tests/count-lines12-wf.cwl

Branch/Commit ID: 5f27e234b4ca88ed1280dedf9e3391a01de12912

https://github.com/Duke-GCB/bespin-cwl.git

Path: subworkflows/exomeseq-02-variantdiscovery.cwl

Branch/Commit ID: e82f3a71183048dd6700ec6725ee526ac1a95238

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **paired-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 paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 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) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. 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.cwl

Branch/Commit ID: 2cad55523d1b4ee7fd9e64df0f6263c6545e4b0e