Explore Workflows

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

Path: tests/output-arrays-int-wf.cwl

Branch/Commit ID: ea9f8634e41824ac3f81c3dde698d5f0eef54f1b

https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git

Path: janis_pipelines/wgs_somatic/cwl/tools/BwaAligner_1_0_0.cwl

Branch/Commit ID: a3d1f3b870eb834fed14ebcc928ea6a2270441a8

https://github.com/E3SM-Project/e3sm_to_cmip.git

Path: scripts/cwl_workflows/atm-unified/atm-unified.cwl

Branch/Commit ID: 662280529757f03a438fc0ad0da0d8ce6d15e25a

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

Path: cwltool/schemas/v1.0/v1.0/dynresreq-workflow.cwl

Branch/Commit ID: e4a52682f3bdefafe5c27e32983fed31116ac489

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

Path: task_types/tt_univec_wnode.cwl

Branch/Commit ID: 89098668413e90519c99b35143bffec509d3599c

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: subworkflows/heatmap-prepare.cwl

Branch/Commit ID: 8d7ba680b7904da84ad611d184caf247da4a5dc7

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: 4f48ee6f8665a34cdf96e89c012ee807f80c7a3d

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

Path: tests/wf/mut3.cwl

Branch/Commit ID: aec33fcfa3459a90cbba8c88ebb991be94d21429

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

Path: definitions/subworkflows/hs_metrics.cwl

Branch/Commit ID: e7e888df9e7d44f036c4c7985e474016ee9e6525

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

Path: tests/wf/1st-workflow.cwl

Branch/Commit ID: ecdfe1ee769d05790f70ac87a711131f441f3753