Explore Workflows

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

Path: tests/count-lines9-wf-noET.cwl

Branch/Commit ID: 31ec48a8d81ef7c1b2c5e9c0a19e7623efe4a1e2

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: e9cc6de8cd1e00345969c646e5e6f27d7d10420f

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: 7b5130d2408bce82ee15c666b37d931ef6f452e3

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

Path: tests/count-lines1-wf.cwl

Branch/Commit ID: e515226f8ac0f7985cd94dae4a301150adae3050

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

Path: tests/wf/mut2.cwl

Branch/Commit ID: aec33fcfa3459a90cbba8c88ebb991be94d21429

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

Path: definitions/pipelines/somatic_exome_mouse.cwl

Branch/Commit ID: 6b365b79675b2aabfb8d5829bb8df0a6e986b037

https://github.com/CompEpigen/ChIPseq_workflows.git

Path: CWL/workflows/CUTnRUN_pipeline.cwl

Branch/Commit ID: b7709bff6bd6e93a28dfc2fee0655f6aceef0901

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

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

Branch/Commit ID: 26870e38cec81af880cd3e4789ae6cee8fc27020

Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow.

https://github.com/datirium/workflows.git

Path: tools/bam-bedgraph-bigwig.cwl

Branch/Commit ID: 57863b6131d8262c5ce864adaf8e4038401e71a2

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: dda9e6e06a656b7b3fa7504156474b962fe3953c