Explore Workflows

https://github.com/pascmont/cwltest.git

Path: myWorkflow2.cwl

Branch/Commit ID: e56456381c2588e3933d91b47c47b7e61023683b

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

Path: tests/scatter-wf3.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3

Packed ID: main

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

Path: tests/count-lines11-null-step-wf.cwl

Branch/Commit ID: a5073143db4155e05df8d2e7eb59d9e62acd65a5

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

Path: tests/wf-loadContents3.cwl

Branch/Commit ID: a5073143db4155e05df8d2e7eb59d9e62acd65a5

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf3.cwl

Branch/Commit ID: 6d2998467fada81e5024c1f8594ae167514cb290

Packed ID: main

Copy genome_fasta file to the folder and run run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome_fasta file basename without extension.

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

Path: workflows/bismark-indices.cwl

Branch/Commit ID: b141f7e73005227d6d02fa03a47151836dd4109b

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

Path: definitions/pipelines/umi_molecular_alignment.cwl

Branch/Commit ID: 49508a2757ff2f49f1c200774a38af1c12b531bf

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-dutp.cwl

Branch/Commit ID: b141f7e73005227d6d02fa03a47151836dd4109b

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

Path: tests/count-lines3-wf.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3

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

Path: tests/count-lines7-wf.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3