Explore Workflows

https://github.com/common-workflow-library/legacy.git

Path: workflows/kallisto-demo.cwl

Branch/Commit ID: 767d700e602805112a4c953d166e570cddfa2605

This workflow takes in appropriate trimming params and demultiplexed reads, and performs the following steps in order: trimx1, trimx2, fastq-sort, filter repeat elements, fastq-sort, genomic mapping, sort alignment, index alignment, namesort, PCR dedup, sort alignment, index alignment

https://github.com/YeoLab/eclip.git

Path: cwl/wf_trim_and_map_se.cwl

Branch/Commit ID: c0fffc4979a92371dc0667a03e3d957bf7f77600

This workflow creates FASTA file from BED coordinates

https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/File-formats/fasta-from-bed.cwl

Branch/Commit ID: 793e327acc1d159ff601043ee88651fca62350dd

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

Path: tests/fail-unconnected.cwl

Branch/Commit ID: a0f2d38e37ff51721fdeaf993bb2ab474b17246b

Modified original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **pair-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 single-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 4. 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 files 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/trim-rnaseq-pe-dutp.cwl

Branch/Commit ID: 7518b100d8cbc80c8be32e9e939dfbb27d6b4361

https://github.com/YeoLab/eclip.git

Path: cwl/wf_demultiplex_pe.cwl

Branch/Commit ID: c0fffc4979a92371dc0667a03e3d957bf7f77600

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

Path: tests/dynresreq-workflow-tooldefault.cwl

Branch/Commit ID: 86c46cb397de029e4c91f02cca40fa2b54d22f37

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: workflows/emg-pipeline-v4-paired.cwl

Branch/Commit ID: 7bb76f33bf40b5cd2604001cac46f967a209c47f

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

Path: tests/wf/scatter-wf4.cwl

Branch/Commit ID: 1441c285e8a5afe399f5d52ca9059cb8bb513edb

Packed ID: main

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

Path: cwltool/schemas/v1.0/v1.0/js-expr-req-wf.cwl

Branch/Commit ID: e835bc0487fe42fb330b6222c9be65d18dd81ec9

Packed ID: wf