Explore Workflows

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

Path: tests/wf/default-wf5.cwl

Branch/Commit ID: 65aedc5e7e1f3ccace7f9022f8a54b3f0d5c9a8c

First computes average per UniProt domain instance and then aligns all the average structures against core average structure. Outputs the alignment results along with the structures passing and failing the threshold for given Kpax score.

https://github.com/HrishiDhondge/CroMaSt.git

Path: Tools/unmapped_unp_avg_align.cwl

Branch/Commit ID: 9f3832867eab6c7a6363f8ca594a4bcf2ff7e96f

Devel version of AltAnalyze Iterative Clustering and Guide-gene Selection =========================================================================

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

Path: workflows/altanalyze-icgs.cwl

Branch/Commit ID: 4a5c59829ff8b9f3c843e66e3c675dcd9c689ed5

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

Path: cwltool/schemas/v1.0/v1.0/search.cwl

Branch/Commit ID: cf9d7cdefa6dfb3b678636da02bc55b6108c04ac

Packed ID: main

AltAnalyze CellHarmony ======================

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

Path: workflows/altanalyze-cellharmony.cwl

Branch/Commit ID: 1a46cb0e8f973481fe5ae3ae6188a41622c8532e

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

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

Branch/Commit ID: 1f501e38ff692a408e16b246ac7d64d32f0822c2

Packed ID: main

https://chipster.csc.fi/manual/library-type-summary.html 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-smarter-dutp.cwl

Branch/Commit ID: 9e3c3e65c19873cd1ed3cf7cc3b94ebc75ae0cc5

https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git

Path: workflows/emg-pipeline-v3.cwl

Branch/Commit ID: 583307878ab83c5845c897f03db920ae8e1929e2

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

Path: v1.0/v1.0/io-int-optional-wf.cwl

Branch/Commit ID: a5ae5ad0c9017ed625fb372f65e72dbb069439b0

https://github.com/ncbi/cwl-demos.git

Path: blast-pipelines/simple_three_step.cwl

Branch/Commit ID: deb45393512c8eb82de1adec82982b439933d7cd