Explore Workflows

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

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

Branch/Commit ID: 50251ef931d108c09bed2d330d3d4fe9c562b1c3

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

Path: subworkflows/xenbase-sra-to-fastq-pe.cwl

Branch/Commit ID: 00ced0fc44ceeb3495e891232e1000235e56ee6b

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/subworkflows/indexing_bed.cwl

Branch/Commit ID: b62c7bfcf5eb7ac3c1ed06879200fdf5db947e4b

Outputs a message using echo

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

Path: workflows/hello/hello.cwl

Branch/Commit ID: 767d700e602805112a4c953d166e570cddfa2605

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

Path: tests/scatter-wf2.cwl

Branch/Commit ID: 5f27e234b4ca88ed1280dedf9e3391a01de12912

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: 91bb63948c0a264334b9007ef85f936768d90d11

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

Path: tests/count-lines11-extra-step-wf-noET.cwl

Branch/Commit ID: 50251ef931d108c09bed2d330d3d4fe9c562b1c3

https://github.com/cr-ste-justine/chujs-alignment-workflow.git

Path: workflows/wesp2.cwl

Branch/Commit ID: 682ec407000059b7f397e5faaeff1317af1d9402

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: c602e3cdd72ff904dd54d46ba2b5146eb1c57022

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

Path: tests/import_schema-def.cwl

Branch/Commit ID: 5f27e234b4ca88ed1280dedf9e3391a01de12912