Explore Workflows

Workflow runs group-isoforms.cwl tool using scatter for isoforms_file input. genes_filename and common_tss_filename inputs are ignored.

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

Path: tools/group-isoforms-batch.cwl

Branch/Commit ID: ce058d892d330125cd03d0a0d5fb3b321cda0be3

https://github.com/hubmapconsortium/hra-workflows.git

Path: steps/run-one.cwl

Branch/Commit ID: f44151f2eae461c916916cc3e323ad909c3900c6

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf2.cwl

Branch/Commit ID: e9c83739a93fa0b18f8dea2f98b632a9e32725c9

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

Path: cwltool/schemas/v1.0/v1.0/count-lines13-wf.cwl

Branch/Commit ID: e9c83739a93fa0b18f8dea2f98b632a9e32725c9

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

Path: definitions/subworkflows/bam_readcount.cwl

Branch/Commit ID: 24e5290aec441665c6976ee3ee8ae3574c49c6b5

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

Path: cwltool/schemas/v1.0/v1.0/echo-wf-default.cwl

Branch/Commit ID: ae401a813472ca453a99ad067a5e6fc3bd71112b

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.cwl

Branch/Commit ID: ce058d892d330125cd03d0a0d5fb3b321cda0be3

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

Path: definitions/subworkflows/pindel_region.cwl

Branch/Commit ID: a9133c999502acf94b433af8d39897e6c2cdf65f

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

Path: definitions/subworkflows/filter_vcf.cwl

Branch/Commit ID: a670f323e77e02d9b77be9a13d73d5276dd3676c

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

Path: task_types/tt_checkm_wnode.cwl

Branch/Commit ID: 8ea3637b0f11eac1ea5599c41d74e00d85fb778d