Explore Workflows

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: 93b844a80f4008cc973ea9b5efedaff32a343895

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

Path: definitions/subworkflows/molecular_alignment.cwl

Branch/Commit ID: 4bc0a4577d626b65a4b44683e5a1ab2f7d7faf4c

Pairwise comparison

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

Path: task_types/tt_kmer_compare_wnode.cwl

Branch/Commit ID: cd97086739ae5988bab09b05e9259675c4b6bce6

Set light guide efficiency as function of wavelength and incident angle.

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

Path: workflows/SetLightGuideEfficiency.cwl

Branch/Commit ID: 789752af87eb190387ff2acb4c95c7a5cdb961e7

https://github.com/kids-first/kf-dev-single-cell-rna.git

Path: workflows/kf_STAR_Solo_10x_alignment_wf.cwl

Branch/Commit ID: 8c1d2315ad46fe0a30bf618e108e55b0263c7c6d

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

Path: testdata/workflow_input_sf_expr_array.cwl

Branch/Commit ID: b76b039edb62dea76c43f173848cdc57e4b4aab7

Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow.

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

Path: tools/bam-bedgraph-bigwig.cwl

Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f

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

Path: testdata/workflow_input_sf_expr_array_v1_1.cwl

Branch/Commit ID: b76b039edb62dea76c43f173848cdc57e4b4aab7

https://github.com/kids-first/kf-alignment-workflow.git

Path: workflows/kfdrc_sentieon_alignment_wf.cwl

Branch/Commit ID: 0e35fb09e15a7a6af52d9906111136a961b2c488

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

Path: tests/wf/count-lines1-wf.cwl

Branch/Commit ID: 63f539ba60e91f0cb3ce7cda2c5da5c65525c375