Explore Workflows

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: 7ae3b75bbe614e59cdeaba06047234a6c40c0fe9

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

Path: cwltool/schemas/v1.0/v1.0/count-lines1-wf.cwl

Branch/Commit ID: 280a852e74aec08cf79687e8004e17b1ab464534

https://github.com/li-xinshan/data_visualization.git

Path: sbg_cwl/sbg_cwl_test.cwl

Branch/Commit ID: dev

CNV ExomeDepth calling

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

Path: structuralvariants/cwl/subworkflows/cnv_exome_depth.cwl

Branch/Commit ID: 572d9e6b9264d98967b33d18110b0e1979b21d6c

Single-cell Assign Cell Types ============================= Assigns cell types to Seurat clusters.

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

Path: workflows/sc-assign-cell-types.cwl

Branch/Commit ID: 7ae3b75bbe614e59cdeaba06047234a6c40c0fe9

This workflow is intended to be used to test the QC module, without having to run the long waltz step

https://github.com/mskcc/ACCESS-Pipeline.git

Path: workflows/QC/qc_workflow_wo_waltz.cwl

Branch/Commit ID: bccb338be356db83ad178be2aa9634ae86cb5211

https://github.com/mskcc/ACCESS-Pipeline.git

Path: workflows/waltz/waltz_workflow_all_bams.cwl

Branch/Commit ID: bccb338be356db83ad178be2aa9634ae86cb5211

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: c0ca7b140d776eec223ceb1c620eda17281860c4

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

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

Branch/Commit ID: 89ccbfc53ff3bb6abe2eb90bb7e0091c54c18f5c

Packed ID: main

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

Path: tests/wf-loadContents4.cwl

Branch/Commit ID: 368b562a1449e8cd39ae8b7f05926b2bfb9b22df