Explore Workflows

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: 46d3d403ddb240d5a8f4f31ab992b6d6a2686745

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: 46d3d403ddb240d5a8f4f31ab992b6d6a2686745

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

Path: workflow/rmats_wf.cwl

Branch/Commit ID: 3fd55a819cda2a1fc48957b5daa2bebdaee843fb

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

Path: task_types/tt_taxonomy_check_16S.cwl

Branch/Commit ID: ce433f771ebf5677c9f40858e2ae91b1a7e75d30

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

Path: task_types/tt_gcaccess_from_list.cwl

Branch/Commit ID: 8ea3637b0f11eac1ea5599c41d74e00d85fb778d

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

Path: definitions/subworkflows/qc_wgs.cwl

Branch/Commit ID: ec45fad68ca10fb64d5c58e704991b146dc31d28

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

Path: bacterial_kmer/wf_bacterial_kmer.cwl

Branch/Commit ID: 2afb5ebafd1353ba063cc74ee9a7eaf347afce5c

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

Path: workflows/kfdrc-gatk-haplotypecaller-wf.cwl

Branch/Commit ID: 9fc3770230e1bd8495f5e6a18665bd21e7c6fafd

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

Path: pipeline.cwl

Branch/Commit ID: f44151f2eae461c916916cc3e323ad909c3900c6

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

Path: testdata/workflow_input_sf_expr_v1_2.cwl

Branch/Commit ID: c1875d54dedc41b1d2fa08634dcf1caa8f1bc631