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Graph Name Retrieved From View
workflow graph Feature expression merge - combines feature expression from several experiments

Feature expression merge - combines feature expression from several experiments ========================================================================= Workflows merges RPKM (by default) gene expression from several experiments based on the values from GeneId, Chrom, TxStart, TxEnd and Strand columns (by default). Reported unique columns are renamed based on the experiments names.

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

Path: workflows/feature-merge.cwl

Branch/Commit ID: 57863b6131d8262c5ce864adaf8e4038401e71a2
workflow graph wgs alignment with qc

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

Path: definitions/pipelines/alignment_wgs.cwl

Branch/Commit ID: adcae308fdccaa1190083616118dfadb4df65dca
workflow graph Seed Protein Alignments

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

Path: protein_alignment/wf_seed_seqids.cwl

Branch/Commit ID: cb15f907132fb90bc66b39bb0af3c211801feba1
workflow graph cnv_manta

CNV Manta calling

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

Path: structuralvariants/subworkflows/cnv_manta.cwl

Branch/Commit ID: 86f2f3fb64e916607637d93cf6715bab90b1f1d3
workflow graph trnascan_wnode and gpx_qdump combined

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

Path: bacterial_trna/wf_scan_and_dump.cwl

Branch/Commit ID: cb15f907132fb90bc66b39bb0af3c211801feba1
workflow graph Varscan Workflow

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

Path: definitions/subworkflows/varscan_germline.cwl

Branch/Commit ID: 60edaf6f57eaaf02cda1a3d8cb9a825aa64a43e2
workflow graph scatter-valuefrom-wf1.cwl

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf1.cwl

Branch/Commit ID: 4700fbee9a5a3271eef8bc9ee595619d0720431b
workflow graph Filter Protein Seeds I; Find ProSplign Alignments I

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

Path: protein_alignment/wf_compart_filter_prosplign.cwl

Branch/Commit ID: e81df43c40bc6849ece095a05cb0247dc53b94b1
workflow graph kfdrc_alignment_wf.cwl

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

Path: workflows/kfdrc_alignment_wf.cwl

Branch/Commit ID: e75f0c96153a484db1f882f6ff2a9764519a3179
workflow graph Trim Galore SMARTer RNA-Seq pipeline paired-end strand specific

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: 57863b6131d8262c5ce864adaf8e4038401e71a2