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Graph Name Retrieved From View
workflow graph dragen-germline-pipeline__4.2.4.cwl

https://github.com/umccr/cwl-ica.git

Path: workflows/dragen-germline-pipeline/4.2.4/dragen-germline-pipeline__4.2.4.cwl

Branch/Commit ID: d6974d10bb47406f8a5f1718301fe27efb5618ec
workflow graph Deprecated. Single-Cell Preprocessing Pipeline

Devel version of Single-Cell Preprocessing Pipeline ===================================================

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

Path: workflows/single-cell-preprocess.cwl

Branch/Commit ID: fa4f172486288a1a9d23864f1d6962d85a453e16
workflow graph count-lines3-wf.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/count-lines3-wf.cwl

Branch/Commit ID: 7d7986a6e852ca6e3239c96d3a05dd536c76c903
workflow graph Set Operations for Called Peaks (ChIP/ATAC/C&R/diffbind)

# Set Operations for Peaks This workflow takes as input multiple peak list TSV files (the `iaintersect_result.tsv` output under the \"Files\" output tab) from the ChIP, ATAC, C&R, or diffbind workflows and performs the user-selected set operation on the group. Set operations include intersection, union, difference, and complement. See the tooltip for the `set_operator` input for more details.

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

Path: workflows/filter-peaks-by-overlap.cwl

Branch/Commit ID: fa4f172486288a1a9d23864f1d6962d85a453e16
workflow graph Single-Cell ATAC-Seq Genome Coverage

Single-Cell ATAC-Seq Genome Coverage Generates genome coverage tracks from chromatin accessibility data of selected cells

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

Path: workflows/sc-atac-coverage.cwl

Branch/Commit ID: fa4f172486288a1a9d23864f1d6962d85a453e16
workflow graph record-output-wf_v1_0.cwl

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

Path: testdata/record-output-wf_v1_0.cwl

Branch/Commit ID: 8058c7477097f90205dd7d8481781eb3737ea9c9
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: fa4f172486288a1a9d23864f1d6962d85a453e16
workflow graph Kraken2 Metagenomic pipeline paired-end

This workflow taxonomically classifies paired-end sequencing reads in FASTQ format, that have been optionally adapter trimmed with trimgalore, using Kraken2 and a user-selected pre-built database from a list of [genomic index files](https://benlangmead.github.io/aws-indexes/k2). ### __Inputs__ Kraken2 database for taxonomic classification: - [Viral (0.5 GB)](https://genome-idx.s3.amazonaws.com/kraken/k2_viral_20221209.tar.gz), all refseq viral genomes - [MinusB (8.7 GB)](https://genome-idx.s3.amazonaws.com/kraken/k2_minusb_20221209.tar.gz), standard minus bacteria (archaea, viral, plasmid, human1, UniVec_Core) - [PlusPFP-16 (15.0 GB)](https://genome-idx.s3.amazonaws.com/kraken/k2_pluspfp_16gb_20221209.tar.gz), standard (archaea, bacteria, viral, plasmid, human1, UniVec_Core) + (protozoa, fungi & plant) capped at 16 GB (shrunk via random kmer downselect) - [EuPathDB46 (34.1 GB)](https://genome-idx.s3.amazonaws.com/kraken/k2_eupathdb48_20201113.tar.gz), eukaryotic pathogen genomes with contaminants removed (https://veupathdb.org/veupathdb/app) - [16S_gg_13_5 (73 MB)](https://genome-idx.s3.amazonaws.com/kraken/16S_Greengenes13.5_20200326.tgz), Greengenes 16S rRNA database ([release 13.5](https://greengenes.secondgenome.com/?prefix=downloads/greengenes_database/gg_13_5/), 20200326)\n - [16S_silva_138 (112 MB)](https://genome-idx.s3.amazonaws.com/kraken/16S_Silva138_20200326.tgz), SILVA 16S rRNA database ([release 138.1](https://www.arb-silva.de/documentation/release-1381/), 20200827) Read 1 file: - FASTA/Q input R1 from a paired end library Read 2 file: - FASTA/Q input R2 from a paired end library Number of threads for steps that support multithreading: - Number of threads for steps that support multithreading - default set to `4` Advanced Inputs Tab (Optional): - Number of bases to clip from the 3p end - Number of bases to clip from the 5p end ### __Outputs__ - k2db, an upstream database used by kraken2 classifier ### __Data Analysis Steps__ 1. Trimming the adapters with TrimGalore. - This step is particularly important when the reads are long and the fragments are short - resulting in sequencing adapters at the ends of reads. If adapter is not removed the read will not map. TrimGalore can recognize standard adapters, such as Illumina or Nextera/Tn5 adapters. 2. Generate quality control statistics of trimmed, unmapped sequence data 3. (Optional) Clipping of 5' and/or 3' end by the specified number of bases. 4. Mapping reads to primary genome index with Bowtie. ### __References__ - Wood, D.E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol 20, 257 (2019). https://doi.org/10.1186/s13059-019-1891-0

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

Path: workflows/kraken2-classify-pe.cwl

Branch/Commit ID: fa4f172486288a1a9d23864f1d6962d85a453e16
workflow graph Deprecated. RNA-Seq pipeline single-read

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **single-read** 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-read RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 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) 5. Generate BigWig file on the base of sorted BAM file 6. Map input FASTQ file 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/rnaseq-se.cwl

Branch/Commit ID: fa4f172486288a1a9d23864f1d6962d85a453e16
workflow graph count-lines7-single-source-wf_v1_2.cwl

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

Path: testdata/count-lines7-single-source-wf_v1_2.cwl

Branch/Commit ID: 8058c7477097f90205dd7d8481781eb3737ea9c9