Explore Workflows

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Graph	Name	Retrieved From	View
	allele-vcf-alignreads-se-pe.cwl Workflow maps FASTQ files from `fastq_files` input into reference genome `reference_star_indices_folder` and insilico generated `insilico_star_indices_folder` genome (concatenated genome for both `strain1` and `strain2` strains). For both genomes STAR is run with `outFilterMultimapNmax` parameter set to 1 to discard all of the multimapped reads. For insilico genome SAM file is generated. Then it's splitted into two SAM files based on strain names and then sorted by coordinates into the BAM format. For reference genome output BAM file from STAR slignment is also coordinate sorted.	https://github.com/datirium/workflows.git Path: subworkflows/allele-vcf-alignreads-se-pe.cwl Branch/Commit ID: ae2b231562822ed66b8e35e5452ae7f012416b2a
	wgs_variant_calling_bam.cwl	https://github.com/cr-ste-justine/chujs-alignment-workflow.git Path: workflows/wgs_variant_calling_bam.cwl Branch/Commit ID: 682ec407000059b7f397e5faaeff1317af1d9402
	heatmap-prepare.cwl Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs - bam_file - fragment_size - total_reads `dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job: 1) bam_file[0] fragment_size[0] total_reads[0] 2) bam_file[1] fragment_size[1] total_reads[1] ... N) bam_file[N] fragment_size[N] total_reads[N] `bam_file`, `fragment_size` and `total_reads` arrays should have the identical order.	https://github.com/Barski-lab/workflows.git Path: subworkflows/heatmap-prepare.cwl Branch/Commit ID: fb355eda4555a7e7182a91ce045212b0a087d73f
	default-wf5.cwl	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/default-wf5.cwl Branch/Commit ID: 03af16c9df2ee77485d4ab092cd64ae096d2e71c
	RNA-Seq pipeline single-read stranded mitochondrial Slightly changed original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) RNA-Seq basic analysis for strand specific single-read experiment. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with single-read strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `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-dutp-mitochondrial.cwl Branch/Commit ID: 91bb63948c0a264334b9007ef85f936768d90d11
	align_sort_sa	https://github.com/ncbi/pgap.git Path: task_types/tt_align_sort_sa.cwl Branch/Commit ID: b0ee40d34d233f1611c2e2c66b6d22a3b7deec05
	rnaseq-se-dutp-mitochondrial.cwl RNA-Seq strand specific mitochondrial workflow for single-read experiment based on BioWardrobe's basic analysis.	https://github.com/datirium/workflows.git Path: workflows/rnaseq-se-dutp-mitochondrial.cwl Branch/Commit ID: cf107bc24a37883ef01b959fd89c19456aaecc02
	Indices builder from GBOL RDF (TTL) Workflow to build different indices for different tools from a genome and transcriptome. This workflow expects an (annotated) genome in GBOL ttl format. Steps: - SAPP: rdf2gtf (genome fasta) - SAPP: rdf2fasta (transcripts fasta) - STAR index (Optional for Eukaryotic origin) - bowtie2 index - kallisto index	https://git.wur.nl/unlock/cwl.git Path: cwl/workflows/workflow_indexbuilder.cwl Branch/Commit ID: 60fafdfbec9b39c860945ef4634e0c28cb5e976c
	Quality assessment, amplicon classification Workflow for quality assessment of paired reads and classification using NGTax 2.0. In addition files are exported to their respective subfolders for easier data management in a later stage. Steps: - FastQC (read quality control) - NGTax 2.0 - Export module	https://git.wur.nl/unlock/cwl.git Path: cwl/workflows/workflow_ngtax.cwl Branch/Commit ID: 60fafdfbec9b39c860945ef4634e0c28cb5e976c
	facets	https://github.com/mskcc/roslin-variant.git Path: setup/cwl/facets.cwl Branch/Commit ID: e96613177b18b76c6fac98b945660bde65ebdd80