Explore Workflows

View already parsed workflows here or click here to add your own

Graph	Name	Retrieved From	View
	FASTQ to BQSR	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/fastq_to_bqsr.cwl Branch/Commit ID: cc3e7f1ccfdc7101c22bf88792608504eea7d53a
	bwa-alignment.cwl	https://github.com/ncbi/cwl-ngs-workflows-cbb.git Path: workflows/Alignments/bwa-alignment.cwl Branch/Commit ID: 0e21d424267367d9dae7b980438ddee14c31a445
	exome alignment and germline variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/germline_exome.cwl Branch/Commit ID: 7638b3075863ae8172f4adaec82fb2eb8e80d3d5
	salmon_wf_pe.cwl	https://github.com/pitagora-network/pitagora-cwl.git Path: workflows/salmon/paired_end/salmon_wf_pe.cwl Branch/Commit ID: f85f2cd5d888ed947f47a391eb32dcb53265f9b3
	salmon_wf_se.cwl	https://github.com/pitagora-network/pitagora-cwl.git Path: workflows/salmon/single_end/salmon_wf_se.cwl Branch/Commit ID: f85f2cd5d888ed947f47a391eb32dcb53265f9b3
	format_rrnas_from_seq_entry	https://github.com/ncbi/pgap.git Path: task_types/tt_format_rrnas_from_seq_entry.cwl Branch/Commit ID: 6ac47e5703d8c8cdac698de91143829b3911e9b2
	bam to trimmed fastqs and HISAT alignments	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl Branch/Commit ID: 7638b3075863ae8172f4adaec82fb2eb8e80d3d5
	Build Bowtie indices Workflow runs [Bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) to build indices for reference genome provided in a single FASTA file as fasta_file input. Generated indices are saved in a folder with the name that corresponds to the input genome	https://github.com/datirium/workflows.git Path: workflows/bowtie-index.cwl Branch/Commit ID: 581156366f91861bd4dbb5bcb59f67d468b32af3
	03-map-se-blacklist-removal.cwl ATAC-seq 03 mapping - reads: SE - blacklist removal	https://github.com/Duke-GCB/GGR-cwl.git Path: v1.0/ATAC-seq_pipeline/03-map-se-blacklist-removal.cwl Branch/Commit ID: 8aabde14169421a7115c5cd48c4740b3a7bd818f
	Bismark Methylation - pipeline for BS-Seq data analysis Sequence reads are first cleaned from adapters and transformed into fully bisulfite-converted forward (C->T) and reverse read (G->A conversion of the forward strand) versions, before they are aligned to similarly converted versions of the genome (also C->T and G->A converted). Sequence reads that produce a unique best alignment from the four alignment processes against the bisulfite genomes (which are running in parallel) are then compared to the normal genomic sequence and the methylation state of all cytosine positions in the read is inferred. A read is considered to align uniquely if an alignment has a unique best alignment score (as reported by the AS:i field). If a read produces several alignments with the same number of mismatches or with the same alignment score (AS:i field), a read (or a read-pair) is discarded altogether. On the next step we extract the methylation call for every single C analysed. The position of every single C will be written out to a new output file, depending on its context (CpG, CHG or CHH), whereby methylated Cs will be labelled as forward reads (+), non-methylated Cs as reverse reads (-). The output of the methylation extractor is then transformed into a bedGraph and coverage file. The bedGraph counts output is then used to generate a genome-wide cytosine report which reports the number on every single CpG (optionally every single cytosine) in the genome, irrespective of whether it was covered by any reads or not. As this type of report is informative for cytosines on both strands the output may be fairly large (~46mn CpG positions or >1.2bn total cytosine positions in the human genome).	https://github.com/datirium/workflows.git Path: workflows/bismark-methylation-se.cwl Branch/Commit ID: 581156366f91861bd4dbb5bcb59f67d468b32af3