Explore Workflows

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Graph	Name	Retrieved From	View
	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: 22fce2dbdada0c4135b6f0677f78535cf980cb07
	Varscan Workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/varscan_pre_and_post_processing.cwl Branch/Commit ID: efbbe5ed51f6ac583e87a348785c72818a33f56e
	chemprodev.cwl Workflow for the synthesis and purification of 5-methoxytryptamine, based on a series of chemical reactions, extractions, filtrations, and other unit operations.	https://github.com/pascmont/cwltest.git Path: chemprodev.cwl Branch/Commit ID: e56456381c2588e3933d91b47c47b7e61023683b
	Prepare user input Prepare user input for NCBI-PGAP pipeline	https://github.com/ncbi/pgap.git Path: prepare_user_input2.cwl Branch/Commit ID: 4ffbad9ffeab15ec8af5f6f91bd352ef96d1ef77
	1st-workflow.cwl	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/1st-workflow.cwl Branch/Commit ID: 6d8c2a41e2c524e8d746020cc91711ecc3418a23
	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: efbbe5ed51f6ac583e87a348785c72818a33f56e
	umi molecular alignment workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/molecular_alignment.cwl Branch/Commit ID: dc2c019c1aa24cc01b451a0f048cf94a35f163c4
	Unaligned BAM to BQSR and VCF	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/bam_to_bqsr_no_dup_marking.cwl Branch/Commit ID: 8cee1920920ed73384fb3ab74272da9c92a20cf2
	downsample unaligned BAM and align	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/downsampled_alignment.cwl Branch/Commit ID: d297528e53b6c1ecb69b1ab27b8e03323b4463ad
	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: dda6e8b5ada3f106a2b3bfcc1b151eccf9977726