Explore Workflows

rna / protein - qc, preprocess, filter, annotation, index, abundance

https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/wgs-noscreen-fastq.workflow.cwl

Branch/Commit ID: 6a8727124baf77416ca797982fd4e0689c2a593a

CNV CODEX2 calling

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

Path: structuralvariants/subworkflows/cnv_codex.cwl

Branch/Commit ID: 86f2f3fb64e916607637d93cf6715bab90b1f1d3

1. Convert input SRA file into FASTQ file (run fastq-dump) 2. Analyze quality of FASTQ file (run fastqc) 3. If any of the following fields in fastqc generated report is marked as failed: \"Per base sequence quality\", \"Per sequence quality scores\", \"Overrepresented sequences\", \"Adapter Content\", - trim adapters (run trimmomatic) 4. Align original or trimmed FASTQ file to reference genome (run Bowtie2) 5. Sort and index generated by Bowtie2 BAM file (run samtools sort, samtools index) 6. Remove duplicates in sorted BAM file (run picard) 7. Sort and index BAM file after duplicates removing (run samtools sort, samtools index) 8. Count mapped reads number in sorted BAM file (run bamtools stats) 9. Generate genome coverage BED file (run bedtools genomecov) 10. Sort genearted BED file (run sort) 11. Generate genome coverage bigWig file from BED file (run bedGraphToBigWig)

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

Path: workflows/xenbase-chipseq-se.cwl

Branch/Commit ID: dda9e6e06a656b7b3fa7504156474b962fe3953c

Genomic regions intersection and visualization ============================================== 1. Merges intervals within each of the filtered peaks files from ChIP/ATAC experiments 2. Overlaps merged intervals and assigns the nearest genes to them

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

Path: workflows/intervene.cwl

Branch/Commit ID: 261c0232a7a40880f2480b811ed2d7e89c463869

Generates tag density heatmap and histogram for the centered list of features in a headerless regions file. - If provided regions file is a gene list with the following columns `chrom start end name score strand` set `Gene TSS` as a re-centering criteria. - If provided regions file is a peak list with the following columns `chrom start end name` set `Peak Center` as a re-centering criteria. `score` column is always ignored.

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

Path: workflows/heatmap.cwl

Branch/Commit ID: 261c0232a7a40880f2480b811ed2d7e89c463869

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

Path: definitions/pipelines/cle_aml_trio.cwl

Branch/Commit ID: 4bc0a4577d626b65a4b44683e5a1ab2f7d7faf4c

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

Path: tests/wf/mut.cwl

Branch/Commit ID: 280a852e74aec08cf79687e8004e17b1ab464534

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/datirium/workflows.git

Path: tools/heatmap-prepare.cwl

Branch/Commit ID: 42dc4f70b117e78785b82865ec4c4b941ac1c259

https://github.com/NAL-i5K/Organism_Onboarding.git

Path: MoveData-workflow.cwl

Branch/Commit ID: 096a9feffe292a1aeb329552661d27bb579e084c

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

Path: tests/wf/nested.cwl

Branch/Commit ID: b82ce7ae901a54c7a062fd5eefd8d5ceb5a4d684