Explore Workflows

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Graph Name Retrieved From View
workflow graph final_filtering

Final filtering

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

Path: structuralvariants/cwl/subworkflows/final_filtering.cwl

Branch/Commit ID: 94bcf49c6f22055a359336d2e593f8289f1c5e48
workflow graph trim-rnaseq-se.cwl

Runs RNA-Seq BioWardrobe basic analysis with single-end data file.

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

Path: workflows/trim-rnaseq-se.cwl

Branch/Commit ID: cf107bc24a37883ef01b959fd89c19456aaecc02
workflow graph cnv_exomedepth

CNV ExomeDepth calling

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

Path: structuralvariants/cwl/subworkflows/cnv_exome_depth.cwl

Branch/Commit ID: 94bcf49c6f22055a359336d2e593f8289f1c5e48
workflow graph cnv_codex

CNV CODEX calling

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

Path: structuralvariants/cwl/subworkflows/cnv_codex.cwl

Branch/Commit ID: 94bcf49c6f22055a359336d2e593f8289f1c5e48
workflow graph count-lines6-wf.cwl

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

Path: tests/count-lines6-wf.cwl

Branch/Commit ID: 5f27e234b4ca88ed1280dedf9e3391a01de12912
workflow graph count-lines11-null-step-wf-noET.cwl

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

Path: tests/count-lines11-null-step-wf-noET.cwl

Branch/Commit ID: 5f27e234b4ca88ed1280dedf9e3391a01de12912
workflow graph Xenbase ChIP-Seq pipeline paired-end

1. Convert input SRA file into pair of upsrtream and downstream FASTQ files (run fastq-dump) 2. Analyze quality of FASTQ files (run fastqc with each of the FASTQ files) 3. If any of the following fields in fastqc generated report is marked as failed for at least one of input FASTQ files: \"Per base sequence quality\", \"Per sequence quality scores\", \"Overrepresented sequences\", \"Adapter Content\", - trim adapters (run trimmomatic) 4. Align original or trimmed FASTQ files 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-pe.cwl

Branch/Commit ID: bfa3843bcf36125ff258d6314f64b41336f06e6b
workflow graph scatter-valuefrom-inputs-wf1.cwl

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

Path: v1.0/v1.0/scatter-valuefrom-inputs-wf1.cwl

Branch/Commit ID: 1f501e38ff692a408e16b246ac7d64d32f0822c2
workflow graph trimmed_fastq

Quality Control (raw data), Raw Data trimming and Quality Control (pre-processed)

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

Path: structuralvariants/cwl/subworkflows/trimmed_fastq.cwl

Branch/Commit ID: 94bcf49c6f22055a359336d2e593f8289f1c5e48
workflow graph io-file-default-wf.cwl

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

Path: v1.0/v1.0/io-file-default-wf.cwl

Branch/Commit ID: 1f501e38ff692a408e16b246ac7d64d32f0822c2