Explore Workflows
View already parsed workflows here or click here to add your own
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Trim Galore RNA-Seq pipeline paired-end strand specific
Modified original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **pair-end** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the single-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 4. Use 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 files 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/trim-rnaseq-pe-dutp.cwl Branch/Commit ID: c6bfa0de917efb536dd385624fc7702e6748e61d |
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Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/pvacseq.cwl Branch/Commit ID: 0c4f4e59c265eb22aed3d2d37b173cb5430773d2 |
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THOR - differential peak calling of ChIP-seq signals with replicates
What is THOR? -------------- THOR is an HMM-based approach to detect and analyze differential peaks in two sets of ChIP-seq data from distinct biological conditions with replicates. THOR performs genomic signal processing, peak calling and p-value calculation in an integrated framework. For more information please refer to: ------------------------------------- Allhoff, M., Sere K., Freitas, J., Zenke, M., Costa, I.G. (2016), Differential Peak Calling of ChIP-seq Signals with Replicates with THOR, Nucleic Acids Research, epub gkw680. |
https://github.com/datirium/workflows.git
Path: workflows/rgt-thor.cwl Branch/Commit ID: 00ea05e22788029370898fd4c17798b11edf0e57 |
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RNA-Seq pipeline paired-end strand specific
The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **paired-end** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 3. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. 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-pe-dutp.cwl Branch/Commit ID: 12e5256de1b680c551c87fd5db6f3bc65428af67 |
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align_merge_sas
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https://github.com/ncbi/pgap.git
Path: task_types/tt_align_merge_sas.cwl Branch/Commit ID: b4a6e46405c08e0b14ad92f0ab38bcc4a69caa5c |
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Pairwise genomic regions intersection
Pairwise genomic regions intersection ============================================= Overlaps peaks from two ChIP/ATAC experiments |
https://github.com/datirium/workflows.git
Path: workflows/peak-intersect.cwl Branch/Commit ID: cc6fa135d04737fdde3b4414d6e214cf8c812f6e |
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count-lines7-wf.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/count-lines7-wf.cwl Branch/Commit ID: 09323506da219ba3ddb5313bd83022b52cac9adc |
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Nested workflow example
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https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/nested.cwl Branch/Commit ID: 875b928ce50a3202f5954843b79ea86683c160fa |
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bam-bedgraph-bigwig.cwl
Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow. |
https://github.com/datirium/workflows.git
Path: tools/bam-bedgraph-bigwig.cwl Branch/Commit ID: 64f7fe4438898218fd83133efa25251078f5b27e |
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echo-wf-default.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/echo-wf-default.cwl Branch/Commit ID: 09323506da219ba3ddb5313bd83022b52cac9adc |
