Explore Workflows

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Graph Name Retrieved From View
workflow graph bact_get_kmer_reference

https://github.com/ncbi/pgap.git

Path: task_types/tt_bact_get_kmer_reference.cwl

Branch/Commit ID: f10de890d1d2271299931349fa8aea660acef4ee
workflow graph RNA-Seq pipeline paired-end stranded mitochondrial

Slightly changed original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific pair-end** experiment. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with the pair-end strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `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 file 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/rnaseq-pe-dutp-mitochondrial.cwl

Branch/Commit ID: 730b40bc403263b724399a952c0f3e2d28f13519
workflow graph revsort-abstract.cwl

Reverse the lines in a document, then sort those lines.

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

Path: tests/revsort-abstract.cwl

Branch/Commit ID: a5073143db4155e05df8d2e7eb59d9e62acd65a5
workflow graph kmer_build_tree

https://github.com/ncbi/pgap.git

Path: task_types/tt_kmer_build_tree.cwl

Branch/Commit ID: cabb1a9a95244e93294727be8cf5816c38992cb0
workflow graph kmer_ref_compare_wnode

https://github.com/ncbi/pgap.git

Path: task_types/tt_kmer_ref_compare_wnode.cwl

Branch/Commit ID: 7b21dc40840852f3942c31b9c472346ea3f9a3ca
workflow graph tt_univec_wnode.cwl

https://github.com/ncbi/pgap.git

Path: task_types/tt_univec_wnode.cwl

Branch/Commit ID: 122aba2dafbb63241413c82b725b877c04523aaf
workflow graph count-lines2-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines2-wf.cwl

Branch/Commit ID: 7c7615c44b80f8e76e659433f8c7875603ae0b25
workflow graph Complete Mapping and Quality Control pipeline for Paired-end data

A workflow which: i) Runs Hisat2 on each fastq pair while generating the fastq files containing unmapped reads ii) Runs Bowtie2 using the --very-sensitive-local option, on the unmapped reads iii) A subworkflow is employed to prepare BAM files, corresponding to the unmapped-remaped reads, to be merged with the mapped reads form Hisat2 iv) After the merged BAMs are created, they are sorted and assigned a user defined name (according to samle identifier) v) Corresponding index file for each sample is generated. vi) At the same time it performs quality control over the FASTQ using fastqc and assembles the MultiQC report

https://github.com/mr-c/elixir-gr-project.git

Path: CWL/workflows/mapping-pe-qc.cwl

Branch/Commit ID: 6a1a6b9d5a152e783fe3f794ccce35387d02fd0d
workflow graph trim-rnaseq-se-dutp.cwl

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

https://github.com/Barski-lab/workflows.git

Path: workflows/trim-rnaseq-se-dutp.cwl

Branch/Commit ID: 812b0ff40dda18ab7a9a872ff13a577be8531ba6
workflow graph count-lines15-wf.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/count-lines15-wf.cwl

Branch/Commit ID: 0e37d46e793e72b7c16b5ec03e22cb3ce1f55ba3