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04-quantification-se-unstranded.cwl
RNA-seq 04 quantification |
![]() Path: v1.0/RNA-seq_pipeline/04-quantification-se-unstranded.cwl Branch/Commit ID: 13826f526a99e151e9cf5f22e70bdcf4feea73f4 |
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Xenbase RNA-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, calculate genes and isoforms expression (run RSEM) 5. Count mapped reads number in sorted BAM file (run bamtools stats) 6. Generate genome coverage BED file (run bedtools genomecov) 7. Sort genearted BED file (run sort) 8. Generate genome coverage bigWig file from BED file (run bedGraphToBigWig) |
![]() Path: workflows/xenbase-rnaseq-pe.cwl Branch/Commit ID: b141f7e73005227d6d02fa03a47151836dd4109b |
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hisat2-stringtie_wf_se.cwl
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![]() Path: workflows/hisat2-stringtie/single_end/hisat2-stringtie_wf_se.cwl Branch/Commit ID: 3affcd5588e273779b8b4084839ed0582ba2ea18 |
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scatter-valuefrom-wf1.cwl
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![]() Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf1.cwl Branch/Commit ID: 4c905b830371eee45188a53510ba0ee9113fd4c8 |
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bam-bedgraph-bigwig.cwl
Workflow converts input BAM file into bigWig and bedGraph files |
![]() Path: subworkflows/bam-bedgraph-bigwig.cwl Branch/Commit ID: 02ffbbd7eb8e06bfb759edea440f78bdc8bb2631 |
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count-lines13-wf.cwl
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![]() Path: cwltool/schemas/v1.0/v1.0/count-lines13-wf.cwl Branch/Commit ID: 4a5fe26e32d244d95f9483c3edfc3df04f3e5f7b |
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04-quantification-pe-unstranded.cwl
RNA-seq 04 quantification |
![]() Path: v1.0/RNA-seq_pipeline/04-quantification-pe-unstranded.cwl Branch/Commit ID: 13826f526a99e151e9cf5f22e70bdcf4feea73f4 |
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Add snv and indel bam-readcount files to a vcf
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![]() Path: definitions/subworkflows/vcf_readcount_annotator.cwl Branch/Commit ID: 5f120e5bc3c0f75bfbc636ea2c6f4393f5d45ca1 |
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hisat2-cufflinks_wf_se.cwl
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![]() Path: workflows/hisat2-cufflinks/single_end/hisat2-cufflinks_wf_se.cwl Branch/Commit ID: 3affcd5588e273779b8b4084839ed0582ba2ea18 |
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hisat2-stringtie_wf_pe.cwl
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![]() Path: workflows/hisat2-stringtie/paired_end/hisat2-stringtie_wf_pe.cwl Branch/Commit ID: 3affcd5588e273779b8b4084839ed0582ba2ea18 |