Workflow: RNA-Seq alignment and transcript/gene abundance workflow
Fetched 2024-04-26 17:43:27 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
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- Default Values
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| strand | String | ||
| refFlat | File | ||
| firststrand | Boolean (Optional) | ||
| sample_name | String | ||
| secondstrand | Boolean (Optional) | ||
| read_group_id | String[] | ||
| kallisto_index | File | ||
| reference_index | File | ||
| read_group_fields | 24ec33a3b66b04e67ea5ad894535da2c[] | ||
| trimming_adapters | File | ||
| ribosomal_intervals | File | ||
| instrument_data_bams | File[] | ||
| reference_annotation | File | ||
| trimming_max_uncalled | Integer | ||
| trimming_min_readlength | Integer | ||
| trimming_adapter_trim_end | String | ||
| gene_transcript_lookup_table | File | ||
| trimming_adapter_min_overlap | Integer |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| merge |
merge.cwl
(CommandLineTool)
|
Sambamba: merge | |
| kallisto |
kallisto.cwl
(CommandLineTool)
|
Kallisto: Quant | |
| index_bam |
../detect_variants/index_bam.cwl
(CommandLineTool)
|
samtools index | |
| stringtie |
stringtie.cwl
(CommandLineTool)
|
StringTie | |
| transcript_to_gene |
transcript_to_gene.cwl
(CommandLineTool)
|
Kallisto: TranscriptToGene | |
| generate_qc_metrics |
generate_qc_metrics.cwl
(CommandLineTool)
|
Picard: RNA Seq Metrics | |
| bam_to_trimmed_fastq_and_hisat_alignments | bam to trimmed fastqs and HISAT alignments |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| chart | File | ||
| metrics | File | ||
| final_bam | File | ||
| gene_abundance | File | ||
| fusion_evidence | File | ||
| transcript_abundance_h5 | File | ||
| stringtie_transcript_gtf | File | ||
| transcript_abundance_tsv | File | ||
| stringtie_gene_expression_tsv | File |
Permalink:
https://w3id.org/cwl/view/git/d1ee6a2a323cee7e4af00c7e0b926c2192038e1d/rnaseq/workflow.cwl
