Workflow: RNA-Seq alignment and transcript/gene abundance workflow
Fetched 2023-01-04 16:54:05 GMT
Verified with cwltool version 3.1.20221201130942
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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 | |||
| refFlat | File | ||
| species | String |
the species being analyzed, such as homo_sapiens or mus_musculus |
|
| assembly | String |
the assembly used, such as GRCh37/38, GRCm37/38 |
|
| reference | File | ||
| sample_name | String | ||
| read_group_id | String[] | ||
| kallisto_index | File | ||
| reference_index | File | ||
| read_group_fields | 090146663104ff800e7d6c6245cd81e6[] | ||
| trimming_adapters | File | ||
| ribosomal_intervals | File (Optional) | ||
| 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 |
../tools/merge_bams.cwl
(CommandLineTool)
|
Sambamba: merge | |
| kallisto |
../tools/kallisto.cwl
(CommandLineTool)
|
Kallisto: Quant | |
| mark_dup |
../tools/mark_duplicates_and_sort.cwl
(CommandLineTool)
|
Mark duplicates and Sort | |
| index_bam |
../tools/index_bam.cwl
(CommandLineTool)
|
samtools index | |
| stringtie |
../tools/stringtie.cwl
(CommandLineTool)
|
StringTie | |
| transcript_to_gene |
../tools/transcript_to_gene.cwl
(CommandLineTool)
|
Kallisto: TranscriptToGene | |
| generate_qc_metrics |
../tools/generate_qc_metrics.cwl
(CommandLineTool)
|
Picard: RNA Seq Metrics | |
| cgpbigwig_bamcoverage |
../tools/bam_to_bigwig.cwl
(CommandLineTool)
|
cgpBigWig Converting BAM to BigWig | |
| bam_to_trimmed_fastq_and_hisat_alignments | bam to trimmed fastqs and HISAT alignments |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| chart | File (Optional) | ||
| metrics | File | ||
| final_bam | File | ||
| gene_abundance | File | ||
| fusion_evidence | File | ||
| bamcoverage_bigwig | 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/97572e3a088d79f6a4166385f79e79ea77b11470/definitions/pipelines/rnaseq.cwl
