61 lines
1.3 KiB
YAML
Executable File
61 lines
1.3 KiB
YAML
Executable File
name: rnaseq-quant
|
|
version: 1.0.0
|
|
description: RNA-seq Quantification - Gene expression quantification using StringTie and featureCounts
|
|
author: xialab
|
|
domain: rna-seq
|
|
stage: rnaseq_quant
|
|
|
|
environment:
|
|
conda: rnaseq
|
|
python: "3.11"
|
|
|
|
dependencies:
|
|
- stringtie >= 2.2.0
|
|
- subread >= 2.0.0 # featureCounts
|
|
|
|
inputs:
|
|
- name: bam_files
|
|
type: bam
|
|
description: Sorted BAM files from RNA-seq Align stage
|
|
required: true
|
|
- name: gtf
|
|
type: gtf
|
|
description: Reference genome GTF annotation
|
|
required: true
|
|
- name: sample_config
|
|
type: yaml
|
|
description: Sample configuration file with explicit library_strandness
|
|
required: true
|
|
|
|
outputs:
|
|
- name: count_matrix
|
|
type: tsv
|
|
description: Gene count matrix
|
|
- name: fpkm_matrix
|
|
type: tsv
|
|
description: FPKM expression matrix
|
|
- name: tpm_matrix
|
|
type: tsv
|
|
description: TPM expression matrix
|
|
- name: stringtie_gtf
|
|
type: gtf
|
|
description: StringTie assembled transcripts
|
|
- name: report
|
|
type: markdown
|
|
description: Quantification summary report
|
|
- name: manifest
|
|
type: json
|
|
description: Analysis manifest
|
|
|
|
metrics:
|
|
- total_genes
|
|
- total_transcripts
|
|
- expressed_genes
|
|
- samples_processed
|
|
|
|
parameters:
|
|
- name: cpu
|
|
type: int
|
|
default: 4
|
|
description: Number of CPU threads
|