60 lines
1.2 KiB
YAML
Executable File
60 lines
1.2 KiB
YAML
Executable File
name: rnaseq-align
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version: 1.0.0
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description: RNA-seq Alignment - Map clean reads to reference genome using HISAT2
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author: xialab
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domain: rna-seq
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stage: rnaseq_align
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environment:
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conda: rnaseq
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python: "3.11"
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dependencies:
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- hisat2 >= 2.2.1
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- samtools >= 1.15
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inputs:
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- name: clean_reads
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type: fastq.gz
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description: Clean FASTQ files from RNA-seq QC stage
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required: true
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- name: hisat2_index
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type: ht2
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description: HISAT2 index files
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required: true
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- name: sample_config
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type: yaml
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description: Sample configuration file with explicit library_strandness
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required: true
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outputs:
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- name: sorted_bam
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type: bam
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description: Sorted BAM alignment files
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- name: bam_index
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type: bai
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description: BAM index files
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- name: alignment_log
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type: log
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description: HISAT2 alignment logs
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- name: report
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type: markdown
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description: Alignment summary report
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- name: manifest
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type: json
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description: Analysis manifest
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metrics:
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- total_reads
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- aligned_reads
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- unaligned_reads
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- alignment_rate
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- unique_alignments
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- multiple_alignments
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parameters:
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- name: cpu
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type: int
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default: 4
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description: Number of CPU threads
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