wehub-resource-sync
188 lines
5.0 KiB
YAML
188 lines
5.0 KiB
YAML
name: atacseq
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version: "2.1.2"
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description: "Chromatin accessibility analysis and peak calling"
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# Documentation and source - NOTE: Update version in URLs when upgrading pipeline
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urls:
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documentation: "https://nf-co.re/atacseq/{version}/"
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parameters: "https://nf-co.re/atacseq/{version}/parameters/"
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output_docs: "https://nf-co.re/atacseq/{version}/docs/output/"
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github: "https://github.com/nf-core/atacseq"
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releases: "https://github.com/nf-core/atacseq/releases"
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data_types:
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- ATAC-seq
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- chromatin accessibility
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- open chromatin
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detection_hints:
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filename:
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- atac
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- atacseq
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- chromatin
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- accessibility
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directory:
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- atac
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- atacseq
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- chromatin
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- epigenome
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- epigenetics
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samplesheet:
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input_types:
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- fastq
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columns:
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- name: sample
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required: true
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type: string
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inference: filename
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description: "Condition/group identifier (replicates share same name)"
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- name: fastq_1
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required: true
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type: path
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inference: auto
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description: "Absolute path to R1 FASTQ"
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- name: fastq_2
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required: true
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type: path
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inference: auto
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description: "Absolute path to R2 FASTQ (paired-end required)"
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- name: replicate
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required: true
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type: integer
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default: 1
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inference: filename
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description: "Replicate number (integer)"
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decision_points:
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- parameter: genome
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prompt: "Which reference genome matches your organism?"
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options:
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- value: GRCh38
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label: "Human GRCh38/hg38 (recommended)"
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description: "Latest human reference"
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- value: GRCh37
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label: "Human GRCh37/hg19 (legacy)"
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description: "Older human reference"
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- value: mm10
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label: "Mouse mm10"
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description: "Mouse reference genome"
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default: GRCh38
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recommendation: "Default to GRCh38 for human samples"
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- parameter: read_length
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prompt: "What is the read length of your sequencing data?"
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options:
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- value: 50
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label: "50 bp"
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description: "Short reads"
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- value: 75
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label: "75 bp"
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description: "Standard length"
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- value: 100
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label: "100 bp"
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description: "Common for modern sequencers"
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- value: 150
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label: "150 bp"
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description: "Long reads"
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default: 50
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recommendation: "Check FASTQ files or sequencing report for exact length"
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- parameter: narrow_peak
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prompt: "What type of peaks are you expecting?"
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options:
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- value: "true"
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label: "Narrow peaks (default for ATAC-seq)"
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description: "Standard ATAC-seq open chromatin regions"
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- value: "false"
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label: "Broad peaks"
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description: "For histone marks or broader accessibility regions"
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default: "true"
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recommendation: "Use narrow peaks for standard ATAC-seq"
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test_profile:
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command: "nextflow run nf-core/atacseq -r 2.1.2 -profile test,docker --outdir test_atacseq"
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duration: "15 minutes"
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success_indicators:
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- "test_atacseq/multiqc/multiqc_report.html"
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log_pattern: "Pipeline completed successfully"
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run_command:
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template: |
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nextflow run nf-core/atacseq \
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-r 2.1.2 \
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-profile docker \
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--input {samplesheet} \
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--outdir {outdir} \
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--genome {genome} \
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--read_length {read_length} \
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-resume
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outputs:
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primary:
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- path: "bwa/mergedLibrary/*.mLb.mkD.sorted.bam"
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description: "Filtered, deduplicated alignments"
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- path: "bwa/mergedLibrary/bigwig/*.bigWig"
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description: "Coverage tracks for genome browsers"
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- path: "macs2/narrowPeak/*.narrowPeak"
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description: "Peak calls (BED format)"
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- path: "macs2/narrowPeak/consensus/consensus_peaks.bed"
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description: "Consensus peaks across replicates"
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validation:
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- file: "multiqc/multiqc_report.html"
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check: exists
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description: "QC report must exist"
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- file: "macs2/narrowPeak"
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check: exists
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description: "Peak calls directory"
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quality_metrics:
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- name: mapped_reads
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good: ">80%"
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acceptable: "60-80%"
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poor: "<60%"
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- name: mitochondrial
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good: "<20%"
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acceptable: "20-40%"
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poor: ">40%"
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- name: duplicates
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good: "<30%"
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acceptable: "30-50%"
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poor: ">50%"
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- name: frip
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good: ">30%"
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acceptable: "15-30%"
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poor: "<15%"
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- name: tss_enrichment
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good: ">6"
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acceptable: "4-6"
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poor: "<4"
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resources:
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min_memory: "8.GB"
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recommended_memory: "32.GB"
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min_cpus: 4
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recommended_cpus: 8
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disk_space: "100.GB"
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troubleshooting:
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- error: "Low FRiP score"
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fix: "Check library complexity in plotFingerprint. May indicate over-transposition or low quality"
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- error: "Few peaks called"
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fix: "Lower threshold with --macs_qvalue 0.1 or use --narrow_peak false for broader peaks"
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- error: "High duplicates"
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fix: "Normal for low-input samples. Pipeline removes by default. Consider deeper sequencing"
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- error: "High mitochondrial reads"
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fix: "Sample quality issue. Pipeline filters mito by default (--keep_mito false)"
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replicate_patterns:
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- "_rep(\\d+)"
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- "_R(\\d+)_"
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- "_(\\d+)$"
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- "_replicate(\\d+)"
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