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Implement nf-schema in pipeline #472

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d87b8f6
feat: enhance JSON schema with comprehensive validation rules
edmundmiller Sep 17, 2025
a0e66a8
refactor: remove legacy Python validation system
edmundmiller Sep 17, 2025
444c3e1
feat: integrate nf-schema samplesheet validation
edmundmiller Sep 17, 2025
d0a5d33
refactor: adapt INPUT_CHECK for nf-schema data structure
edmundmiller Sep 17, 2025
c4c7fc9
feat: connect nf-schema validated data to main workflow
edmundmiller Sep 17, 2025
3970818
refactor: consolidate INPUT_CHECK into pipeline utils
edmundmiller Sep 17, 2025
01d3761
fix: correct nf-schema metadata extraction and control ID matching
edmundmiller Sep 19, 2025
753836a
fix: resolve MultiQC input staging path conflicts
edmundmiller Sep 19, 2025
c1c8dd6
test: update snapshots to reflect nf-schema integration fixes
edmundmiller Sep 19, 2025
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20 changes: 13 additions & 7 deletions assets/schema_input.json
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Original file line number Diff line number Diff line change
Expand Up @@ -35,27 +35,33 @@
},
"replicate": {
"type": "integer",
"errorMessage": "Replicate id not an integer!",
"minimum": 1,
"errorMessage": "Replicate id must be a positive integer!",
"meta": ["replicate"]
},
"antibody": {
"type": "string",
"pattern": "^\\S+$",
"errorMessage": "Antibody entry cannot contain spaces",
"pattern": "^[\\w.-]+$",
"errorMessage": "Antibody entry must contain only alphanumeric characters, dots, and hyphens",
"meta": ["antibody"]
},
"control": {
"type": "string",
"pattern": "^\\S+$",
"errorMessage": "Control entry cannot contain spaces",
"pattern": "^[\\w.-]+$",
"errorMessage": "Control entry must contain only alphanumeric characters, dots, and hyphens",
"meta": ["control"]
},
"control_replicate": {
"type": "integer",
"errorMessage": "Replicate id not an integer!",
"minimum": 1,
"errorMessage": "Control replicate id must be a positive integer!",
"meta": ["control_replicate"]
}
},
"required": ["sample", "fastq_1"]
"required": ["sample", "fastq_1"],
"dependentRequired": {
"antibody": ["control"],
"control": ["antibody"]
}
}
}
247 changes: 0 additions & 247 deletions bin/check_samplesheet.py
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11 changes: 7 additions & 4 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -48,6 +48,9 @@ include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_chip
//
workflow NFCORE_CHIPSEQ {

take:
samplesheet // channel: pre-validated samplesheet data from nf-schema

main:
ch_versions = Channel.empty()

Expand All @@ -71,10 +74,8 @@ workflow NFCORE_CHIPSEQ {
//
// WORKFLOW: Run nf-core/chipseq workflow
//
ch_samplesheet = Channel.value(file(params.input, checkIfExists: true))

CHIPSEQ(
ch_samplesheet,
samplesheet,
ch_versions,
PREPARE_GENOME.out.fasta,
PREPARE_GENOME.out.fai,
Expand Down Expand Up @@ -116,7 +117,9 @@ workflow {
//
// WORKFLOW: Run main workflow
//
NFCORE_CHIPSEQ ( )
NFCORE_CHIPSEQ (
PIPELINE_INITIALISATION.out.samplesheet
)

//
// SUBWORKFLOW: Run completion tasks
Expand Down
38 changes: 19 additions & 19 deletions modules/local/multiqc.nf
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Expand Up @@ -15,37 +15,37 @@ process MULTIQC {
path "trimgalore/fastqc/*"
path "trimgalore/*"

path "alignment/library/*"
path "alignment/library/*"
path "alignment/library/*"
path "alignment/library/samtools_stats/*"
path "alignment/library/samtools_flagstat/*"
path "alignment/library/samtools_idxstats/*"

path "alignment/merged_library/unfiltered/*"
path "alignment/merged_library/unfiltered/*"
path "alignment/merged_library/unfiltered/*"
path "alignment/merged_library/unfiltered/samtools_stats/*"
path "alignment/merged_library/unfiltered/samtools_flagstat/*"
path "alignment/merged_library/unfiltered/samtools_idxstats/*"
path "alignment/merged_library/unfiltered/picard_metrics/*"

path "alignment/merged_library/filtered/*"
path "alignment/merged_library/filtered/*"
path "alignment/merged_library/filtered/*"
path "alignment/merged_library/filtered/samtools_stats/*"
path "alignment/merged_library/filtered/samtools_flagstat/*"
path "alignment/merged_library/filtered/samtools_idxstats/*"
path "alignment/merged_library/filtered/picard_metrics/*"

path "preseq/*"

path "deeptools/*"
path "deeptools/*"
path "deeptools/plotprofile/*"
path "deeptools/plotfingerprint/*"

path "phantompeakqualtools/*"
path "phantompeakqualtools/*"
path "phantompeakqualtools/*"
path "phantompeakqualtools/*"
path "phantompeakqualtools/spp/*"
path "phantompeakqualtools/nsc/*"
path "phantompeakqualtools/rsc/*"
path "phantompeakqualtools/correlation/*"

path "macs3/peaks/*"
path "macs3/peaks/*"
path "macs3/peaks/frip/*"
path "macs3/peaks/count/*"
path "macs3/annotation/*"
path "macs3/featurecounts/*"

path "deseq2/*"
path "deseq2/*"
path "deseq2/pca/*"
path "deseq2/clustering/*"

output:
path "*multiqc_report.html", emit: report
Expand Down
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