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Merge pull request nf-core#1013 from nf-core/dsl2-nf-validation
DSL2: replaces input_check with fromSamplesheet (nf-validation)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,129 @@ | ||
| { | ||
| "$schema": "http://json-schema.org/draft-07/schema", | ||
| "$id": "https://raw.githubusercontent.com/nf-core/eager/master/assets/schema_fasta.json", | ||
| "title": "nf-core/eager pipeline - params.fasta schema", | ||
| "description": "Schema for the file provided with params.fasta", | ||
| "type": "array", | ||
| "items": { | ||
| "type": "object", | ||
| "properties": { | ||
| "reference_name": { | ||
| "type": "string", | ||
| "pattern": "^\\S+$", | ||
| "meta": ["id"], | ||
| "unique": true, | ||
| "errorMessage": "Reference name must be provided and cannot contain spaces." | ||
| }, | ||
| "fasta": { | ||
| "type": "string", | ||
| "format": "file-path", | ||
| "pattern": "^\\S+\\.f(na|asta|a|as)(\\.gz)?$", | ||
| "exists": true, | ||
| "unique": true, | ||
| "errorMessage": "Fasta files for the mapping reference must be provided with file extensions '.fasta', '.fa', '.fas', '.fna', '.fasta.gz','.fa.gz','.fas.gz', '.fna.gz' and cannot contain any spaces." | ||
| }, | ||
| "fai": { | ||
| "type": "string", | ||
| "format": "file-path", | ||
| "pattern": "^\\S+\\.fai$", | ||
| "exists": true, | ||
| "errorMessage": "Fasta index files for the mapping reference cannot have any spaces and must have file extension '.fai'." | ||
| }, | ||
| "dict": { | ||
| "type": "string", | ||
| "format": "file-path", | ||
| "pattern": "^\\S+\\.dict$", | ||
| "exists": true, | ||
| "errorMessage": "Picard sequence dictionary files for the mapping reference cannot have any spaces and must have file extensions '.dict'." | ||
| }, | ||
| "mapper_index": { | ||
| "type": "string", | ||
| "format": "directory-path", | ||
| "pattern": "^\\S+$", | ||
| "exists": true, | ||
| "errorMessage": "The directories of the index files for the mapping reference for a given mapper must not contain any spaces and have file extensions ''." | ||
| }, | ||
| "circular_target": { | ||
| "type": "string", | ||
| "pattern": "^\\S+$", | ||
| "errorMessage": "The headers of the chromosome to be extended by circularmapper must not contain any spaces and no leading '>'." | ||
| }, | ||
| "mitochondrion_header": { | ||
| "type": "string", | ||
| "pattern": "^\\S+$", | ||
| "errorMessage": "The names of the fasta entry of the mapping reference corresponding to the mitochondrial genome must not contain any spaces and no leading '>'." | ||
| }, | ||
| "snpcapture_bed": { | ||
| "type": "string", | ||
| "format": "file-path", | ||
| "pattern": "^\\S+\\.bed(\\.gz)?$", | ||
| "exists": true, | ||
| "errorMessage": "SNP capture bed files must not contain any spaces and have file extensions '.bed' or '.bed.gz'." | ||
| }, | ||
| "pileupcaller_bedfile": { | ||
| "type": "string", | ||
| "format": "file-path", | ||
| "pattern": "^\\S+\\.bed(\\.gz)?$", | ||
| "exists": true, | ||
| "dependentRequired": ["pileupcaller_snpfile"], | ||
| "errorMessage": "SNP capture bed files for pileupcaller must not contain any spaces, have file extensions '.bed' or '.bed.gz' and be provided alongside a pileupcall_bedfile." | ||
| }, | ||
| "pileupcaller_snpfile": { | ||
| "type": "string", | ||
| "format": "file-path", | ||
| "pattern": "^\\S+\\.snp$", | ||
| "exists": true, | ||
| "dependentRequired": ["pileupcaller_bedfile"], | ||
| "errorMessage": "SNP panel files for pileupcaller must not contain any spaces, have file extension '.snp' and be provided alongside a pileupcaller_snpfile." | ||
| }, | ||
| "hapmap_file": { | ||
| "type": "string", | ||
| "format": "file-path", | ||
| "pattern": "^\\S+$", | ||
| "exists": true, | ||
| "errorMessage": "HapMap files for contamination estimation with ANGSD must not contain any spaces." | ||
| }, | ||
| "pmdtools_masked_fasta": { | ||
| "type": "string", | ||
| "format": "file-path", | ||
| "pattern": "^\\S+\\.f(na|asta|a|as)(\\.gz)?$", | ||
| "exists": true, | ||
| "errorMessage": "Masked fasta files for PMDtools must not contain any spaces and have file extensions '.fasta', '.fa', '.fas', '.fna', '.fasta.gz','.fa.gz','.fas.gz' or '.fna.gz'." | ||
| }, | ||
| "pmdtools_bed_for_masking": { | ||
| "type": "string", | ||
| "format": "file-path", | ||
| "pattern": "^\\S+\\.bed(\\.gz)?$", | ||
| "exists": true, | ||
| "errorMessage": "SNP capture bed files to mask the reference for PMDtools must not contain any spaces and have file extensions '.bed' or '.bed.gz'." | ||
| }, | ||
| "sexdeterrmine_snp_bed": { | ||
| "type": "string", | ||
| "format": "file-path", | ||
| "pattern": "^\\S+\\.bed?(\\.gz)$", | ||
| "exists": true, | ||
| "errorMessage": "SNP capture bed files for SexDetERRmine must not contain any spaces and have file extensions '.bed' or '.bed.gz'." | ||
| }, | ||
| "bedtools_feature_file": { | ||
| "type": "string", | ||
| "format": "file-path", | ||
| "pattern": "^\\S+\\.(bed|gff|gff3)(\\.gz)?$", | ||
| "exists": true, | ||
| "errorMessage": "Feature files must not contain any spaces and have file extensions '.bed', '.bed.gz', '.gff', '.gff.gz', '.gff3' or '.gff3.gz'." | ||
| }, | ||
| "genotyping_reference_ploidy": { | ||
| "type": "integer", | ||
| "meta": ["genotyping_ploidy"], | ||
| "errorMessage": "Organism ploidy for GATK or FreeBayes must be provided as integers." | ||
| }, | ||
| "genotyping_gatk_dbsnp": { | ||
| "type": "string", | ||
| "format": "file-path", | ||
| "pattern": "^\\S+\\.vcf$", | ||
| "exists": true, | ||
| "errorMessage": "SNP annotation files for GATK must not contain any spaces and have file extension '.vcf'." | ||
| } | ||
| }, | ||
| "required": ["reference_name", "fasta"] | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,46 @@ | ||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Nextflow config file for running minimal tests | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Defines input files and everything required to run a fast and simple pipeline test. | ||
| Use as follows: | ||
| nextflow run nf-core/eager -profile test_nothing,<docker/singularity> --outdir <OUTDIR> | ||
| ---------------------------------------------------------------------------------------- | ||
| */ | ||
|
|
||
| params { | ||
| config_profile_name = 'Test profile' | ||
| config_profile_description = 'Minimal test dataset to check pipeline function' | ||
|
|
||
| // Limit resources so that this can run on GitHub Actions | ||
| max_cpus = 2 | ||
| max_memory = '6.GB' | ||
| max_time = '6.h' | ||
|
|
||
| // Input data | ||
| // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets | ||
| // TODO nf-core: Give any required params for the test so that command line flags are not needed | ||
| input = params.pipelines_testdata_base_path + 'eager/testdata/Human/human_design_bam_eager3.tsv' | ||
|
|
||
| // Genome references | ||
| fasta = params.pipelines_testdata_base_path + 'eager/reference/Human/hs37d5_chr21-MT.fa.gz' | ||
|
|
||
| skip_preprocessing = true | ||
| skip_deduplication = true | ||
| skip_qualimap = true | ||
| skip_damage_calculation = true | ||
| mapstats_skip_preseq = true | ||
|
|
||
| run_fastq_sharding = false | ||
| run_bamfiltering = false | ||
| run_bedtools_coverage = false | ||
| run_metagenomicscreening = false | ||
| run_contamination_estimation_angsd = false | ||
| run_mtnucratio = false | ||
| run_mapdamage_rescaling = false | ||
| run_pmd_filtering = false | ||
| run_trim_bam = false | ||
|
|
||
| } |
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