Closed rafalstepien closed 1 year ago
When running eido validate --st-index sample -f samplesheet.csv -s samplesheet_schema.yaml -e command with following schema:
eido validate --st-index sample -f samplesheet.csv -s samplesheet_schema.yaml -e
description: A schema for validation of samplesheet.csv for taxprofiler pipeline. imports: - https://schema.databio.org/pep/2.1.0.yaml properties: samples: type: array items: type: object properties: sample: type: string description: "Sample identifier." pattern: "^\\S*$" run_accession: type: string description: "Run accession number." instrument_platform: type: string description: "Name of the platform that sequenced the samples." enum: ["ABI_SOLID", "BGISEQ", "CAPILLARY", "COMPLETE_GENOMICS", "DNBSEQ", "HELICOS", "ILLUMINA", "ION_TORRENT", "LS454", "OXFORD_NANOPORE", "PACBIO_SMRT"] fastq1: type: string description: "FASTQ file for read 1." pattern: "^[\\S]+.(fq\\.gz|fastq\\.gz)$" fastq2: type: string description: "FASTQ file for read 2." pattern: "^[\\S]+.(fq\\.gz|fastq\\.gz)$" fasta: type: string description: "Path to FASTA file." pattern: "^[\\S]+.(fa\\.gz|fasta\\.gz)$" required: - sample - run_accession - instrument_platform files: - fastq1 - fastq2 - fasta required: - samples
On the samplesheet attached samplesheet.csv, then peppy.Project.to_dict creates following structure:
peppy.Project.to_dict
{'pep_version': '2.1.0', '_samples': [{'sample': '2611', 'instrument_platform': 'ILLUMINA', 'run_accession': 'ERR5766174', 'fastq_1': 'NaN', 'fastq_2': 'NaN', 'fasta': 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fasta/ERX5474930_ERR5766174_1.fa.gz'}, {'sample': '2614', 'instrument_platform': 'ILLUMINA', 'run_accession': 'ERR5766176', 'fastq_1': 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_1.fastq.gz', 'fastq_2': 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_2.fastq.gz', 'fasta': 'NaN'}, {'sample': '2615', 'instrument_platform': 'ILLUMINA', 'run_accession': 'ERR5766176_B', 'fastq_1': 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_B_1.fastq.gz', 'fastq_2': 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_B_2.fastq.gz', 'fasta': 'NaN'}, {'sample': '2612', 'instrument_platform': 'ILLUMINA', 'run_accession': 'ERR5766180', 'fastq_1': 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474936_ERR5766180_1.fastq.gz', 'fastq_2': 'NaN', 'fasta': 'NaN'}, {'sample': '2613', 'instrument_platform': 'ILLUMINA', 'run_accession': 'ERR5766181', 'fastq_1': 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474937_ERR5766181_1.fastq.gz', 'fastq_2': 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474937_ERR5766181_2.fastq.gz', 'fasta': 'NaN'}, {'sample': 'ERR3201952', 'instrument_platform': 'OXFORD_NANOPORE', 'run_accession': 'ERR3201952', 'fastq_1': 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERR3201952.fastq.gz', 'fastq_2': 'NaN', 'fasta': 'NaN'}]}
This is not correct, because we don't want to have NaNs in our data structures.
NaN
When running
eido validate --st-index sample -f samplesheet.csv -s samplesheet_schema.yaml -e
command with following schema:On the samplesheet attached samplesheet.csv, then
peppy.Project.to_dict
creates following structure:This is not correct, because we don't want to have
NaN
s in our data structures.