Adding Integration Testing

[emarinier]

Remember to update test data paths after merging.

final_report.json:

{
    "CSE": {
        "meta": {
            "metagenomic": null,
            "assembly": false,
            "hybrid": false,
            "single_end": false,
            "merge": false,
            "downsampled": false
        },
        "CSE": {
            "FastP": {
                "summary": {
                    "fastp_version": "0.23.2",
                    "sequencing": "paired end (150 cycles + 150 cycles)",
                    "before_filtering": {
                        "total_reads": 248,
                        "total_bases": 37200,
                        "q20_bases": 36357,
                        "q30_bases": 33763,
                        "q20_rate": 0.977339,
                        "q30_rate": 0.907608,
                        "read1_mean_length": 150,
                        "read2_mean_length": 150,
                        "gc_content": 0.325188
                    },
                    "after_filtering": {
                        "total_reads": 248,
                        "total_bases": 37200,
                        "q20_bases": 36357,
                        "q30_bases": 33763,
                        "q20_rate": 0.977339,
                        "q30_rate": 0.907608,
                        "read1_mean_length": 150,
                        "read2_mean_length": 150,
                        "gc_content": 0.325188
                    }
                },
                "filtering_result": {
                    "passed_filter_reads": 248,
                    "low_quality_reads": 0,
                    "too_many_N_reads": 0,
                    "low_complexity_reads": 0,
                    "too_short_reads": 0,
                    "too_long_reads": 0
                },
                "duplication": {
                    "rate": 0
                },
                "insert_size": {
                    "peak": 196,
                    "unknown": 0
                },
                "adapter_cutting": {
                    "adapter_trimmed_reads": 0,
                    "adapter_trimmed_bases": 0,
                    "read1_adapter_sequence": "unspecified",
                    "read2_adapter_sequence": "unspecified",
                    "read1_adapter_counts": {
                        
                    },
                    "read2_adapter_counts": {
                        
                    }
                },
                "polyx_trimming": {
                    "total_polyx_trimmed_reads": 0,
                    "polyx_trimmed_reads": {
                        "A": 0,
                        "T": 0,
                        "C": 0,
                        "G": 0
                    },
                    "total_polyx_trimmed_bases": 0,
                    "polyx_trimmed_bases": {
                        "A": 0,
                        "T": 0,
                        "C": 0,
                        "G": 0
                    }
                },
                "read1_before_filtering": {
                    "total_reads": 124,
                    "total_bases": 18600,
                    "q20_bases": 18235,
                    "q30_bases": 17049,
                    "total_cycles": 150
                },
                "read2_before_filtering": {
                    "total_reads": 124,
                    "total_bases": 18600,
                    "q20_bases": 18122,
                    "q30_bases": 16714,
                    "total_cycles": 150
                },
                "read1_after_filtering": {
                    "total_reads": 124,
                    "total_bases": 18600,
                    "q20_bases": 18235,
                    "q30_bases": 17049,
                    "total_cycles": 150
                },
                "read2_after_filtering": {
                    "total_reads": 124,
                    "total_bases": 18600,
                    "q20_bases": 18122,
                    "q30_bases": 16714,
                    "total_cycles": 150
                },
                "command": "fastp --overrepresentation_analysis --trim_poly_g --poly_g_min_len 10 --trim_poly_x --poly_x_min_len 10 --cut_tail --cut_tail_window_size 4 --cut_tail_mean_quality 15 --low_complexity_filter --complexity_threshold 20 --average_qual 25 --qualified_quality_phred 15 --unqualified_percent_limit 40 --length_limit 400 --length_required 35 --detect_adapter_for_pe -i CSE.R1.deconned.fastq.gz -I CSE.R2.deconned.fastq.gz -o CSE.R1.trimmed.fastq.gz -O CSE.R2.trimmed.fastq.gz --json CSE.json --html CSE.html "
            },
            "MeetsReadThreshold": false
        },
        "QualityAnalysis": {
            "raw_average_quality": {
                "field": "raw_average_quality",
                "message": "[raw_average_quality] No data"
            },
            "average_coverage": {
                "field": "average_coverage",
                "message": "[average_coverage] No data"
            },
            "n50_value": {
                "field": "n50_value",
                "message": "[n50_value] No data"
            },
            "nr_contigs": {
                "field": "nr_contigs",
                "message": "[nr_contigs] No data"
            },
            "length": {
                "field": "length",
                "message": "[length] No data"
            },
            "checkm_contamination": {
                "field": "checkm_contamination",
                "message": "[checkm_contamination] No data"
            }
        },
        "QCStatus": "FAILED",
        "QCSummary": "[FAILED] Sample is likely contaminated, REISOLATION AND RESEQUENCING RECOMMENDED\nPassed Tests: 0/6\nSpecies ID: null"
    }
}

[apetkau]

Thanks so much for all your work with this @emarinier . It looks amazing 😄 . I'm so glad you got it working.

I have a few comments below.

[apetkau]

This looks amazing @emarinier. Thanks so much. I just have two additional suggestions.

[apetkau]

Everything looks good. Thanks so much @emarinier 😄