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biocore / oecophylla

shotgun pipeline
MIT License
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Samples with multiple lines on sample sheets leading to duplicate input? #133

Open tanaes opened 6 years ago

tanaes commented 6 years ago

@qiyunzhu and I noticed that a sample that has the following lines on the sample sheet:

1,3559,3559,AGP_1-4,H15,iTru7_110_05,CGCTTAAC,iTru5_20_D,CGGCATTA,AGP,10317.000003559
2,3559,3559,AGP_1-4,H15,iTru7_110_05,CGCTTAAC,iTru5_20_D,CGGCATTA,AGP,10317.000003559
2,3559,3559,AGP_5-6_16_168,H5,iTru7_111_08,TCCGTATG,iTru5_21_D,ACTCGATC,AGP,10317.000003559
1,3559,3559,AGP_5-6_16_168,H5,iTru7_111_08,TCCGTATG,iTru5_21_D,ACTCGATC,AGP,10317.000003559

leads to a config file with lines that look like this:

  '10317.000003559':
    forward:
    - /projects/ag500/qiyun_ag500/KHP/RKL0005/raw/3559_S212_L001_R1_001.fastq.gz
    - /projects/ag500/qiyun_ag500/KHP/RKL0005/raw/3559_S212_L001_R1_001.fastq.gz
    - /projects/ag500/qiyun_ag500/KHP/RKL0005/raw/3559_S212_L002_R1_001.fastq.gz
    - /projects/ag500/qiyun_ag500/KHP/RKL0005/raw/3559_S212_L002_R1_001.fastq.gz
    - /projects/ag500/qiyun_ag500/KHP/RKL0005/raw/3559_S252_L001_R1_001.fastq.gz
    - /projects/ag500/qiyun_ag500/KHP/RKL0005/raw/3559_S252_L001_R1_001.fastq.gz
    - /projects/ag500/qiyun_ag500/KHP/RKL0005/raw/3559_S252_L002_R1_001.fastq.gz
    - /projects/ag500/qiyun_ag500/KHP/RKL0005/raw/3559_S252_L002_R1_001.fastq.gz
    reverse:
    - /projects/ag500/qiyun_ag500/KHP/RKL0005/raw/3559_S212_L001_R2_001.fastq.gz
    - /projects/ag500/qiyun_ag500/KHP/RKL0005/raw/3559_S212_L001_R2_001.fastq.gz
    - /projects/ag500/qiyun_ag500/KHP/RKL0005/raw/3559_S212_L002_R2_001.fastq.gz
    - /projects/ag500/qiyun_ag500/KHP/RKL0005/raw/3559_S212_L002_R2_001.fastq.gz
    - /projects/ag500/qiyun_ag500/KHP/RKL0005/raw/3559_S252_L001_R2_001.fastq.gz
    - /projects/ag500/qiyun_ag500/KHP/RKL0005/raw/3559_S252_L001_R2_001.fastq.gz
    - /projects/ag500/qiyun_ag500/KHP/RKL0005/raw/3559_S252_L002_R2_001.fastq.gz
    - /projects/ag500/qiyun_ag500/KHP/RKL0005/raw/3559_S252_L002_R2_001.fastq.gz

need to investigate and fix.