showfastqstats

Shows fastq stats using cprogs and python

Install the module, then:

include { Main as ShowFastqStats } from './modules/showfastqstats/main.nf'

workflow {
    ShowFastqStats(stats)
    ShowFastqStats.out.view()
}

Inputs

| name | description | |-----------|----------------------------| | stats (path) | JSON file with stats generated by collectfastqstats module |

JSON stats format

Properties

• lengths: array of read counts of each size
• quality-scores: array of quality scores distribution
• quality-scores-at-position: array of average quality across read nucleotide position

Example

{
    "lengths":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,10000],
    "quality-scores":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,2,1,3,2,2,5,7,5,10,11,15,13,24,18,28,40,54,73,146,398,2672,6470],
    "quality-scores-at-position":[36.7241,36.6437,36.6594,36.6336,36.6804,36.6706,36.6876,36.6598,36.721,36.6272,36.6792,36.6166,36.64,36.6396,36.6662,36.6578,36.6828,36.6136,36.6134,36.6154,36.6152,36.6548,36.6346,36.626,36.6166,36.6082,36.5784,36.5848,36.529,36.5368,36.5348,36.5856,36.5196,36.5412,36.5378,36.4903,36.5564,36.5926,36.5496,36.5762,36.4988,36.528,36.414,36.457,36.4814,36.5162,36.516,36.4446,36.5374,36.4706,36.4336,36.4074,36.4932,36.5126,36.4766,36.4948,36.4738,36.4594,36.4462,36.4478,36.3612,36.4066,36.4932,36.4113,36.4402,36.4283,36.4278,36.4316,36.3652,36.3456,36.3708,36.2836,36.3461,36.3244,36.359,36.3214,36.278,36.3376,36.3314,36.3336,36.273,36.2604,36.2934,36.3378,36.3586,36.3492,36.3252,36.388,36.322,36.3032,36.2916,36.2704,36.3292,36.2894,36.2818,36.2722,36.2814,36.2542,36.186,36.2566,36.2328,36.1702,36.1074,36.1338,36.0736,36.2312,36.1274,36.185,36.1626,36.129,36.0816,36.0792,36.0642,36.1566,36.1114,36.0892,35.9698,36.0966,36.0252,36.031,36.0046,36.0244,35.8486,35.8702,35.8112,35.8644,35.7792,35.7692,35.6984,35.9008,35.7152,35.871,35.7566,35.8,35.796,35.614,35.8124,35.7816,35.6656,35.7172,35.738,35.646,35.6196,35.6392,35.6202,35.5254,35.6102,35.5627,35.5989,35.5679]
}

Outputs

| name | description | |-----------|----------------------------| | plot (path) | plot of quality-scores-at-position property in PNG |

Dependencies

Modules

• collectfastqstats:
  • module

Container-images

• python-matplotlib:
  • artifactory.internal.sophiagenetics.com/docker-release-local/python-matplotlib:1.0.0
  • source