mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-20 23:32:05 +00:00
Fixing MULTIQC module and adding tests (#1)
* fix multiqc process * fix multiqc tests * move multiqc test input data into tests/data/fastqc/ folder Move input tests data into tests/data/fastqc/ and linking those files into software/multiqc/test/input/ as stated from the project documentation * add multiqc github workflow * remove unused file * generalize multiqc input data User must collect all desidered files in a channel (as described in https://seqera.io/training/#_multiqc_report * update meta information
This commit is contained in:
Paolo Cozzi
Abhinav Sharma
parent
2783913122
commit
835ac48565
21 changed files with 920 additions and 757 deletions
30
.github/workflows/multiqc.yml
vendored
Normal file
30
.github/workflows/multiqc.yml
vendored
Normal file
|
|
@ -0,0 +1,30 @@
|
||||||
|
name: multiqc
|
||||||
|
on:
|
||||||
|
push:
|
||||||
|
paths:
|
||||||
|
- software/multiqc/**
|
||||||
|
- .github/workflows/multiqc.yml
|
||||||
|
- tests
|
||||||
|
pull_request:
|
||||||
|
paths:
|
||||||
|
- software/multiqc/**
|
||||||
|
- .github/workflows/multiqc.yml
|
||||||
|
- tests
|
||||||
|
|
||||||
|
jobs:
|
||||||
|
ci_test:
|
||||||
|
runs-on: ubuntu-latest
|
||||||
|
env:
|
||||||
|
NXF_ANSI_LOG: false
|
||||||
|
steps:
|
||||||
|
|
||||||
|
- uses: actions/checkout@v2
|
||||||
|
|
||||||
|
- name: Install Nextflow
|
||||||
|
run: |
|
||||||
|
export NXF_VER="20.07.1"
|
||||||
|
wget -qO- get.nextflow.io | bash
|
||||||
|
sudo mv nextflow /usr/local/bin/
|
||||||
|
|
||||||
|
# Test the module
|
||||||
|
- run: nextflow run ./software/multiqc/test/ -profile docker
|
||||||
|
|
@ -4,29 +4,29 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||||
params.options = [:]
|
params.options = [:]
|
||||||
def options = initOptions(params.options)
|
def options = initOptions(params.options)
|
||||||
|
|
||||||
process FASTQC {
|
process MULTIQC {
|
||||||
tag "$meta.id"
|
tag "multiqc"
|
||||||
label 'process_medium'
|
label 'process_medium'
|
||||||
publishDir "${params.outdir}",
|
publishDir "${params.outdir}",
|
||||||
mode: params.publish_dir_mode,
|
mode: params.publish_dir_mode,
|
||||||
saveAs: { filename -> saveFiles(filename: filename, options: params.options, publish_dir: getSoftwareName(task.process), publish_id: meta.id) }
|
saveAs: { filename -> saveFiles(filename: filename, options: params.options, publish_dir: getSoftwareName(task.process), publish_id:'') }
|
||||||
|
|
||||||
conda(params.enable_conda ? "bioconda::multiqc=1.9" : null)
|
conda(params.enable_conda ? "bioconda::multiqc=1.9" : null)
|
||||||
container "quay.io/biocontainers/multiqc:1.9--py_1"
|
container "quay.io/biocontainers/multiqc:1.9--py_1"
|
||||||
|
|
||||||
input:
|
input:
|
||||||
tuple val(meta), path("*.html")
|
path(generic_report)
|
||||||
|
|
||||||
output:
|
output:
|
||||||
tuple val(meta), path("multiqc_data"), emit: dir
|
path("multiqc_data"), emit: dir
|
||||||
tuple val(meta), path("*.html"), emit: html
|
path("multiqc_report.html"), emit: html
|
||||||
path "*.version.txt", emit: version
|
path "*.version.txt", emit: version
|
||||||
|
|
||||||
script:
|
script:
|
||||||
def software = getSoftwareName(task.process)
|
def software = getSoftwareName(task.process)
|
||||||
def prefix = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
|
|
||||||
"""
|
"""
|
||||||
multiqc --version | sed -e "s/version//g" > ${software}.version.txt
|
multiqc .
|
||||||
"""
|
multiqc --version | sed -e "s/multiqc, version //g" > ${software}.version.txt
|
||||||
}
|
"""
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -1,20 +1,16 @@
|
||||||
name: fastqc
|
name: MultiQC
|
||||||
description: Run FastQC on sequenced reads
|
description: Aggregate results from bioinformatics analyses across many samples into a single report
|
||||||
keywords:
|
keywords:
|
||||||
- quality control
|
- QC
|
||||||
- qc
|
- bioinformatics tools
|
||||||
- adapters
|
- Beautiful stand-alone HTML report
|
||||||
- fastq
|
|
||||||
tools:
|
tools:
|
||||||
- fastqc:
|
- multiqc:
|
||||||
description: |
|
description: |
|
||||||
FastQC gives general quality metrics about your reads.
|
MultiQC searches a given directory for analysis logs and compiles a HTML report.
|
||||||
It provides information about the quality score distribution
|
It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
|
||||||
across your reads, the per base sequence content (%A/C/G/T).
|
homepage: https://multiqc.info/
|
||||||
You get information about adapter contamination and other
|
documentation: https://multiqc.info/docs/
|
||||||
overrepresented sequences.
|
|
||||||
homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
|
|
||||||
documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
|
|
||||||
params:
|
params:
|
||||||
- outdir:
|
- outdir:
|
||||||
type: string
|
type: string
|
||||||
|
|
@ -32,36 +28,23 @@ params:
|
||||||
Run the module with Conda using the software specified
|
Run the module with Conda using the software specified
|
||||||
via the `conda` directive
|
via the `conda` directive
|
||||||
input:
|
input:
|
||||||
- meta:
|
- generic_report:
|
||||||
type: map
|
|
||||||
description: |
|
|
||||||
Groovy Map containing sample information
|
|
||||||
e.g. [ id:'test', single_end:false ]
|
|
||||||
- reads:
|
|
||||||
type: file
|
type: file
|
||||||
description: |
|
description: |
|
||||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
List of report, for example the html and zip output of FastQC
|
||||||
respectively.
|
|
||||||
output:
|
output:
|
||||||
- meta:
|
- dir:
|
||||||
type: map
|
type: dir
|
||||||
description: |
|
description: MultiQC data dir
|
||||||
Groovy Map containing sample information
|
pattern: "multiqc_data"
|
||||||
e.g. [ id:'test', single_end:false ]
|
|
||||||
- html:
|
- html:
|
||||||
type: file
|
type: file
|
||||||
description: FastQC report
|
description: MultiQC report file
|
||||||
pattern: "*_{fastqc.html}"
|
pattern: "multiqc_report.html"
|
||||||
- zip:
|
|
||||||
type: file
|
|
||||||
description: FastQC report archive
|
|
||||||
pattern: "*_{fastqc.zip}"
|
|
||||||
- version:
|
- version:
|
||||||
type: file
|
type: file
|
||||||
description: File containing software version
|
description: File containing software version
|
||||||
pattern: "*.{version.txt}"
|
pattern: "*.{version.txt}"
|
||||||
authors:
|
authors:
|
||||||
- "@drpatelh"
|
- "@abhi18av"
|
||||||
- "@grst"
|
- "@bunop"
|
||||||
- "@ewels"
|
|
||||||
- "@FelixKrueger"
|
|
||||||
|
|
|
||||||
File diff suppressed because one or more lines are too long
1
software/multiqc/test/input/test_1_fastqc.html
Symbolic link
1
software/multiqc/test/input/test_1_fastqc.html
Symbolic link
|
|
@ -0,0 +1 @@
|
||||||
|
../../../../tests/data/fastqc/test_1_fastqc.html
|
||||||
Binary file not shown.
1
software/multiqc/test/input/test_1_fastqc.zip
Symbolic link
1
software/multiqc/test/input/test_1_fastqc.zip
Symbolic link
|
|
@ -0,0 +1 @@
|
||||||
|
../../../../tests/data/fastqc/test_1_fastqc.zip
|
||||||
File diff suppressed because one or more lines are too long
1
software/multiqc/test/input/test_2_fastqc.html
Symbolic link
1
software/multiqc/test/input/test_2_fastqc.html
Symbolic link
|
|
@ -0,0 +1 @@
|
||||||
|
../../../../tests/data/fastqc/test_2_fastqc.html
|
||||||
Binary file not shown.
1
software/multiqc/test/input/test_2_fastqc.zip
Symbolic link
1
software/multiqc/test/input/test_2_fastqc.zip
Symbolic link
|
|
@ -0,0 +1 @@
|
||||||
|
../../../../tests/data/fastqc/test_2_fastqc.zip
|
||||||
|
|
@ -2,20 +2,24 @@
|
||||||
|
|
||||||
nextflow.enable.dsl = 2
|
nextflow.enable.dsl = 2
|
||||||
|
|
||||||
include { MULTIQC } from '../main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
|
include { MULTIQC } from '../main.nf' addParams( options: [ publish_dir:'test_multi' ] )
|
||||||
|
|
||||||
/*
|
/*
|
||||||
* Test with single-end data
|
* Test with single-end data
|
||||||
*/
|
*/
|
||||||
workflow test_single_end {
|
workflow test_multi {
|
||||||
|
|
||||||
def input = []
|
def input = []
|
||||||
input = [ [ id:'test', single_end:true ], // meta map
|
input = [
|
||||||
[ file("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ]
|
file("${baseDir}/input/test_1_fastqc.html", checkIfExists: true),
|
||||||
|
file("${baseDir}/input/test_2_fastqc.html", checkIfExists: true),
|
||||||
|
file("${baseDir}/input/test_1_fastqc.zip", checkIfExists: true),
|
||||||
|
file("${baseDir}/input/test_2_fastqc.zip", checkIfExists: true)
|
||||||
|
]
|
||||||
|
|
||||||
FASTQC_SE ( input )
|
MULTIQC ( input )
|
||||||
}
|
}
|
||||||
|
|
||||||
workflow {
|
workflow {
|
||||||
test_single_end()
|
test_multi()
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -1,105 +0,0 @@
|
||||||
[2020-11-23 18:25:23,742] multiqc [DEBUG ] No MultiQC config found: /Users/eklavya/.pyenv/versions/miniconda3-latest/lib/python3.7/site-packages/multiqc_config.yaml
|
|
||||||
[2020-11-23 18:25:23,742] multiqc [DEBUG ] No MultiQC config found: /Users/eklavya/.multiqc_config.yaml
|
|
||||||
[2020-11-23 18:25:23,742] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml
|
|
||||||
[2020-11-23 18:25:23,742] multiqc [DEBUG ] Command used: /Users/eklavya/.pyenv/versions/miniconda3-latest/bin/multiqc input/
|
|
||||||
[2020-11-23 18:25:25,158] multiqc [WARNING] MultiQC Version v1.9 now available!
|
|
||||||
[2020-11-23 18:25:25,158] multiqc [INFO ] This is MultiQC v1.8
|
|
||||||
[2020-11-23 18:25:25,158] multiqc [DEBUG ] Command : /Users/eklavya/.pyenv/versions/miniconda3-latest/bin/multiqc input/
|
|
||||||
[2020-11-23 18:25:25,158] multiqc [DEBUG ] Working dir : /Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test
|
|
||||||
[2020-11-23 18:25:25,158] multiqc [INFO ] Template : default
|
|
||||||
[2020-11-23 18:25:25,158] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 16:54:48) [Clang 4.0.1 (tags/RELEASE_401/final)]
|
|
||||||
[2020-11-23 18:25:25,159] multiqc [INFO ] Searching : /Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test/input
|
|
||||||
[2020-11-23 18:25:25,159] multiqc [DEBUG ] Analysing modules: custom_content, conpair, peddy, methylQA, phantompeakqualtools, qualimap, preseq, quast, qorts, rna_seqc, rsem, rseqc, busco, goleft_indexcov, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, homer, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, fgbio, dedup, damageprofiler, biobambam2, mtnucratio, picard, prokka, samblaster, samtools, sexdeterrmine, bamtools, jellyfish, vcftools, longranger, stacks, bbmap, bismark, biscuit, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, kat, leehom, adapterRemoval, clipandmerge, cutadapt, flexbar, trimmomatic, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastp, fastqc, minionqc, mosdepth, clusterflow, bcl2fastq, interop, flash, seqyclean
|
|
||||||
[2020-11-23 18:25:25,159] multiqc [DEBUG ] Using temporary directory for creating report: /var/folders/zp/63677vtx23d_b2_nd7mm92040000gn/T/tmph8bg8w5g
|
|
||||||
[2020-11-23 18:25:25,251] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: test_1_fastqc.html
|
|
||||||
[2020-11-23 18:25:25,251] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: test_2_fastqc.html
|
|
||||||
[2020-11-23 18:25:25,624] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.1.1
|
|
||||||
[2020-11-23 18:25:25,625] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.1.1
|
|
||||||
[2020-11-23 18:25:25,626] multiqc [DEBUG ] No samples found: custom_content
|
|
||||||
[2020-11-23 18:25:25,630] multiqc [DEBUG ] No samples found: conpair
|
|
||||||
[2020-11-23 18:25:25,634] multiqc [DEBUG ] No samples found: peddy
|
|
||||||
[2020-11-23 18:25:25,638] multiqc [DEBUG ] No samples found: methylQA
|
|
||||||
[2020-11-23 18:25:25,642] multiqc [DEBUG ] No samples found: phantompeakqualtools
|
|
||||||
[2020-11-23 18:25:25,647] multiqc [DEBUG ] No samples found: qualimap
|
|
||||||
[2020-11-23 18:25:25,651] multiqc [DEBUG ] No samples found: preseq
|
|
||||||
[2020-11-23 18:25:25,655] multiqc [DEBUG ] No samples found: quast
|
|
||||||
[2020-11-23 18:25:25,659] multiqc [DEBUG ] No samples found: qorts
|
|
||||||
[2020-11-23 18:25:25,663] multiqc [DEBUG ] No samples found: rna_seqc
|
|
||||||
[2020-11-23 18:25:25,666] multiqc [DEBUG ] No samples found: rsem
|
|
||||||
[2020-11-23 18:25:25,675] multiqc [DEBUG ] No samples found: rseqc
|
|
||||||
[2020-11-23 18:25:25,679] multiqc [DEBUG ] No samples found: busco
|
|
||||||
[2020-11-23 18:25:25,683] multiqc [DEBUG ] No samples found: goleft_indexcov
|
|
||||||
[2020-11-23 18:25:25,687] multiqc [DEBUG ] No samples found: disambiguate
|
|
||||||
[2020-11-23 18:25:25,691] multiqc [DEBUG ] No samples found: supernova
|
|
||||||
[2020-11-23 18:25:25,700] multiqc [DEBUG ] No samples found: deeptools
|
|
||||||
[2020-11-23 18:25:25,703] multiqc [DEBUG ] No samples found: sargasso
|
|
||||||
[2020-11-23 18:25:25,707] multiqc [DEBUG ] No samples found: verifybamid
|
|
||||||
[2020-11-23 18:25:25,711] multiqc [DEBUG ] No samples found: mirtrace
|
|
||||||
[2020-11-23 18:25:25,715] multiqc [DEBUG ] No samples found: happy
|
|
||||||
[2020-11-23 18:25:25,720] multiqc [DEBUG ] No samples found: homer
|
|
||||||
[2020-11-23 18:25:25,723] multiqc [DEBUG ] No samples found: macs2
|
|
||||||
[2020-11-23 18:25:25,727] multiqc [DEBUG ] No samples found: theta2
|
|
||||||
[2020-11-23 18:25:25,731] multiqc [DEBUG ] No samples found: snpeff
|
|
||||||
[2020-11-23 18:25:25,736] multiqc [DEBUG ] No samples found: gatk
|
|
||||||
[2020-11-23 18:25:25,741] multiqc [DEBUG ] No samples found: htseq
|
|
||||||
[2020-11-23 18:25:25,745] multiqc [DEBUG ] No samples found: bcftools
|
|
||||||
[2020-11-23 18:25:25,750] multiqc [DEBUG ] No samples found: featureCounts
|
|
||||||
[2020-11-23 18:25:25,754] multiqc [DEBUG ] No samples found: fgbio
|
|
||||||
[2020-11-23 18:25:25,758] multiqc [DEBUG ] No samples found: dedup
|
|
||||||
[2020-11-23 18:25:25,762] multiqc [DEBUG ] No samples found: damageprofiler
|
|
||||||
[2020-11-23 18:25:25,774] multiqc [DEBUG ] No samples found: biobambam2
|
|
||||||
[2020-11-23 18:25:25,778] multiqc [DEBUG ] No samples found: mtnucratio
|
|
||||||
[2020-11-23 18:25:25,781] multiqc [DEBUG ] No samples found: picard
|
|
||||||
[2020-11-23 18:25:25,785] multiqc [DEBUG ] No samples found: prokka
|
|
||||||
[2020-11-23 18:25:25,789] multiqc [DEBUG ] No samples found: samblaster
|
|
||||||
[2020-11-23 18:25:25,795] multiqc [DEBUG ] No samples found: samtools
|
|
||||||
[2020-11-23 18:25:25,799] multiqc [DEBUG ] No samples found: sexdeterrmine
|
|
||||||
[2020-11-23 18:25:25,803] multiqc [DEBUG ] No samples found: bamtools
|
|
||||||
[2020-11-23 18:25:25,806] multiqc [DEBUG ] No samples found: jellyfish
|
|
||||||
[2020-11-23 18:25:25,812] multiqc [DEBUG ] No samples found: vcftools
|
|
||||||
[2020-11-23 18:25:25,816] multiqc [DEBUG ] No samples found: longranger
|
|
||||||
[2020-11-23 18:25:25,820] multiqc [DEBUG ] No samples found: stacks
|
|
||||||
[2020-11-23 18:25:25,830] multiqc [DEBUG ] No samples found: bbmap
|
|
||||||
[2020-11-23 18:25:25,834] multiqc [DEBUG ] No samples found: bismark
|
|
||||||
[2020-11-23 18:25:25,838] multiqc [DEBUG ] No samples found: biscuit
|
|
||||||
[2020-11-23 18:25:25,842] multiqc [DEBUG ] No samples found: hicexplorer
|
|
||||||
[2020-11-23 18:25:25,846] multiqc [DEBUG ] No samples found: hicup
|
|
||||||
[2020-11-23 18:25:25,850] multiqc [DEBUG ] No samples found: hicpro
|
|
||||||
[2020-11-23 18:25:25,853] multiqc [DEBUG ] No samples found: salmon
|
|
||||||
[2020-11-23 18:25:25,857] multiqc [DEBUG ] No samples found: kallisto
|
|
||||||
[2020-11-23 18:25:25,861] multiqc [DEBUG ] No samples found: slamdunk
|
|
||||||
[2020-11-23 18:25:25,865] multiqc [DEBUG ] No samples found: star
|
|
||||||
[2020-11-23 18:25:25,868] multiqc [DEBUG ] No samples found: hisat2
|
|
||||||
[2020-11-23 18:25:25,872] multiqc [DEBUG ] No samples found: tophat
|
|
||||||
[2020-11-23 18:25:25,875] multiqc [DEBUG ] No samples found: bowtie2
|
|
||||||
[2020-11-23 18:25:25,879] multiqc [DEBUG ] No samples found: bowtie1
|
|
||||||
[2020-11-23 18:25:25,883] multiqc [DEBUG ] No samples found: kat
|
|
||||||
[2020-11-23 18:25:25,886] multiqc [DEBUG ] No samples found: leehom
|
|
||||||
[2020-11-23 18:25:25,890] multiqc [DEBUG ] No samples found: adapterRemoval
|
|
||||||
[2020-11-23 18:25:25,893] multiqc [DEBUG ] No samples found: clipandmerge
|
|
||||||
[2020-11-23 18:25:25,897] multiqc [DEBUG ] No samples found: cutadapt
|
|
||||||
[2020-11-23 18:25:25,901] multiqc [DEBUG ] No samples found: flexbar
|
|
||||||
[2020-11-23 18:25:25,904] multiqc [DEBUG ] No samples found: trimmomatic
|
|
||||||
[2020-11-23 18:25:25,908] multiqc [DEBUG ] No samples found: skewer
|
|
||||||
[2020-11-23 18:25:25,912] multiqc [DEBUG ] No samples found: sortmerna
|
|
||||||
[2020-11-23 18:25:25,915] multiqc [DEBUG ] No samples found: biobloomtools
|
|
||||||
[2020-11-23 18:25:25,919] multiqc [DEBUG ] No samples found: fastq_screen
|
|
||||||
[2020-11-23 18:25:25,922] multiqc [DEBUG ] No samples found: afterqc
|
|
||||||
[2020-11-23 18:25:25,926] multiqc [DEBUG ] No samples found: fastp
|
|
||||||
[2020-11-23 18:25:25,947] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports
|
|
||||||
[2020-11-23 18:25:26,023] multiqc [DEBUG ] No samples found: minionqc
|
|
||||||
[2020-11-23 18:25:26,027] multiqc [DEBUG ] No samples found: mosdepth
|
|
||||||
[2020-11-23 18:25:26,031] multiqc [DEBUG ] No samples found: clusterflow
|
|
||||||
[2020-11-23 18:25:26,035] multiqc [DEBUG ] No samples found: bcl2fastq
|
|
||||||
[2020-11-23 18:25:26,039] multiqc [DEBUG ] No samples found: interop
|
|
||||||
[2020-11-23 18:25:26,043] multiqc [DEBUG ] No samples found: flash
|
|
||||||
[2020-11-23 18:25:26,046] multiqc [DEBUG ] No samples found: seqyclean
|
|
||||||
[2020-11-23 18:25:26,050] multiqc [INFO ] Compressing plot data
|
|
||||||
[2020-11-23 18:25:26,086] multiqc [INFO ] Report : multiqc_report.html
|
|
||||||
[2020-11-23 18:25:26,086] multiqc [INFO ] Data : multiqc_data
|
|
||||||
[2020-11-23 18:25:26,087] multiqc [DEBUG ] Moving data file from '/var/folders/zp/63677vtx23d_b2_nd7mm92040000gn/T/tmph8bg8w5g/multiqc_data/multiqc_fastqc.txt' to '/Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test/multiqc_data'
|
|
||||||
[2020-11-23 18:25:26,087] multiqc [DEBUG ] Moving data file from '/var/folders/zp/63677vtx23d_b2_nd7mm92040000gn/T/tmph8bg8w5g/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test/multiqc_data'
|
|
||||||
[2020-11-23 18:25:26,087] multiqc [DEBUG ] Moving data file from '/var/folders/zp/63677vtx23d_b2_nd7mm92040000gn/T/tmph8bg8w5g/multiqc_data/multiqc_general_stats.txt' to '/Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test/multiqc_data'
|
|
||||||
[2020-11-23 18:25:26,087] multiqc [DEBUG ] Moving data file from '/var/folders/zp/63677vtx23d_b2_nd7mm92040000gn/T/tmph8bg8w5g/multiqc_data/multiqc_sources.txt' to '/Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test/multiqc_data'
|
|
||||||
[2020-11-23 18:25:26,088] multiqc [DEBUG ] Moving data file from '/var/folders/zp/63677vtx23d_b2_nd7mm92040000gn/T/tmph8bg8w5g/multiqc_data/multiqc_data.json' to '/Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test/multiqc_data'
|
|
||||||
[2020-11-23 18:25:26,231] multiqc [INFO ] MultiQC complete
|
|
||||||
127
software/multiqc/test/output/multiqc_data/multiqc.log
Normal file
127
software/multiqc/test/output/multiqc_data/multiqc.log
Normal file
|
|
@ -0,0 +1,127 @@
|
||||||
|
[2020-11-28 16:22:29,678] multiqc [DEBUG ] No MultiQC config found: /usr/local/lib/python3.8/site-packages/multiqc_config.yaml
|
||||||
|
[2020-11-28 16:22:29,678] multiqc [DEBUG ] No MultiQC config found: /.multiqc_config.yaml
|
||||||
|
[2020-11-28 16:22:29,678] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml
|
||||||
|
[2020-11-28 16:22:29,678] multiqc [DEBUG ] Command used: /usr/local/bin/multiqc .
|
||||||
|
[2020-11-28 16:22:30,040] multiqc [DEBUG ] Latest MultiQC version is v1.9
|
||||||
|
[2020-11-28 16:22:30,040] multiqc [INFO ] This is MultiQC v1.9
|
||||||
|
[2020-11-28 16:22:30,040] multiqc [DEBUG ] Command : /usr/local/bin/multiqc .
|
||||||
|
[2020-11-28 16:22:30,040] multiqc [DEBUG ] Working dir : /home/paolo/Projects/NEXTFLOWetude/nf-core-modules/work/cc/e69df4c4d3d33e79fbb670c7f14b52
|
||||||
|
[2020-11-28 16:22:30,040] multiqc [INFO ] Template : default
|
||||||
|
[2020-11-28 16:22:30,040] multiqc [DEBUG ] Running Python 3.8.5 | packaged by conda-forge | (default, Jul 24 2020, 01:25:15) [GCC 7.5.0]
|
||||||
|
[2020-11-28 16:22:30,041] multiqc [INFO ] Searching : /home/paolo/Projects/NEXTFLOWetude/nf-core-modules/work/cc/e69df4c4d3d33e79fbb670c7f14b52
|
||||||
|
[2020-11-28 16:22:30,041] multiqc [DEBUG ] Analysing modules: custom_content, conpair, peddy, somalier, methylQA, mosdepth, phantompeakqualtools, qualimap, preseq, quast, qorts, rna_seqc, rockhopper, rsem, rseqc, busco, goleft_indexcov, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, mirtop, homer, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, fgbio, dragen, dedup, damageprofiler, biobambam2, mtnucratio, picard, prokka, samblaster, samtools, sexdeterrmine, bamtools, jellyfish, vcftools, longranger, stacks, varscan2, bbmap, bismark, biscuit, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, snpsplit, kat, leehom, adapterRemoval, clipandmerge, cutadapt, flexbar, kaiju, kraken, malt, trimmomatic, sickle, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastp, fastqc, pycoqc, minionqc, multivcfanalyzer, clusterflow, bcl2fastq, interop, ivar, flash, seqyclean
|
||||||
|
[2020-11-28 16:22:30,041] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp2h0fqr8s
|
||||||
|
[2020-11-28 16:22:30,124] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: test_2_fastqc.html
|
||||||
|
[2020-11-28 16:22:30,126] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: test_2_fastqc.html
|
||||||
|
[2020-11-28 16:22:30,126] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: test_2_fastqc.html
|
||||||
|
[2020-11-28 16:22:30,126] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: test_2_fastqc.html
|
||||||
|
[2020-11-28 16:22:30,126] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: test_2_fastqc.html
|
||||||
|
[2020-11-28 16:22:30,126] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: test_2_fastqc.html
|
||||||
|
[2020-11-28 16:22:30,126] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: test_2_fastqc.html
|
||||||
|
[2020-11-28 16:22:30,160] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: .command.run
|
||||||
|
[2020-11-28 16:22:30,184] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: test_1_fastqc.html
|
||||||
|
[2020-11-28 16:22:30,185] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: test_1_fastqc.html
|
||||||
|
[2020-11-28 16:22:30,185] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: test_1_fastqc.html
|
||||||
|
[2020-11-28 16:22:30,185] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: test_1_fastqc.html
|
||||||
|
[2020-11-28 16:22:30,185] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: test_1_fastqc.html
|
||||||
|
[2020-11-28 16:22:30,185] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: test_1_fastqc.html
|
||||||
|
[2020-11-28 16:22:30,185] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: test_1_fastqc.html
|
||||||
|
[2020-11-28 16:22:30,607] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.0
|
||||||
|
[2020-11-28 16:22:30,607] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.0
|
||||||
|
[2020-11-28 16:22:30,608] multiqc [DEBUG ] No samples found: custom_content
|
||||||
|
[2020-11-28 16:22:30,611] multiqc [DEBUG ] No samples found: conpair
|
||||||
|
[2020-11-28 16:22:30,613] multiqc [DEBUG ] No samples found: peddy
|
||||||
|
[2020-11-28 16:22:30,616] multiqc [DEBUG ] No samples found: somalier
|
||||||
|
[2020-11-28 16:22:30,618] multiqc [DEBUG ] No samples found: methylQA
|
||||||
|
[2020-11-28 16:22:30,621] multiqc [DEBUG ] No samples found: mosdepth
|
||||||
|
[2020-11-28 16:22:30,624] multiqc [DEBUG ] No samples found: phantompeakqualtools
|
||||||
|
[2020-11-28 16:22:30,626] multiqc [DEBUG ] No samples found: qualimap
|
||||||
|
[2020-11-28 16:22:30,629] multiqc [DEBUG ] No samples found: preseq
|
||||||
|
[2020-11-28 16:22:30,631] multiqc [DEBUG ] No samples found: quast
|
||||||
|
[2020-11-28 16:22:30,633] multiqc [DEBUG ] No samples found: qorts
|
||||||
|
[2020-11-28 16:22:30,636] multiqc [DEBUG ] No samples found: rna_seqc
|
||||||
|
[2020-11-28 16:22:30,638] multiqc [DEBUG ] No samples found: rockhopper
|
||||||
|
[2020-11-28 16:22:30,640] multiqc [DEBUG ] No samples found: rsem
|
||||||
|
[2020-11-28 16:22:30,644] multiqc [DEBUG ] No samples found: rseqc
|
||||||
|
[2020-11-28 16:22:30,647] multiqc [DEBUG ] No samples found: busco
|
||||||
|
[2020-11-28 16:22:30,649] multiqc [DEBUG ] No samples found: goleft_indexcov
|
||||||
|
[2020-11-28 16:22:30,651] multiqc [DEBUG ] No samples found: disambiguate
|
||||||
|
[2020-11-28 16:22:30,654] multiqc [DEBUG ] No samples found: supernova
|
||||||
|
[2020-11-28 16:22:30,658] multiqc [DEBUG ] No samples found: deeptools
|
||||||
|
[2020-11-28 16:22:30,660] multiqc [DEBUG ] No samples found: sargasso
|
||||||
|
[2020-11-28 16:22:30,663] multiqc [DEBUG ] No samples found: verifybamid
|
||||||
|
[2020-11-28 16:22:30,665] multiqc [DEBUG ] No samples found: mirtrace
|
||||||
|
[2020-11-28 16:22:30,667] multiqc [DEBUG ] No samples found: happy
|
||||||
|
[2020-11-28 16:22:30,670] multiqc [DEBUG ] No samples found: mirtop
|
||||||
|
[2020-11-28 16:22:30,673] multiqc [DEBUG ] No samples found: homer
|
||||||
|
[2020-11-28 16:22:30,675] multiqc [DEBUG ] No samples found: macs2
|
||||||
|
[2020-11-28 16:22:30,677] multiqc [DEBUG ] No samples found: theta2
|
||||||
|
[2020-11-28 16:22:30,680] multiqc [DEBUG ] No samples found: snpeff
|
||||||
|
[2020-11-28 16:22:30,683] multiqc [DEBUG ] No samples found: gatk
|
||||||
|
[2020-11-28 16:22:30,685] multiqc [DEBUG ] No samples found: htseq
|
||||||
|
[2020-11-28 16:22:30,687] multiqc [DEBUG ] No samples found: bcftools
|
||||||
|
[2020-11-28 16:22:30,690] multiqc [DEBUG ] No samples found: featureCounts
|
||||||
|
[2020-11-28 16:22:30,692] multiqc [DEBUG ] No samples found: fgbio
|
||||||
|
[2020-11-28 16:22:30,697] multiqc [DEBUG ] No samples found: dragen
|
||||||
|
[2020-11-28 16:22:30,700] multiqc [DEBUG ] No samples found: dedup
|
||||||
|
[2020-11-28 16:22:30,703] multiqc [DEBUG ] No samples found: damageprofiler
|
||||||
|
[2020-11-28 16:22:30,709] multiqc [DEBUG ] No samples found: biobambam2
|
||||||
|
[2020-11-28 16:22:30,711] multiqc [DEBUG ] No samples found: mtnucratio
|
||||||
|
[2020-11-28 16:22:30,714] multiqc [DEBUG ] No samples found: picard
|
||||||
|
[2020-11-28 16:22:30,717] multiqc [DEBUG ] No samples found: prokka
|
||||||
|
[2020-11-28 16:22:30,720] multiqc [DEBUG ] No samples found: samblaster
|
||||||
|
[2020-11-28 16:22:30,723] multiqc [DEBUG ] No samples found: samtools
|
||||||
|
[2020-11-28 16:22:30,726] multiqc [DEBUG ] No samples found: sexdeterrmine
|
||||||
|
[2020-11-28 16:22:30,729] multiqc [DEBUG ] No samples found: bamtools
|
||||||
|
[2020-11-28 16:22:30,731] multiqc [DEBUG ] No samples found: jellyfish
|
||||||
|
[2020-11-28 16:22:30,735] multiqc [DEBUG ] No samples found: vcftools
|
||||||
|
[2020-11-28 16:22:30,739] multiqc [DEBUG ] No samples found: longranger
|
||||||
|
[2020-11-28 16:22:30,742] multiqc [DEBUG ] No samples found: stacks
|
||||||
|
[2020-11-28 16:22:30,745] multiqc [DEBUG ] No samples found: varscan2
|
||||||
|
[2020-11-28 16:22:30,750] multiqc [DEBUG ] No samples found: bbmap
|
||||||
|
[2020-11-28 16:22:30,753] multiqc [DEBUG ] No samples found: bismark
|
||||||
|
[2020-11-28 16:22:30,756] multiqc [DEBUG ] No samples found: biscuit
|
||||||
|
[2020-11-28 16:22:30,759] multiqc [DEBUG ] No samples found: hicexplorer
|
||||||
|
[2020-11-28 16:22:30,762] multiqc [DEBUG ] No samples found: hicup
|
||||||
|
[2020-11-28 16:22:30,765] multiqc [DEBUG ] No samples found: hicpro
|
||||||
|
[2020-11-28 16:22:30,767] multiqc [DEBUG ] No samples found: salmon
|
||||||
|
[2020-11-28 16:22:30,770] multiqc [DEBUG ] No samples found: kallisto
|
||||||
|
[2020-11-28 16:22:30,772] multiqc [DEBUG ] No samples found: slamdunk
|
||||||
|
[2020-11-28 16:22:30,775] multiqc [DEBUG ] No samples found: star
|
||||||
|
[2020-11-28 16:22:30,777] multiqc [DEBUG ] No samples found: hisat2
|
||||||
|
[2020-11-28 16:22:30,780] multiqc [DEBUG ] No samples found: tophat
|
||||||
|
[2020-11-28 16:22:30,783] multiqc [DEBUG ] No samples found: bowtie2
|
||||||
|
[2020-11-28 16:22:30,786] multiqc [DEBUG ] No samples found: bowtie1
|
||||||
|
[2020-11-28 16:22:30,788] multiqc [DEBUG ] No samples found: snpsplit
|
||||||
|
[2020-11-28 16:22:30,791] multiqc [DEBUG ] No samples found: kat
|
||||||
|
[2020-11-28 16:22:30,794] multiqc [DEBUG ] No samples found: leehom
|
||||||
|
[2020-11-28 16:22:30,796] multiqc [DEBUG ] No samples found: adapterRemoval
|
||||||
|
[2020-11-28 16:22:30,798] multiqc [DEBUG ] No samples found: clipandmerge
|
||||||
|
[2020-11-28 16:22:30,801] multiqc [DEBUG ] No samples found: cutadapt
|
||||||
|
[2020-11-28 16:22:30,803] multiqc [DEBUG ] No samples found: flexbar
|
||||||
|
[2020-11-28 16:22:30,806] multiqc [DEBUG ] No samples found: kaiju
|
||||||
|
[2020-11-28 16:22:30,808] multiqc [DEBUG ] No samples found: kraken
|
||||||
|
[2020-11-28 16:22:30,811] multiqc [DEBUG ] No samples found: malt
|
||||||
|
[2020-11-28 16:22:30,813] multiqc [DEBUG ] No samples found: trimmomatic
|
||||||
|
[2020-11-28 16:22:30,816] multiqc [DEBUG ] No samples found: sickle
|
||||||
|
[2020-11-28 16:22:30,818] multiqc [DEBUG ] No samples found: skewer
|
||||||
|
[2020-11-28 16:22:30,820] multiqc [DEBUG ] No samples found: sortmerna
|
||||||
|
[2020-11-28 16:22:30,823] multiqc [DEBUG ] No samples found: biobloomtools
|
||||||
|
[2020-11-28 16:22:30,825] multiqc [DEBUG ] No samples found: fastq_screen
|
||||||
|
[2020-11-28 16:22:30,828] multiqc [DEBUG ] No samples found: afterqc
|
||||||
|
[2020-11-28 16:22:30,830] multiqc [DEBUG ] No samples found: fastp
|
||||||
|
[2020-11-28 16:22:30,845] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports
|
||||||
|
[2020-11-28 16:22:30,896] multiqc [DEBUG ] No samples found: pycoqc
|
||||||
|
[2020-11-28 16:22:30,899] multiqc [DEBUG ] No samples found: minionqc
|
||||||
|
[2020-11-28 16:22:30,901] multiqc [DEBUG ] No samples found: multivcfanalyzer
|
||||||
|
[2020-11-28 16:22:30,904] multiqc [DEBUG ] No samples found: clusterflow
|
||||||
|
[2020-11-28 16:22:30,906] multiqc [DEBUG ] No samples found: bcl2fastq
|
||||||
|
[2020-11-28 16:22:30,908] multiqc [DEBUG ] No samples found: interop
|
||||||
|
[2020-11-28 16:22:30,911] multiqc [DEBUG ] No samples found: ivar
|
||||||
|
[2020-11-28 16:22:30,914] multiqc [DEBUG ] No samples found: flash
|
||||||
|
[2020-11-28 16:22:30,916] multiqc [DEBUG ] No samples found: seqyclean
|
||||||
|
[2020-11-28 16:22:30,921] multiqc [INFO ] Compressing plot data
|
||||||
|
[2020-11-28 16:22:30,951] multiqc [INFO ] Report : multiqc_report.html
|
||||||
|
[2020-11-28 16:22:30,951] multiqc [INFO ] Data : multiqc_data
|
||||||
|
[2020-11-28 16:22:30,951] multiqc [DEBUG ] Moving data file from '/tmp/tmp2h0fqr8s/multiqc_data' to '/home/paolo/Projects/NEXTFLOWetude/nf-core-modules/work/cc/e69df4c4d3d33e79fbb670c7f14b52/multiqc_data'
|
||||||
|
[2020-11-28 16:22:31,035] multiqc [INFO ] MultiQC complete
|
||||||
|
|
@ -2,26 +2,26 @@
|
||||||
"report_data_sources": {
|
"report_data_sources": {
|
||||||
"FastQC": {
|
"FastQC": {
|
||||||
"all_sections": {
|
"all_sections": {
|
||||||
"test_2": "/Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test/input/test_2_fastqc.zip",
|
"test_1": "/home/paolo/Projects/NEXTFLOWetude/nf-core-modules/work/cc/e69df4c4d3d33e79fbb670c7f14b52/test_1_fastqc.zip",
|
||||||
"test_1": "/Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test/input/test_1_fastqc.zip"
|
"test_2": "/home/paolo/Projects/NEXTFLOWetude/nf-core-modules/work/cc/e69df4c4d3d33e79fbb670c7f14b52/test_2_fastqc.zip"
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
},
|
},
|
||||||
"report_general_stats_data": [
|
"report_general_stats_data": [
|
||||||
{
|
{
|
||||||
"test_2": {
|
|
||||||
"percent_gc": 44.0,
|
|
||||||
"avg_sequence_length": 76.0,
|
|
||||||
"total_sequences": 10000.0,
|
|
||||||
"percent_duplicates": 8.370000000000005,
|
|
||||||
"percent_fails": 9.090909090909092
|
|
||||||
},
|
|
||||||
"test_1": {
|
"test_1": {
|
||||||
"percent_gc": 44.0,
|
"percent_gc": 44.0,
|
||||||
"avg_sequence_length": 76.0,
|
"avg_sequence_length": 76.0,
|
||||||
"total_sequences": 10000.0,
|
"total_sequences": 10000.0,
|
||||||
"percent_duplicates": 8.280000000000001,
|
"percent_duplicates": 8.280000000000001,
|
||||||
"percent_fails": 9.090909090909092
|
"percent_fails": 9.090909090909092
|
||||||
|
},
|
||||||
|
"test_2": {
|
||||||
|
"percent_gc": 44.0,
|
||||||
|
"avg_sequence_length": 76.0,
|
||||||
|
"total_sequences": 10000.0,
|
||||||
|
"percent_duplicates": 8.370000000000005,
|
||||||
|
"percent_fails": 9.090909090909092
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
],
|
],
|
||||||
|
|
@ -133,7 +133,7 @@
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
],
|
],
|
||||||
"report_multiqc_command": "/Users/eklavya/.pyenv/versions/miniconda3-latest/bin/multiqc input/",
|
"report_multiqc_command": "/usr/local/bin/multiqc .",
|
||||||
"report_plot_data": {
|
"report_plot_data": {
|
||||||
"fastqc_sequence_counts_plot": {
|
"fastqc_sequence_counts_plot": {
|
||||||
"plot_type": "bar_graph",
|
"plot_type": "bar_graph",
|
||||||
|
|
@ -540,8 +540,8 @@
|
||||||
"xDecimals": false,
|
"xDecimals": false,
|
||||||
"tt_label": "<b>Base {point.x}</b>: {point.y:.2f}",
|
"tt_label": "<b>Base {point.x}</b>: {point.y:.2f}",
|
||||||
"colors": {
|
"colors": {
|
||||||
"test_2": "#5cb85c",
|
"test_1": "#5cb85c",
|
||||||
"test_1": "#5cb85c"
|
"test_2": "#5cb85c"
|
||||||
},
|
},
|
||||||
"yPlotBands": [
|
"yPlotBands": [
|
||||||
{
|
{
|
||||||
|
|
@ -749,8 +749,8 @@
|
||||||
"xmin": 0,
|
"xmin": 0,
|
||||||
"xDecimals": false,
|
"xDecimals": false,
|
||||||
"colors": {
|
"colors": {
|
||||||
"test_2": "#5cb85c",
|
"test_1": "#5cb85c",
|
||||||
"test_1": "#5cb85c"
|
"test_2": "#5cb85c"
|
||||||
},
|
},
|
||||||
"tt_label": "<b>Phred {point.x}</b>: {point.y} reads",
|
"tt_label": "<b>Phred {point.x}</b>: {point.y} reads",
|
||||||
"xPlotBands": [
|
"xPlotBands": [
|
||||||
|
|
@ -2424,14 +2424,15 @@
|
||||||
"id": "fastqc_per_sequence_gc_content_plot",
|
"id": "fastqc_per_sequence_gc_content_plot",
|
||||||
"title": "FastQC: Per Sequence GC Content",
|
"title": "FastQC: Per Sequence GC Content",
|
||||||
"xlab": "% GC",
|
"xlab": "% GC",
|
||||||
|
"ylab": "Percentage",
|
||||||
"ymin": 0,
|
"ymin": 0,
|
||||||
"xmax": 100,
|
"xmax": 100,
|
||||||
"xmin": 0,
|
"xmin": 0,
|
||||||
"yDecimals": false,
|
"yDecimals": false,
|
||||||
"tt_label": "<b>{point.x}% GC</b>: {point.y}",
|
"tt_label": "<b>{point.x}% GC</b>: {point.y}",
|
||||||
"colors": {
|
"colors": {
|
||||||
"test_2": "#5cb85c",
|
"test_1": "#5cb85c",
|
||||||
"test_1": "#5cb85c"
|
"test_2": "#5cb85c"
|
||||||
},
|
},
|
||||||
"data_labels": [
|
"data_labels": [
|
||||||
{
|
{
|
||||||
|
|
@ -2442,8 +2443,7 @@
|
||||||
"name": "Counts",
|
"name": "Counts",
|
||||||
"ylab": "Count"
|
"ylab": "Count"
|
||||||
}
|
}
|
||||||
],
|
]
|
||||||
"ylab": "Percentage"
|
|
||||||
}
|
}
|
||||||
},
|
},
|
||||||
"fastqc_per_base_n_content_plot": {
|
"fastqc_per_base_n_content_plot": {
|
||||||
|
|
@ -2819,8 +2819,8 @@
|
||||||
"xmin": 0,
|
"xmin": 0,
|
||||||
"xDecimals": false,
|
"xDecimals": false,
|
||||||
"colors": {
|
"colors": {
|
||||||
"test_2": "#5cb85c",
|
"test_1": "#5cb85c",
|
||||||
"test_1": "#5cb85c"
|
"test_2": "#5cb85c"
|
||||||
},
|
},
|
||||||
"tt_label": "<b>Base {point.x}</b>: {point.y:.2f}%",
|
"tt_label": "<b>Base {point.x}</b>: {point.y:.2f}%",
|
||||||
"yPlotBands": [
|
"yPlotBands": [
|
||||||
|
|
@ -2918,11 +2918,13 @@
|
||||||
"ymax": 100,
|
"ymax": 100,
|
||||||
"ymin": 0,
|
"ymin": 0,
|
||||||
"yMinTickInterval": 0.1,
|
"yMinTickInterval": 0.1,
|
||||||
|
"yLabelFormat": "{value:.0f}%",
|
||||||
"colors": {
|
"colors": {
|
||||||
"test_2": "#5cb85c",
|
"test_1": "#5cb85c",
|
||||||
"test_1": "#5cb85c"
|
"test_2": "#5cb85c"
|
||||||
},
|
},
|
||||||
"tt_label": "<b>{point.x}</b>: {point.y:.1f}%"
|
"tt_decimals": 2,
|
||||||
|
"tt_suffix": "%"
|
||||||
}
|
}
|
||||||
},
|
},
|
||||||
"fastqc_adapter_content_plot": {
|
"fastqc_adapter_content_plot": {
|
||||||
|
|
@ -3650,35 +3652,13 @@
|
||||||
],
|
],
|
||||||
"decimalPlaces": 1,
|
"decimalPlaces": 1,
|
||||||
"legend": false,
|
"legend": false,
|
||||||
"datalabels": false
|
"datalabels": false,
|
||||||
|
"xcats_samples": false
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
},
|
},
|
||||||
"report_saved_raw_data": {
|
"report_saved_raw_data": {
|
||||||
"multiqc_qualimap_bamqc_genome_results": {},
|
|
||||||
"multiqc_fastqc": {
|
"multiqc_fastqc": {
|
||||||
"test_2": {
|
|
||||||
"Filename": "test_2.fastq.gz",
|
|
||||||
"File type": "Conventional base calls",
|
|
||||||
"Encoding": "Sanger / Illumina 1.9",
|
|
||||||
"Total Sequences": 10000.0,
|
|
||||||
"Sequences flagged as poor quality": 0.0,
|
|
||||||
"Sequence length": 76.0,
|
|
||||||
"%GC": 44.0,
|
|
||||||
"total_deduplicated_percentage": 91.63,
|
|
||||||
"avg_sequence_length": 76.0,
|
|
||||||
"basic_statistics": "pass",
|
|
||||||
"per_base_sequence_quality": "pass",
|
|
||||||
"per_tile_sequence_quality": "pass",
|
|
||||||
"per_sequence_quality_scores": "pass",
|
|
||||||
"per_base_sequence_content": "fail",
|
|
||||||
"per_sequence_gc_content": "pass",
|
|
||||||
"per_base_n_content": "pass",
|
|
||||||
"sequence_length_distribution": "pass",
|
|
||||||
"sequence_duplication_levels": "pass",
|
|
||||||
"overrepresented_sequences": "warn",
|
|
||||||
"adapter_content": "pass"
|
|
||||||
},
|
|
||||||
"test_1": {
|
"test_1": {
|
||||||
"Filename": "test_1.fastq.gz",
|
"Filename": "test_1.fastq.gz",
|
||||||
"File type": "Conventional base calls",
|
"File type": "Conventional base calls",
|
||||||
|
|
@ -3700,18 +3680,40 @@
|
||||||
"sequence_duplication_levels": "pass",
|
"sequence_duplication_levels": "pass",
|
||||||
"overrepresented_sequences": "warn",
|
"overrepresented_sequences": "warn",
|
||||||
"adapter_content": "pass"
|
"adapter_content": "pass"
|
||||||
|
},
|
||||||
|
"test_2": {
|
||||||
|
"Filename": "test_2.fastq.gz",
|
||||||
|
"File type": "Conventional base calls",
|
||||||
|
"Encoding": "Sanger / Illumina 1.9",
|
||||||
|
"Total Sequences": 10000.0,
|
||||||
|
"Sequences flagged as poor quality": 0.0,
|
||||||
|
"Sequence length": 76.0,
|
||||||
|
"%GC": 44.0,
|
||||||
|
"total_deduplicated_percentage": 91.63,
|
||||||
|
"avg_sequence_length": 76.0,
|
||||||
|
"basic_statistics": "pass",
|
||||||
|
"per_base_sequence_quality": "pass",
|
||||||
|
"per_tile_sequence_quality": "pass",
|
||||||
|
"per_sequence_quality_scores": "pass",
|
||||||
|
"per_base_sequence_content": "fail",
|
||||||
|
"per_sequence_gc_content": "pass",
|
||||||
|
"per_base_n_content": "pass",
|
||||||
|
"sequence_length_distribution": "pass",
|
||||||
|
"sequence_duplication_levels": "pass",
|
||||||
|
"overrepresented_sequences": "warn",
|
||||||
|
"adapter_content": "pass"
|
||||||
}
|
}
|
||||||
},
|
},
|
||||||
"multiqc_general_stats": {
|
"multiqc_general_stats": {
|
||||||
"test_2": {
|
"test_1": {
|
||||||
"FastQC_mqc-generalstats-fastqc-percent_duplicates": 8.370000000000005,
|
"FastQC_mqc-generalstats-fastqc-percent_duplicates": 8.280000000000001,
|
||||||
"FastQC_mqc-generalstats-fastqc-percent_gc": 44.0,
|
"FastQC_mqc-generalstats-fastqc-percent_gc": 44.0,
|
||||||
"FastQC_mqc-generalstats-fastqc-avg_sequence_length": 76.0,
|
"FastQC_mqc-generalstats-fastqc-avg_sequence_length": 76.0,
|
||||||
"FastQC_mqc-generalstats-fastqc-percent_fails": 9.090909090909092,
|
"FastQC_mqc-generalstats-fastqc-percent_fails": 9.090909090909092,
|
||||||
"FastQC_mqc-generalstats-fastqc-total_sequences": 10000.0
|
"FastQC_mqc-generalstats-fastqc-total_sequences": 10000.0
|
||||||
},
|
},
|
||||||
"test_1": {
|
"test_2": {
|
||||||
"FastQC_mqc-generalstats-fastqc-percent_duplicates": 8.280000000000001,
|
"FastQC_mqc-generalstats-fastqc-percent_duplicates": 8.370000000000005,
|
||||||
"FastQC_mqc-generalstats-fastqc-percent_gc": 44.0,
|
"FastQC_mqc-generalstats-fastqc-percent_gc": 44.0,
|
||||||
"FastQC_mqc-generalstats-fastqc-avg_sequence_length": 76.0,
|
"FastQC_mqc-generalstats-fastqc-avg_sequence_length": 76.0,
|
||||||
"FastQC_mqc-generalstats-fastqc-percent_fails": 9.090909090909092,
|
"FastQC_mqc-generalstats-fastqc-percent_fails": 9.090909090909092,
|
||||||
|
|
@ -3720,19 +3722,19 @@
|
||||||
}
|
}
|
||||||
},
|
},
|
||||||
"config_analysis_dir_abs": [
|
"config_analysis_dir_abs": [
|
||||||
"/Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test/input"
|
"/home/paolo/Projects/NEXTFLOWetude/nf-core-modules/work/cc/e69df4c4d3d33e79fbb670c7f14b52"
|
||||||
],
|
],
|
||||||
"config_analysis_dir": [
|
"config_analysis_dir": [
|
||||||
"input/"
|
"."
|
||||||
],
|
],
|
||||||
"config_creation_date": "2020-11-23, 18:25",
|
"config_creation_date": "2020-11-28, 16:22",
|
||||||
"config_git_hash": null,
|
"config_git_hash": null,
|
||||||
"config_intro_text": null,
|
"config_intro_text": null,
|
||||||
"config_report_comment": null,
|
"config_report_comment": null,
|
||||||
"config_report_header_info": null,
|
"config_report_header_info": null,
|
||||||
"config_script_path": "/Users/eklavya/.pyenv/versions/miniconda3-latest/lib/python3.7/site-packages/multiqc/utils",
|
"config_script_path": "/usr/local/lib/python3.8/site-packages/multiqc/utils",
|
||||||
"config_short_version": "1.8",
|
"config_short_version": "1.9",
|
||||||
"config_subtitle": null,
|
"config_subtitle": null,
|
||||||
"config_title": null,
|
"config_title": null,
|
||||||
"config_version": "1.8"
|
"config_version": "1.9"
|
||||||
}
|
}
|
||||||
|
|
@ -0,0 +1,3 @@
|
||||||
|
Module Section Sample Name Source
|
||||||
|
FastQC all_sections test_1 /home/paolo/Projects/NEXTFLOWetude/nf-core-modules/work/cc/e69df4c4d3d33e79fbb670c7f14b52/test_1_fastqc.zip
|
||||||
|
FastQC all_sections test_2 /home/paolo/Projects/NEXTFLOWetude/nf-core-modules/work/cc/e69df4c4d3d33e79fbb670c7f14b52/test_2_fastqc.zip
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Sample
|
|
||||||
File diff suppressed because one or more lines are too long
|
|
@ -1,3 +0,0 @@
|
||||||
Module Section Sample Name Source
|
|
||||||
FastQC all_sections test_2 /Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test/input/test_2_fastqc.zip
|
|
||||||
FastQC all_sections test_1 /Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test/input/test_1_fastqc.zip
|
|
||||||
187
tests/data/fastqc/test_1_fastqc.html
Normal file
187
tests/data/fastqc/test_1_fastqc.html
Normal file
File diff suppressed because one or more lines are too long
BIN
tests/data/fastqc/test_1_fastqc.zip
Normal file
BIN
tests/data/fastqc/test_1_fastqc.zip
Normal file
Binary file not shown.
187
tests/data/fastqc/test_2_fastqc.html
Normal file
187
tests/data/fastqc/test_2_fastqc.html
Normal file
File diff suppressed because one or more lines are too long
BIN
tests/data/fastqc/test_2_fastqc.zip
Normal file
BIN
tests/data/fastqc/test_2_fastqc.zip
Normal file
Binary file not shown.
Loading…
Reference in a new issue