angelovangel/nxf-fastqc

A simple fastp-MultiQC nextflow pipeline

• 💻 Mostly R, Shiny, nextflow & shell
• 📚 Learning Rust, awk
• 🧬 Interested in bioinformatics

nxf-fastqc's Issues

integer overflow in 'cumsum'

For big fastq files, the N50 calculation gets an integer overflow in 'cumsum'

GC-content distribution is not smooth for Illumina data

Zig-zag curves...

Set correct working directory

The nf execution directory does not match the pwd. Rather, the wd of the main.nf is used.

`bam2fastq`

Hi @angelovangel

Do you have any plans for inclusion of pbtk/bam2fastq in your workflow?

I am planning to fork your repo and add pbtk/bam2fastq. I thought I should ask you if you already have any such plans? Secondly, are you open to the use of nf-core DSL2 modules in your pipeline?

Cheers

fails with big numbers of reads or bases

process multiqc fails with big numbers of reads or bases. Presumably the formatter is causing this (java.text.DecimalFormat)

Get rid of "WARN: Failed to publish file:..."

The multiqc report file is published OK, this message is due to FileAlreadyExistsException. When the pipeline is run for a second time (and multiqc report is already there), no warning. Check script if there is somehow duplication of the published file.

use parallel for the seqTools process

Because the seqtools.R script takes all fastq as arguments, it does not parallelize natively with nextflow.
Use parallel in R

reduce with mergeFastqq fails for Nanopore fastq files

This here:
Reduce( mergeFastqq, mclapply(params$fqfiles, fastqq, k = 3) )

causes this error with Nanopore reads:

Quitting from lines 30-91 (fastq-stats-report.Rmd)
  Error in cbind(lhs@seqLenCount, rhs@seqLenCount) :
    number of rows of matrices must match (see arg 2)
  Calls: <Anonymous> ... withVisible -> eval -> eval -> Reduce -> f -> f -> cbind

find fastq files recursively in input folder

Go recursively in input folder (--readsdir) and include all fastq files found in the report. Simple change in the search pattern to **_R{1,2}_001.fastq.gz should be enough.