- ๐ป Mostly
R, Shiny, nextflow & shell
- ๐ Learning
Rust, awk
- ๐งฌ Interested in bioinformatics
angelovangel / nxf-fastqc Goto Github PK
View Code? Open in Web Editor NEWA simple fastp-MultiQC nextflow pipeline
A simple fastp-MultiQC nextflow pipeline
R, Shiny, nextflow & shell
Rust, awk
For big fastq files, the N50 calculation gets an integer overflow in 'cumsum'
Zig-zag curves...
The nf execution directory does not match the pwd. Rather, the wd of the main.nf is used.
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
process multiqc
fails with big numbers of reads or bases. Presumably the formatter is causing this (java.text.DecimalFormat)
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.
Because the seqtools.R script takes all fastq as arguments, it does not parallelize natively with nextflow.
Use parallel in R
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
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.
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