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Code and Data to include in WGS Build

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isugifnf aseetharam zm-git-dev

maize_wgs_build's Issues

Merging multiple sequencing lane fastq-files

Hi,

Good job on automating this pipeline through nextflow!
I have several fastq-files of the same sample, sequenced on different sequencing lanes, and I was wondering at what stage these should be merged together.
I tried giving them the same sample name in my reads_file and running the pipeline, but then I get an "input file name collision" error at the run_gatk_snp stage because I have multiple sample_merged.bam files.

Thanks in advance!

Best regards,

Thomas

add feature: java options

Add a --java-options parameter

params{
  java_options = false     // example "-Xmx60g -XX:+UseParallelGC"
}
env {
  java_options = params.java_options ? "--java-options \\\"$params.java_options\\\"" : "--java-options \\\"-Xmx80g -XX:+UseParallelGC -Djava.io.tmpdir=\$TMPDIR\\\""
}

bwa-mem2

Switch default from using bwa to bwa-mem2

Other notes:

https://github.com/bwa-mem2/bwa-mem2
check RAM usage if possible

FASTQ and FASTQ.gz input

Verify that the pipeline can take a mix of uncompressed fastq as well as compressed fastq.gz.

Update the help statement

Why isn't this called FASTQ to BAM?

Maize_WGS_Build/modules/fastqToSAM.nf

Lines 17 to 44 in 2eabcad

    
           process fastqToSAM_run { 
        
               tag "$readname" 
        
               label 'picard' 
        
               publishDir "${params.outdir}/fastqToSAM", mode: 'copy' 
        
               input: 
        
               tuple val(readname), path(readpairs) 
        
           //    val read1 
        
           //    val read2 
        
           //    val readgroup 
        
           //    val readname 
        
           //    val platform 
        
           //    val rundate 
        
           //    var center 
        
               output: 
        
               path "${readname}_fastqtosam.bam" 
        
               script: 
        
               """ 
        
               #! /usr/bin/env bash 
        
               picard FastqToSam \ 
        
                 FASTQ=${readpairs.get(0)} \ 
        
                 FASTQ2=${readpairs.get(1)} \ 
        
                 OUTPUT=${readname}_fastqtosam.bam \ 
        
                 SAMPLE_NAME=${readname} 
        
               """ 
        
           }

huffordlab / maize_wgs_build Goto Github PK

maize_wgs_build's People

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maize_wgs_build's Issues

Merging multiple sequencing lane fastq-files

add feature: java options

bwa-mem2

FASTQ and FASTQ.gz input

Why isn't this called FASTQ to BAM?

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	process fastqToSAM_run {
	tag "$readname"
	label 'picard'
	publishDir "${params.outdir}/fastqToSAM", mode: 'copy'

	input:
	tuple val(readname), path(readpairs)
	// val read1
	// val read2
	// val readgroup
	// val readname
	// val platform
	// val rundate
	// var center

	output:
	path "${readname}_fastqtosam.bam"

	script:
	"""
	#! /usr/bin/env bash
	picard FastqToSam \
	FASTQ=${readpairs.get(0)} \
	FASTQ2=${readpairs.get(1)} \
	OUTPUT=${readname}_fastqtosam.bam \
	SAMPLE_NAME=${readname}
	"""
	}