Convert paired-end bwa SA coordinate files to SAM format
meta{:bash}
:map
Groovy Map containing sample information. e.g. [ id:‘test’, single_end:false ]
reads{:bash}
:file
FASTQ files specified alongside meta in input channel.
*.{fastq,fq}.gz
sai{:bash}
SAI file specified alongside meta and reads in input channel.
*.sai
meta2{:bash}
Groovy Map containing reference information. e.g. [ id:‘test’, single_end:false ]
index{:bash}
:directory
Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX
bwa/
bam{:bash}
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
*.bam{:bash}
BAM file
*.bam
versions_bwa{:bash}
${task.process}{:bash}
:string
The process the versions were collected from
bwa{:bash}
The tool name
bwa 2>&1 | sed -n "s/^Version: //p"{:bash}
The command used to generate the version of the tool
versions_samtools{:bash}
samtools{:bash}
samtools version | sed '1!d;s/.* //'{:bash}
versions{:bash}
BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
