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