converts sam/bam/cram/pairs into genome contact map
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
input{:bash}
:file
BAM/CRAM/SAM file or pairs formatted reads file
*.{bam,cram,sam,pairs.gz}
meta2{:bash}
fasta{:bash}
Reference sequence file
*.{fasta,fna,fa}
fai{:bash}
Reference sequence index file
*.{fai}
pretext{:bash}
*.pretext{:bash}
pretext map
*.pretext
versions_pretextmap{:bash}
${task.process}{:bash}
:string
Name of the process
PretextMap{:bash}
Name of the tool
PretextMap | sed "/Version/!d; s/.*Version //"{:bash}
:eval
The expression to obtain the version of the tool
versions_samtools{:bash}
samtools{:bash}
samtools --version | sed "1!d; s/samtools //"{:bash}
versions{:bash}
Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.
