filter/convert SAM/BAM/CRAM file
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
input{:bash}
:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
index{:bash}
BAM.BAI/BAM.CSI/CRAM.CRAI file (optional)
*.{.bai,.csi,.crai}
meta2{:bash}
Groovy Map containing reference information e.g. [ id:‘genome’ ]
fasta{:bash}
Fasta reference file
*.{fasta,fa}
fai{:bash}
Fasta reference file index
*.{fai}
qname{:bash}
Optional file with read names to output only select alignments
*.{txt,list}
index_format{:bash}
:string
Index format, used together with ext.args = ‘—write-index’
bai|csi|crai
bam{:bash}
${prefix}.bam{:bash}
optional filtered/converted BAM file
*.{bam}
cram{:bash}
${prefix}.cram{:bash}
optional filtered/converted CRAM file
*.{cram}
sam{:bash}
${prefix}.sam{:bash}
optional filtered/converted SAM file
*.{sam}
bai{:bash}
${prefix}.${file_type}.bai{:bash}
optional BAM file index
*.{bai}
csi{:bash}
${prefix}.${file_type}.csi{:bash}
optional tabix BAM file index
*.{csi}
crai{:bash}
${prefix}.${file_type}.crai{:bash}
optional CRAM file index
*.{crai}
unselected{:bash}
${prefix}.unselected.${file_type}{:bash}
optional file with unselected alignments
*.unselected.{bam,cram,sam}
unselected_index{:bash}
${prefix}.unselected.${file_type}.{csi,crai}{:bash}
index for the “unselected” file
*.unselected.{csi,crai}
versions_samtools{:bash}
${task.process}{:bash}
Name of the process
samtools{:bash}
Name of the tool
samtools version | sed "1!d;s/.* //"{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
