Extracts reads mapped to chromosome 6 and any HLA decoys or chromosome 6 alternates.
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam{:bash}
:file
BAM file. If the BAM file is not indexed, this tool will run samtools index before extracting reads.
*.bam
extracted_reads_fastq{:bash}
*.fq.gz{:bash}
FASTQ file(s) containing chromosome 6 reads and related HLA sequences
*.fq.gz
log{:bash}
*.log{:bash}
Log file for run summary
*.log
intermediate_sam{:bash}
temp_files/**.sam{:bash}
Optional intermediate SAM file
*.sam
intermediate_bam{:bash}
temp_files/**.bam{:bash}
Optional intermediate BAM file
intermediate_sorted_bam{:bash}
temp_files/**.sorted.bam{:bash}
Optional intermediate sorted BAM file
*.sorted.bam
versions_arcashla{:bash}
${task.process}{:bash}
:string
The name of the process
arcashla{:bash}
The name of the tool
echo 0.5.0{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
arcasHLA performs high resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples.
