Precision HLA typing and expression from RNA-seq data using seq2HLA
meta
:map
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
reads
:file
Paired-end FASTQ files for RNA-seq data
*.{fastq.gz,fq.gz}
class1_genotype_2d
*ClassI-class.HLAgenotype2digits
HLA Class I 2-digit genotype results
class2_genotype_2d
*ClassII.HLAgenotype2digits
HLA Class II 2-digit genotype results
class1_genotype_4d
*ClassI-class.HLAgenotype4digits
HLA Class I 4-digit genotype results
class2_genotype_4d
*ClassII.HLAgenotype4digits
HLA Class II 4-digit genotype results
class1_bowtielog
*ClassI-class.bowtielog
HLA Class I Bowtie alignment log
class2_bowtielog
*ClassII.bowtielog
HLA Class II Bowtie alignment log
class1_expression
*ClassI-class.expression
HLA Class I expression results
class2_expression
*ClassII.expression
HLA Class II expression results
class1_nonclass_genotype_2d
*ClassI-nonclass.HLAgenotype2digits
HLA Class I non-classical 2-digit genotype results
ambiguity
*.ambiguity
HLA typing ambiguity results
class1_nonclass_genotype_4d
*ClassI-nonclass.HLAgenotype4digits
HLA Class I non-classical 4-digit genotype results
class1_nonclass_bowtielog
*ClassI-nonclass.bowtielog
HLA Class I non-classical Bowtie alignment log
class1_nonclass_expression
*ClassI-nonclass.expression
HLA Class I non-classical expression results
versions_seq2hla
${task.process}
:string
The name of the process
seq2hla
The name of the tool
seq2HLA --version | sed 's/seq2HLA.py //'
:eval
The expression to obtain the version of the tool
versions
Precision HLA typing and expression from next-generation RNA sequencing data
