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