modules/star_genomegenerate

Create index for STAR

indexfastagenomereferencemulti-toolstarsamtoolsgawk

https://github.com/nf-core/modules/[...]/modules/nf-core/star/genomegenerate

Description

Create index for STAR

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`fasta`
`:file`

Fasta file of the reference genome

`meta2`
`:map`

Groovy Map containing reference information e.g. [ id:‘test’ ]

`gtf`
`:file`

Optional GTF file of the reference genome, used to build the splice junction database

Output

name:type

description

pattern

`index`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`star`
`:directory`

Folder containing the star index files

star

`versions_star`

`${task.process}`
`:string`

The name of the process

`star`
`:string`

The name of the tool

`STAR --version | sed -e "s/STAR_//g"`
`:eval`

The expression to obtain the version of the tool

`versions_samtools`

`${task.process}`
`:string`

The name of the process

`samtools`
`:string`

The name of the tool

`samtools --version | sed -n '1s/samtools //p'`
`:eval`

The expression to obtain the version of the tool

`versions_gawk`

`${task.process}`
`:string`

The name of the process

`gawk`
`:string`

The name of the tool

`gawk --version | sed -n '1{s/GNU Awk //;s/,.*//;p}'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`star`
`:string`

The name of the tool

`STAR --version | sed -e "s/STAR_//g"`
`:eval`

The expression to obtain the version of the tool

`${task.process}`
`:string`

The name of the process

`samtools`
`:string`

The name of the tool

`samtools --version | sed -n '1s/samtools //p'`
`:eval`

The expression to obtain the version of the tool

`${task.process}`
`:string`

The name of the process

`gawk`
`:string`

The name of the tool

`gawk --version | sed -n '1{s/GNU Awk //;s/,.*//;p}'`
`:eval`

The expression to obtain the version of the tool

Tools

star
MIT

STAR is a software package for mapping DNA sequences against a large reference genome, such as the human genome.

args_id: $args

github.com/alexdobin/STAR 10.1093/bioinformatics/bts635

samtools
MIT

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.

args_id: $args2

http://www.htslib.org http://www.htslib.org/doc/samtools 10.1093/bioinformatics/btp352

gawk
GPL v3

GNU awk

args_id: $args3

gnu.org/software/gawk gnu.org/software/gawk/manual https://www.gnu.org/prep/ftp.html

modules/star_genomegenerate

Description

Input

meta :map

fasta :file

meta2 :map

gtf :file

Output

index

meta :map

star :directory

versions_star

${task.process} :string

star :string

STAR --version | sed -e "s/STAR_//g" :eval

versions_samtools

${task.process} :string

samtools :string

samtools --version | sed -n '1s/samtools //p' :eval

versions_gawk

${task.process} :string

gawk :string

gawk --version | sed -n '1{s/GNU Awk //;s/,.*//;p}' :eval

Topics

versions

${task.process} :string

star :string

STAR --version | sed -e "s/STAR_//g" :eval

${task.process} :string

samtools :string

samtools --version | sed -n '1s/samtools //p' :eval

${task.process} :string

gawk :string

gawk --version | sed -n '1{s/GNU Awk //;s/,.*//;p}' :eval

Tools

starMIT

samtoolsMIT

gawkGPL v3

included in

maintainers

get in touch

`meta`
`:map`

`fasta`
`:file`

`meta2`
`:map`

`gtf`
`:file`

`index`

`meta`
`:map`

`star`
`:directory`

`versions_star`

`${task.process}`
`:string`

`star`
`:string`

`STAR --version | sed -e "s/STAR_//g"`
`:eval`

`versions_samtools`

`${task.process}`
`:string`

`samtools`
`:string`

`samtools --version | sed -n '1s/samtools //p'`
`:eval`

`versions_gawk`

`${task.process}`
`:string`

`gawk`
`:string`

`gawk --version | sed -n '1{s/GNU Awk //;s/,.*//;p}'`
`:eval`

`versions`

`${task.process}`
`:string`

`star`
`:string`

`STAR --version | sed -e "s/STAR_//g"`
`:eval`

`${task.process}`
`:string`

`samtools`
`:string`

`samtools --version | sed -n '1s/samtools //p'`
`:eval`

`${task.process}`
`:string`

`gawk`
`:string`

`gawk --version | sed -n '1{s/GNU Awk //;s/,.*//;p}'`
`:eval`

star
MIT

samtools
MIT

gawk
GPL v3