modules/simpleaf_index

Indexing of transcriptome for gene expression quantification using SimpleAF

indexingtranscriptomegene expressionSimpleAF

https://github.com/nf-core/modules/[...]/modules/nf-core/simpleaf/index

Description

Indexing of transcriptome for gene expression quantification using SimpleAF

Input

name:type

description

pattern

`meta:map`

Groovy Map containing information on genome_fasta

`genome_fasta:file`

FASTA file containing the genome sequence

`meta2:map`

Groovy Map containing information on genome_gtf

`genome_gtf:file`

GTF file containing transcript annotations. Optional if transcript FASTA file is provided.

`meta3:map`

Groovy Map containing information on transcript_fasta

`transcript_fasta:file`

FASTA file containing the transcript sequences. Optional if transcript GTF file is provided.

Output

name:type

description

pattern

`index`

`meta:map`

Groovy Map containing information on genome_fasta or transcript_fasta (whichever was used)

`${prefix}/index:directory`

Folder containing the Salmon index files

salmon/index

`transcript_tsv`

`meta:map`

Groovy Map containing information on genome_fasta or transcript_fasta (whichever was used)

`${prefix}/ref/t2g_3col.tsv:file`

Transcript-to-gene mapping file in 3-column TSV format

salmon/ref/*_t2g_3col.tsv

`salmon`

`meta:map`

Groovy Map containing information on genome_fasta or transcript_fasta (whichever was used)

`${prefix}:directory`

Folder containing the Salmon files

salmon

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

simpleaf
BSD-3-Clause

SimpleAF is a tool for quantification of gene expression from RNA-seq data

github.com/COMBINE-lab/simpleaf

modules/simpleaf_index

Description

Input

`meta:map`

`genome_fasta:file`

`meta2:map`

`genome_gtf:file`

`meta3:map`

`transcript_fasta:file`

Output

`index`

`meta:map`

`${prefix}/index:directory`

`transcript_tsv`

`meta:map`

`${prefix}/ref/t2g_3col.tsv:file`

`salmon`

`meta:map`

`${prefix}:directory`

`versions`

`versions.yml:file`

Tools

simpleaf
BSD-3-Clause

maintainers

get in touch

modules/simpleaf_index

Description

Input

meta:map

genome_fasta:file

meta2:map

genome_gtf:file

meta3:map

transcript_fasta:file

Output

index

meta:map

${prefix}/index:directory

transcript_tsv

meta:map

${prefix}/ref/t2g_3col.tsv:file

salmon

meta:map

${prefix}:directory

versions

versions.yml:file

Tools

simpleaf BSD-3-Clause

maintainers

get in touch

`meta:map`

`genome_fasta:file`

`meta2:map`

`genome_gtf:file`

`meta3:map`

`transcript_fasta:file`

`index`

`meta:map`

`${prefix}/index:directory`

`transcript_tsv`

`meta:map`

`${prefix}/ref/t2g_3col.tsv:file`

`salmon`

`meta:map`

`${prefix}:directory`

`versions`

`versions.yml:file`

simpleaf
BSD-3-Clause