modules/tximeta_tximport

Import transcript-level abundances and estimated counts for gene-level analysis packages

genekallistopseudoalignmentrsemsalmontranscript

https://github.com/nf-core/modules/[...]/modules/nf-core/tximeta/tximport

Description

Import transcript-level abundances and estimated counts for gene-level analysis packages

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing information related to the experiment as a whole e.g. [ id:'SRP123456' ]

`quants/*`
`:file`

Quantification files

`meta2`
`:map`

Groovy Map containing reference information related to the species reference e.g. [ id:'yeast' ]

`tx2gene`
`:file`

A transcript to gene mapping table such as those generated by custom/tx2gene

*.{csv,tsv}

`quant_type`
`:string`

Quantification type, kallisto, salmon, or rsem

Output

name:type

description

pattern

`tpm_gene`

`meta`
`:map`

Groovy Map containing information related to the experiment as a whole e.g. [ id:'SRP123456' ]

`*gene_tpm.tsv`
`:file`

Abundance (TPM) values derived from tximport output after summarizeToGene(), without a ‘countsFromAbundance’ specification

*gene_tpm.tsv

`counts_gene`

`meta`
`:map`

Groovy Map containing information related to the experiment as a whole e.g. [ id:'SRP123456' ]

`*gene_counts.tsv`
`:file`

Count values derived from tximport output after summarizeToGene(), without a ‘countsFromAbundance’ specification

*gene_counts.tsv

`counts_gene_length_scaled`

`meta`
`:map`

Groovy Map containing information related to the experiment as a whole e.g. [ id:'SRP123456' ]

`*gene_counts_length_scaled.tsv`
`:file`

Count values derived from tximport output after summarizeToGene(), with a ‘countsFromAbundance’ specification of ‘lengthScaledTPM’

*gene_counts_length_scaled.tsv

`counts_gene_scaled`

`meta`
`:map`

Groovy Map containing information related to the experiment as a whole e.g. [ id:'SRP123456' ]

`*gene_counts_scaled.tsv`
`:file`

Count values derived from tximport output after summarizeToGene(), with a ‘countsFromAbundance’ specification of ‘scaledTPM’

*gene_counts_scaled.tsv

`lengths_gene`

`meta`
`:map`

Groovy Map containing information related to the experiment as a whole e.g. [ id:'SRP123456' ]

`*gene_lengths.tsv`
`:file`

Length values derived from tximport output after summarizeToGene(), without a ‘countsFromAbundance’ specification

*gene_lengths.tsv

`tpm_transcript`

`meta`
`:map`

Groovy Map containing information related to the experiment as a whole e.g. [ id:'SRP123456' ]

`*transcript_tpm.tsv`
`:file`

Abundance (TPM) values derived from tximport output without summarizeToGene(), without a ‘countsFromAbundance’ specification

*transcript_tpm.tsv

`counts_transcript`

`meta`
`:map`

Groovy Map containing information related to the experiment as a whole e.g. [ id:'SRP123456' ]

`*transcript_counts.tsv`
`:file`

Count values derived from tximport output without summarizeToGene(), without a ‘countsFromAbundance’ specification

*transcript_counts.tsv

`lengths_transcript`

`meta`
`:map`

Groovy Map containing information related to the experiment as a whole e.g. [ id:'SRP123456' ]

`*transcript_lengths.tsv`
`:file`

Length values derived from tximport output without summarizeToGene(), without a ‘countsFromAbundance’ specification

*transcript_lengths.tsv

`tx2gene_augmented`

`meta`
`:map`

Groovy Map containing information related to the experiment as a whole e.g. [ id:'SRP123456' ]

`*tx2gene_augmented.tsv`
`:file`

tx2gene mapping table actually used by tximport, equal to the input tx2gene with self-mappings appended for any transcripts present in the quantification output but missing from the input. Use this file (not the input tx2gene) to reproduce the published gene-level outputs from the per-sample quantification files.

*tx2gene_augmented.tsv

`versions`

`versions.yml`
`:file`

YAML file containing versions of tools used in the module

Topics

name:type

description

pattern

`versions`

`versions.yml`
`:string`

The name of the process

Tools

tximeta
GPL-2

Transcript Quantification Import with Automatic Metadata

bioconductor.org/packages/release/bioc/html/tximeta bioconductor.org/packages/release/bioc/vignettes/tximeta/inst/doc/tximeta https://github.com/thelovelab/tximeta 10.1371/journal.pcbi.1007664

modules/tximeta_tximport

Description

Input

meta:map

quants/*:file

meta2:map

tx2gene:file

quant_type:string

Output

tpm_gene

meta:map

*gene_tpm.tsv:file

counts_gene

meta:map

*gene_counts.tsv:file

counts_gene_length_scaled

meta:map

*gene_counts_length_scaled.tsv:file

counts_gene_scaled

meta:map

*gene_counts_scaled.tsv:file

lengths_gene

meta:map

*gene_lengths.tsv:file

tpm_transcript

meta:map

*transcript_tpm.tsv:file

counts_transcript

meta:map

*transcript_counts.tsv:file

lengths_transcript

meta:map

*transcript_lengths.tsv:file

tx2gene_augmented

meta:map

*tx2gene_augmented.tsv:file

versions

versions.yml:file

Topics

versions

versions.yml:string

Tools

tximeta GPL-2

included in

maintainer

get in touch

`meta`
`:map`

`quants/*`
`:file`

`meta2`
`:map`

`tx2gene`
`:file`

`quant_type`
`:string`

`tpm_gene`

`meta`
`:map`

`*gene_tpm.tsv`
`:file`

`counts_gene`

`meta`
`:map`

`*gene_counts.tsv`
`:file`

`counts_gene_length_scaled`

`meta`
`:map`

`*gene_counts_length_scaled.tsv`
`:file`

`counts_gene_scaled`

`meta`
`:map`

`*gene_counts_scaled.tsv`
`:file`

`lengths_gene`

`meta`
`:map`

`*gene_lengths.tsv`
`:file`

`tpm_transcript`

`meta`
`:map`

`*transcript_tpm.tsv`
`:file`

`counts_transcript`

`meta`
`:map`

`*transcript_counts.tsv`
`:file`

`lengths_transcript`

`meta`
`:map`

`*transcript_lengths.tsv`
`:file`

`tx2gene_augmented`

`meta`
`:map`

`*tx2gene_augmented.tsv`
`:file`

`versions`

`versions.yml`
`:file`

`versions`

`versions.yml`
`:string`

tximeta
GPL-2