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nf-core/tximeta/tximport @ 0.0.0-6c4ed3a

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

gene kallisto pseudoalignment rsem salmon transcript
Latest version: 0.0.0-6c4ed3a
Total downloads: 10
Source: nf-core/modules
Authors: @pinin4fjords
Maintainers: @pinin4fjords

Summary

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

Get started

Add the following snippet to your workflow script to include this module.

include { TXIMETA_TXIMPORT } from 'nf-core/tximeta/tximport'

License

MIT License

Process
Name TXIMETA_TXIMPORT
Input 3 channels
#1 tuple
meta map

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

Quantification files
#2 tuple
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 9 channels
#1 tpm_gene tuple
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
#2 versions
versions.yml file

YAML file containing versions of tools used in the module
#3 counts_gene tuple
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
#4 lengths_gene tuple
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
#5 tpm_transcript tuple
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
#6 counts_transcript tuple
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
#7 counts_gene_scaled tuple
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
#8 lengths_transcript tuple
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

 *gene_lengths.tsv
#9 counts_gene_length_scaled tuple
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
Tool Description Homepage
tximeta Transcript Quantification Import with Automatic Metadata