Nextflow Registry | nf-core/custom/rsemmergecounts@0.0.0-6c4ed3a

nf-core/custom/rsemmergecounts @ 0.0.0-6c4ed3a

Merge per-sample RSEM results into wide and long format TSV matrices

rsem merge counts gene expression

Latest version: 0.0.0-6c4ed3a

Total downloads: 8

Source: nf-core/modules

Authors: @pinin4fjords

Maintainers: @pinin4fjords

Merge per-sample RSEM results into wide and long format TSV matrices

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

include { CUSTOM_RSEMMERGECOUNTS } from 'nf-core/custom/rsemmergecounts'

MIT License

Process

`Name`	`CUSTOM_RSEMMERGECOUNTS`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information. e.g. [ id:'all_samples' ].
`genes/*` file	Collected RSEM gene-level results files across all samples. `*.genes.results`

`isoforms/*` file	Collected RSEM isoform-level results files across all samples. `*.isoforms.results`

Output 7 channels

#1 tpm_gene tuple

`meta` map	Groovy Map containing sample information. e.g. [ id:'all_samples' ].
`${prefix}.gene_tpm.tsv` file	Wide-format gene-level TPM matrix with samples as columns. `*.gene_tpm.tsv`

#2 genes_long tuple

`meta` map	Groovy Map containing sample information. e.g. [ id:'all_samples' ].
`${prefix}.genes_long.tsv` file	Long-format gene-level results with all RSEM fields and a sample_name column. `*.genes_long.tsv`

#3 counts_gene tuple

`meta` map	Groovy Map containing sample information. e.g. [ id:'all_samples' ].
`${prefix}.gene_counts.tsv` file	Wide-format gene-level count matrix (expected_count column from RSEM) with samples as columns. `*.gene_counts.tsv`

#4 versions_sed tuple

`${task.process}` string	The name of the process
`sed` string	The name of the tool
`sed --version 2>&1 \| sed '1!d;s/^.*) //'` eval	The expression to obtain the version of the tool

#5 isoforms_long tuple

`meta` map	Groovy Map containing sample information. e.g. [ id:'all_samples' ].
`${prefix}.isoforms_long.tsv` file	Long-format isoform-level results with all RSEM fields and a sample_name column. `*.isoforms_long.tsv`

#6 tpm_transcript tuple

`meta` map	Groovy Map containing sample information. e.g. [ id:'all_samples' ].
`${prefix}.transcript_tpm.tsv` file	Wide-format transcript-level TPM matrix with samples as columns. `*.transcript_tpm.tsv`

#7 counts_transcript tuple

`meta` map	Groovy Map containing sample information. e.g. [ id:'all_samples' ].
`${prefix}.transcript_counts.tsv` file	Wide-format transcript-level count matrix (expected_count column from RSEM) with samples as columns. `*.transcript_counts.tsv`

Tool	Description	Homepage
custom	Custom module to merge RSEM gene and isoform count results across samples into count/TPM matrices and long-format tables.	n/a

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:12:14 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fcustom%2Frsemmergecounts/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/custom/rsemmergecounts/blobs/sha256:861dff531b7288e10d39234b83370a887ae40dc9f0f84c0ec88cfeca3a7994ba
Size	3.4 KB
Checksum	sha256:861dff531b7288e10d39234b83370a887ae40dc9f0f84c0ec88cfeca3a7994ba