nf-core/imc2mc @ 0.0.0-0c7146d
Summary
Staging module transforming Imaging Mass Cytometry .txt files to .tif files with OME-XML metadata. Includes optional hot pixel removal.
Get started
Add the following snippet to your workflow script to include this module.
include { IMC2MC } from 'nf-core/imc2mc'
License
MIT License
Process
Name
|
IMC2MC |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
txtfile
file
|
Acquisition TXT file *.{txt}
|
Output
2 channels
#1
tif
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.tif
file
|
One output .tif file containing acquisition and metadata *.{tif}
|
#2
versions_imc2mc
tuple
${task.process}
string
|
The name of the process |
|---|---|
imc2mc
string
|
The name of the tool |
imc2mc --version | sed 's/v//g'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| imc2mc | Formatting Imaging Mass Cytrometry (IMC) output files to be compatible with the MCMICRO pipeline. | https://github.com/SchapiroLabor/imc2mc |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 0c7146d85582628b5d1034504702fa808632b1af |
| Release Date | 08 Apr 2026 18:49:01 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fimc2mc/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/imc2mc/blobs/sha256:b4bf0481f65ebbbd87e9b012d54f6ad0e384e628d8ad716836a9f1be7cd21743 |
| Size | 2.3 KB |
| Checksum | sha256:b4bf0481f65ebbbd87e9b012d54f6ad0e384e628d8ad716836a9f1be7cd21743 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:49:01 (UTC) | 1 | 2.3 KB | - |