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Clarify antibody documentation #515

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Merged
Kevin-Brockers merged 4 commits into from
May 19, 2026
Merged

Clarify antibody documentation #515

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58a7c49
Changed antibody description to be more explicit
Kevin-Brockers May 18, 2026
6663c83
Updated CHANGELOG
Kevin-Brockers May 18, 2026
97ed47a
Added PR review suggestion
Kevin-Brockers May 19, 2026
0235032
[automated] Fix code linting
nf-core-bot May 19, 2026
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -25,6 +25,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
naming collisions when sample and replicate combination is identical for multiple antibodies see.
- [[#467](https://github.com/nf-core/chipseq/issues/467), [#510](https://github.com/nf-core/chipseq/issues/510)] -
Restrict the usage to one IP against one control replicate.
- [[ #479](https://github.com/nf-core/chipseq/issues/479)] - Changed the usage documentation for antibodies to be
required for IP samples. Since a ChIP IP sample will always have an antibody, it should be specified to distinguish
the sample from input/controls.

### Parameters

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2 changes: 1 addition & 1 deletion docs/usage.md
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Expand Up @@ -127,7 +127,7 @@ NAIVE_INPUT,BLA203A49_S1_L006_R1_001.fastq.gz,,3,,,
| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". |
| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". |
| `replicate` | Integer representing replicate number. This will be identical for re-sequenced libraries. Must start from `1..<number of replicates>`. |
| `antibody` | Antibody name. This is required to segregate downstream analysis for different antibodies. Required when `control` is specified. |
| `antibody` | Antibody name. This is required to segregate downstream analysis for different antibodies. Required for IP samples. |
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| `control` | Sample name for control sample. |
| `control_replicate` | Integer representing replicate number for control sample. |

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