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Kevin-BrockersKevin-Brockers
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Sample sheet check will raise error when one sample-replicate has more than one antibody specified, added further explanation in usage
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Lines changed: 26 additions & 13 deletions

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‎CHANGELOG.md‎

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@@ -21,8 +21,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- [[PR #493](https://github.com/nf-core/chipseq/pull/493)] - Follow up to #487.
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- [[#492](https://github.com/nf-core/chipseq/issues/492), [#417](https://github.com/nf-core/chipseq/issues/417)] - Refactor local modules to nf-core standard.
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- [[#416](https://github.com/nf-core/chipseq/issues/416)] - Moved the KHMER_UNIQUEKMERS logic to prepare_genome
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- [[#510](https://github.com/nf-core/chipseq/issues/510)] - Restrict the usage to one IP replicate against one control see: [#440](https://github.com/nf-core/chipseq/issues/440)
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replicate.
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- [[#440](https://github.com/nf-core/chipseq/issues/440), [#510](https://github.com/nf-core/chipseq/issues/510)] - Fix
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naming collisions when sample and replicate combination is identical for multiple antibodies see.
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- [[#467](https://github.com/nf-core/chipseq/issues/467), [#510](https://github.com/nf-core/chipseq/issues/510)] -
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Restrict the usage to one IP against one control replicate.
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### Parameters
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‎bin/check_samplesheet.py‎

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@@ -212,11 +212,13 @@ def check_samplesheet(file_in, file_out):
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sample,
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)
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set_antibodies = set()
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set_control_replicates = set()
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for idx, val in enumerate(sample_mapping_dict[sample][replicate]):
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control = "_REP".join(val[-1].split("_REP")[:-1])
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control_replicate = val[-1].split("_REP")[-1]
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set_control_replicates.update(control_replicate)
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set_control_replicates.add(control_replicate)
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if control and (
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control not in sample_mapping_dict.keys()
@@ -228,10 +230,19 @@ def check_samplesheet(file_in, file_out):
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val[-1],
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)
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for x in sample_mapping_dict[sample][replicate]:
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set_antibodies.add(x[4])
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# Check that a given sample replicate only uses one antibody
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if len(set_antibodies) > 1:
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print_error(
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f"Sample: {sample}, replicate {replicate} has more than one antibody specified!"
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)
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# Check that a given sample-replicate have only one control replicate
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if len(set_control_replicates) > 1:
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print_error(
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f"Sample: {sample}, replicate {replicate} has more than one control replicate! Revise the experimental design, see: 'Note on IP and control replicates'"
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f"Sample: {sample}, replicate {replicate} has more than one control replicate specified! Revise the experimental design, see: 'Note on IP and control replicates'"
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)
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## Write to file

‎docs/usage.md‎

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NAIVE_INPUT,BLA203A49_S1_L006_R1_001.fastq.gz,,3,,,
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```
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| Column | Description |
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| ------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
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| `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
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| `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". |
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| `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". |
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| `replicate` | Integer representing replicate number. This will be identical for re-sequenced libraries. Must start from `1..<number of replicates>`. |
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| `antibody` | Antibody name. This is required to segregate downstream analysis for different antibodies. Required when `control` is specified. |
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| `control` | Sample name for control sample. |
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| `control_replicate` | Integer representing replicate number for control sample. |
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| Column | Description |
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| ------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
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| `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). It should be unique and contain the antibody name. E.g: `{Treatment or cell type}_{antibody}_IP` |
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| `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". |
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| `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". |
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| `replicate` | Integer representing replicate number. This will be identical for re-sequenced libraries. Must start from `1..<number of replicates>`. |
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| `antibody` | Antibody name. This is required to segregate downstream analysis for different antibodies. Required when `control` is specified. |
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| `control` | Sample name for control sample. |
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| `control_replicate` | Integer representing replicate number for control sample. |
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Example design files have been provided with the pipeline for [paired-end](../assets/samplesheet_pe.csv) and [single-end](../assets/samplesheet_se.csv) data.
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