Fix naming collisions

CHANGELOG.md

@@ -21,6 +21,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[PR #493](https://github.com/nf-core/chipseq/pull/493)] - Follow up to #487.
 - [[#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.
 - [[#416](https://github.com/nf-core/chipseq/issues/416)] - Moved the KHMER_UNIQUEKMERS logic to prepare_genome
+- [[#440](https://github.com/nf-core/chipseq/issues/440), [#510](https://github.com/nf-core/chipseq/issues/510)] - Fix
+  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.
 
 ### Parameters
 

README.md

@@ -116,7 +116,13 @@ These scripts were originally written by Chuan Wang ([@chuan-wang](https://githu
 
 The pipeline workflow diagram was designed by Sarah Guinchard ([@G-Sarah](https://github.com/G-Sarah)).
 
-Many thanks to others who have helped out and contributed along the way too, including (but not limited to): [@apeltzer](https://github.com/apeltzer), [@bc2zb](https://github.com/bc2zb), [@bjlang](https://github.com/bjlang), [@crickbabs](https://github.com/crickbabs), [@drejom](https://github.com/drejom), [@houghtos](https://github.com/houghtos), [@KevinMenden](https://github.com/KevinMenden), [@mashehu](https://github.com/mashehu), [@pditommaso](https://github.com/pditommaso), [@Rotholandus](https://github.com/Rotholandus), [@sofiahaglund](https://github.com/sofiahaglund), [@tiagochst](https://github.com/tiagochst) and [@winni2k](https://github.com/winni2k).
+Many thanks to others who have helped out and contributed along the way too, including (but not limited to):
+[@apeltzer](https://github.com/apeltzer), [@bc2zb](https://github.com/bc2zb), [@bjlang](https://github.com/bjlang),
+[@crickbabs](https://github.com/crickbabs), [@drejom](https://github.com/drejom),
+[@houghtos](https://github.com/houghtos), [@KevinMenden](https://github.com/KevinMenden),
+[@mashehu](https://github.com/mashehu), [@pditommaso](https://github.com/pditommaso),
+[@Rotholandus](https://github.com/Rotholandus), [@sofiahaglund](https://github.com/sofiahaglund),
+[@tiagochst](https://github.com/tiagochst), [@winni2k](https://github.com/winni2k) and [@Kevin-Brockers](https://github.com/Kevin-Brockers).
 
 ## Contributions and Support
 

bin/check_samplesheet.py

@@ -212,9 +212,14 @@ def check_samplesheet(file_in, file_out):
                             sample,
                         )
 
+                    set_antibodies = set()
+                    set_control_replicates = set()
+
                     for idx, val in enumerate(sample_mapping_dict[sample][replicate]):
                         control = "_REP".join(val[-1].split("_REP")[:-1])
                         control_replicate = val[-1].split("_REP")[-1]
+                        set_control_replicates.add(control_replicate)
+
                         if control and (
                             control not in sample_mapping_dict.keys()
                             or int(control_replicate) not in sample_mapping_dict[control].keys()
@@ -225,6 +230,21 @@ def check_samplesheet(file_in, file_out):
                                 val[-1],
                             )
 
+                        for x in sample_mapping_dict[sample][replicate]:
+                            set_antibodies.add(x[4])
+
+                    # Check that a given sample replicate only uses one antibody
+                    if len(set_antibodies) > 1:
+                        print_error(
+                            f"Sample: {sample}, replicate {replicate} has more than one antibody specified!"
+                        )
+
+                    # Check that a given sample-replicate have only one control replicate
+                    if len(set_control_replicates) > 1:
+                        print_error(
+                            f"Sample: {sample}, replicate {replicate} has more than one control replicate specified! Revise the experimental design, see: 'Note on IP and control replicates'"
+                        )
+
                     ## Write to file
                     for idx in range(len(sample_mapping_dict[sample][replicate])):
                         fastq_files = sample_mapping_dict[sample][replicate][idx]

docs/usage.md

@@ -47,6 +47,50 @@ WT_INPUT,BLA203A30_S21_L002_R1_001.fastq.gz,,2,,,
 WT_INPUT,BLA203A31_S21_L003_R1_001.fastq.gz,,3,,,
 ```
 
+### Note on IP and control replicates - Comparisons of one IP sample against multiple controls
+
+The pipeline is designed to handle one IP and matching control replicate, see section above. However there can be
+situations where one might want to make multiple comparisons of the IP sample against several different controls. In
+those cases it is advisable to encode these comparisons either in the sample column or as another replicate. Since it is
+rather unusual in ChIP-Seq experiments, this feature is considered experimental. Please open a github issue in case you
+need further assistance.
+
+- Encoding in sample names:
+
+```csv title="samplesheet.csv"
+sample,fastq_1,fastq_2,replicate,antibody,control,control_replicate
+WT_BCATENIN_IP,BLA203A1_S27_L006_R1_001.fastq.gz,,1,BCATENIN,WT_INPUT,1
+WT_BCATENIN_IP_CONTROL_2,BLA203A1_S27_L006_R1_001.fastq.gz,,1,BCATENIN,WT_INPUT,2
+WT_BCATENIN_IP_CONTROL_3,BLA203A1_S27_L006_R1_001.fastq.gz,,1,BCATENIN,WT_INPUT,3
+WT_INPUT,BLA203A6_S32_L006_R1_001.fastq.gz,,1,,,
+WT_INPUT,BLA203A30_S21_L001_R1_001.fastq.gz,,2,,,
+WT_INPUT,BLA203A31_S21_L003_R1_001.fastq.gz,,3,,,
+```
+
+- Encoding as new biological replicates:
+
+```csv title="samplesheet.csv"
+sample,fastq_1,fastq_2,replicate,antibody,control,control_replicate
+WT_BCATENIN_IP,BLA203A1_S27_L006_R1_001.fastq.gz,,1,BCATENIN,WT_INPUT,1
+WT_BCATENIN_IP,BLA203A1_S27_L006_R1_001.fastq.gz,,2,BCATENIN,WT_INPUT,2
+WT_BCATENIN_IP,BLA203A1_S27_L006_R1_001.fastq.gz,,3,BCATENIN,WT_INPUT,3
+WT_INPUT,BLA203A6_S32_L006_R1_001.fastq.gz,,1,,,
+WT_INPUT,BLA203A30_S21_L001_R1_001.fastq.gz,,2,,,
+WT_INPUT,BLA203A31_S21_L003_R1_001.fastq.gz,,3,,,
+```
+
+- The following design, one IP replicate against more than one control replicate, is not allowed:
+
+```csv title="samplesheet.csv"
+sample,fastq_1,fastq_2,replicate,antibody,control,control_replicate
+WT_BCATENIN_IP,BLA203A1_S27_L006_R1_001.fastq.gz,,1,BCATENIN,WT_INPUT,1
+WT_BCATENIN_IP,BLA203A1_S27_L006_R1_001.fastq.gz,,1,BCATENIN,WT_INPUT,2
+WT_BCATENIN_IP,BLA203A1_S27_L006_R1_001.fastq.gz,,1,BCATENIN,WT_INPUT,3
+WT_INPUT,BLA203A6_S32_L006_R1_001.fastq.gz,,1,,,
+WT_INPUT,BLA203A30_S21_L001_R1_001.fastq.gz,,2,,,
+WT_INPUT,BLA203A31_S21_L003_R1_001.fastq.gz,,3,,,
+```
+
 ### Full design
 
 The pipeline will auto-detect whether a sample is single- or paired-end using the information provided in the samplesheet. The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 7 columns to match those defined in the table below.
@@ -77,15 +121,15 @@ NAIVE_INPUT,BLA203A48_S39_L001_R1_001.fastq.gz,,2,,,
 NAIVE_INPUT,BLA203A49_S1_L006_R1_001.fastq.gz,,3,,,
 ```
 
-| Column              | Description                                                                                                                                                                            |
-| ------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `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 (`_`). |
-| `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.                                                       |
-| `control`           | Sample name for control sample.                                                                                                                                                        |
-| `control_replicate` | Integer representing replicate number for control sample.                                                                                                                              |
+| Column              | Description                                                                                                                                                                                                                                                                                                                                                       |
+| ------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `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 per sample and contain sufficient informations, such as the antibody name. E.g: `{Treatment or cell type}_{antibody}_IP` -> `{WT/NAIVE}_{BCATENIN}_IP` |
+| `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.                                                                                                                                                                                                                                  |
+| `control`           | Sample name for control sample.                                                                                                                                                                                                                                                                                                                                   |
+| `control_replicate` | Integer representing replicate number for control sample.                                                                                                                                                                                                                                                                                                         |
 
 Example design files have been provided with the pipeline for [paired-end](../assets/samplesheet_pe.csv) and [single-end](../assets/samplesheet_se.csv) data.