Adding mgikit demultiplexing

README.md

@@ -42,6 +42,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 - [sgdemux](#sgdemux) - demultiplexing bgzipped fastq files produced by Singular Genomics (CONDITIONAL)
 - [fqtk](#fqtk) - a toolkit for working with FASTQ files, written in Rust (CONDITIONAL)
 - [mkfastq](#mkfastq) - converting bcl files to fastq, and demultiplexing for single-cell sequencing data (CONDITIONAL)
+- [mgikit](#mgikit) - Demultiplex fastq files generated by MGI sequencers using [mgikit](https://github.com/sagc-bioinformatics/mgikit) (CONDITIONAL).
 
 3. [checkqc](#checkqc) - (optional) Check quality criteria after demultiplexing (bcl2fastq only)
 4. [fastp](#fastp) - Adapter and quality trimming

conf/test_mgikit.config

@@ -0,0 +1,32 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/demultiplex -profile test,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+// Limit resources so that this can run on GitHub Actions
+process {
+    resourceLimits = [
+        cpus: 1,
+        memory: '7.GB',
+        time: '4.h'
+    ]
+}
+
+params {
+    config_profile_name        = 'Test mgikit profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function with mgikit'
+
+    // Input data
+    input         = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/demultiplex/testdata/mgi/mgikit_input.csv'
+    demultiplexer = 'mgikit'
+    skip_tools    = "checkqc,samshee"
+}
+
+

docs/output.md

@@ -16,6 +16,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [sgdemux](#sgdemux) - demultiplexing bgzipped fastq files produced by Singular Genomics (CONDITIONAL)
 - [fqtk](#fqtk) - demultiplexing fastq files (CONDITIONAL)
 - [mkfastq](#mkfastq) - converting bcl files to fastq, and demultiplexing for single-cell sequencing data (CONDITIONAL)
+- [mgikit](#mgikit) - Demultiplex fastq files generated by MGI sequencers using [mgikit](https://github.com/sagc-bioinformatics/mgikit) (CONDITIONAL).
 - [checkqc](#checkqc) - (optional) Check quality criteria after demultiplexing (bcl2fastq only)
 - [fastp](#fastp) - Adapter and quality trimming
 - [Falco](#falco) - Raw read QC
@@ -136,6 +137,10 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 </details>
 
+### mgikit
+
+[mgikit](https://github.com/sagc-bioinformatics/mgikit) demultiplexes fastq files generated by MGI sequencers (CONDITIONAL).
+
 ### fastp
 
 <details markdown="1">

docs/usage.md

@@ -22,7 +22,7 @@ When using the demultiplexer fqtk, the _pipeline_ samplesheet must contain an ad
 --input '[path to pipeline samplesheet file]'
 ```
 
-#### Example: Pipeline samplesheet
+### Example: Pipeline samplesheet
 
 ```csv title="samplesheet.csv"
 id,samplesheet,lane,flowcell
@@ -32,18 +32,18 @@ DDMMYY_SERIAL_NUMBER_FC2,/path/to/SampleSheet2.csv,1,/path/to/sequencer/output2
 DDMMYY_SERIAL_NUMBER_FC3,/path/to/SampleSheet3.csv,3,/path/to/sequencer/output3
 ```
 
-| Column        | Description                                                                                                                                         |
-| ------------- | --------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `id`          | Flowcell id                                                                                                                                         |
-| `samplesheet` | Full path to the _flowcell_ `SampleSheet.csv` file containing the sample information and indexes                                                    |
-| `lane`        | Optional lane number. When a lane number is provided, only the given lane will be demultiplexed                                                     |
-| `flowcell`    | Full path to the Illumina sequencer output directory (often referred as run directory) or a `tar.gz` file containing the contents of said directory |
+| Column        | Description                                                                                                                                                                                                                                                                   |
+| ------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `id`          | Flowcell id                                                                                                                                                                                                                                                                   |
+| `samplesheet` | Full path to the _flowcell_ `SampleSheet.csv` file containing the sample information and indexes                                                                                                                                                                              |
+| `lane`        | Optional lane number. When a lane number is provided, only the given lane will be demultiplexed                                                                                                                                                                               |
+| `flowcell`    | Full path to the Illumina sequencer output directory (often referred as run directory) or a `tar.gz` file containing the contents of said directory. `mgikit` demultiplexing expects a path to a directory here containing the compressed fastq files and `BioInfo.csv` file. |
 
 An [example _pipeline_ samplesheet](https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/flowcell_input.csv) has been provided with the pipeline.
 
 Note that the run directory in the `flowcell` column must lead to a `tar.gz` for compatibility with the demultiplexers sgdemux and fqtk.
 
-#### Example: Pipeline samplesheet for fqtk
+### Example: Pipeline samplesheet for fqtk
 
 ```csv title="samplesheet.csv"
 id,samplesheet,lane,flowcell,per_flowcell_manifest
@@ -70,6 +70,7 @@ Each demultiplexing software uses a distinct _flowcell_ samplesheet format. Belo
 | **sgdemux**                  | [sgdemux SampleSheet.csv](https://github.com/nf-core/test-datasets/blob/demultiplex/testdata/sim-data/out.sample_meta.csv)                             |
 | **fqtk**                     | [fqtk SampleSheet.csv](https://github.com/fulcrumgenomics/nf-core-test-datasets/raw/fqtk/testdata/sim-data/fqtk_samplesheet.csv)                       |
 | **bcl2fastq and bclconvert** | [bcl2fastq and bclconvert SampleSheet.csv](https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/b2fq-samplesheet.csv) |
+| **mgikit**                   | [mgikit samplesheet.csv](https://github.com/nf-core/test-datasets/blob/demultiplex/testdata/mgi/fc01_sample_sheet.csv)                                 |
 
 ## Running the pipeline
 
@@ -198,7 +199,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
 - `apptainer`
   - A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
 - `wave`
-  - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later).
+  - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow `24.03.0-edge` or later).
 - `conda`
   - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.
 

modules.json

@@ -60,6 +60,11 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
+                    "mgikit/demultiplex": {
+                        "branch": "master",
+                        "git_sha": "0bf42a3bdf105ddc58f6cc5523c86b4617c4ed04",
+                        "installed_by": ["modules"]
+                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",