Feat: add bbmap/clumpify

CHANGELOG.md

@@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#226](https://github.com/nf-core/seqinspector/pull/226) Add pipeline level stub tests
 - [#228](https://github.com/nf-core/seqinspector/pull/228) Update all modules/subworkflows
 - [#234](https://github.com/nf-core/seqinspector/pull/234) Add pipeline level PICARD tests
+- [#236](https://github.com/nf-core/seqinspector/pull/236) Added bbmap/clumpify module for FASTQ deduplication and compression
 
 ### `Fixed`
 
@@ -58,6 +59,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | multiqcsav |             | 0.2.0       |
 | samtools   | 1.22.1      | 1.23.1      |
 | toulligqc  |             | 2.8.4       |
+| bbmap      |             | 39.18       |
 | tar        |             | 1.34        |
 
 ### `Deprecated`

CITATIONS.md

@@ -10,6 +10,10 @@
 
 ## Pipeline tools
 
+- [BBMap](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/clumpify-guide/)
+
+  > Bushnell B. BBTools: a collection of bioinformatics tools for processing short sequencing reads. https://jgi.doe.gov/data-and-tools/software-tools/bbtools/
+
 - [BWAMEM2](https://ieeexplore.ieee.org/abstract/document/8820962)
 
   > Vasimuddin Md, Misra S, Li H, Aluru S. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. In: 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS). IEEE; 2019:314-324. doi:10.1109/IPDPS.2019.00041

README.md

@@ -35,6 +35,7 @@ If provided, nf-core/seqinspector can also parse statistics from an Illumina run
 | `Subsampling`              | [`Seqtk`](https://github.com/lh3/seqtk)                                                                             | Global subsampling of reads. Only performs subsampling if `--sample_size` parameter is given. | [RNA, DNA]              | [N/A]                                                                                   | no           |
 | `Lint FASTQs`              | [`fq`](https://github.com/stjude-rust-labs/fq)                                                                      | fq filters, generates, subsamples, and validates FASTQ files. [RNA, DNA, synthetic]           | [N/A]                   | yes                                                                                     |
 | `Trimming`                 | [`Fastp`](https://github.com/OpenGene/fastp)                                                                        | Trimming of reads. Only performs trimming if `--tools` parameter is given.                    | [RNA, DNA, synthetic]   | [N/A]                                                                                   | no           |
+| `Compression`              | [`BBMap Clumpify`](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/clumpify-guide/)   | Deduplicate and compress FASTQ files. Only performs clumpify if `--tools` parameter is given. | [RNA, DNA]              | [N/A]                                                                                   | no           |
 | `Indexing, Mapping`        | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                                                   | Align reads to reference                                                                      | [RNA, DNA]              | [N/A]                                                                                   | yes          |
 | `Indexing`                 | [`SAMtools`](http://github.com/samtools)                                                                            | Index aligned BAM files, create FASTA index                                                   | [DNA]                   | [N/A]                                                                                   | yes          |
 | `QC`                       | [`checkQC`](https://github.com/Molmed/checkQC)                                                                      | Read QC                                                                                       | [RNA, DNA]              | Illumina rundir                                                                         | no           |
@@ -62,6 +63,7 @@ If provided, nf-core/seqinspector can also parse statistics from an Illumina run
 | Tool        | Version |
 | ----------- | ------- |
 | bwamem2     | 2.3     |
+| bbmap       | 39.18   |
 | checkQC     | 4.1.0   |
 | fq/lint     | 0.12.0  |
 | fastp       | 1.1.0   |
@@ -130,6 +132,7 @@ We thank the following people for their extensive assistance in the development
 - [@ctuni](https://github.com/ctuni)
 - [@edmundmiller](https://github.com/edmundmiller)
 - [@EliottBo](https://github.com/EliottBo)
+- [@erkutilaslan](https://github.com/erkutilaslan)
 - [@KarNair](https://github.com/KarNair)
 - [@kjellinjonas](https://github.com/kjellinjonas)
 - [@mahesh-panchal](https://github.com/mahesh-panchal)

conf/modules.config

@@ -11,6 +11,10 @@
 */
 
 process {
+    withName: BBMAP_CLUMPIFY {
+        ext.args = ''
+    }
+
     withName: CHECKQC {
         tag = { "${run_dir.simpleName}" }
     }

docs/output.md

@@ -18,6 +18,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and can generat
 - [Rundirparser](#rundirparser) - Parse rundir metadata from Illumina runs
 - [ToulligQC](#toulligqc) - Raw read QC for Oxford Nanopore runs
 - [SeqFu](#seqfu) - Statistics for FASTA or FASTQ files
+- [BBMap Clumpify](#bbmap-clumpify) - Deduplication and compression of FASTQ files
 - [Seqtk](#seqtk) - Subsample a specific number of reads per sample
 - [FastQC](#fastqc) - Raw read QC
 - [Sequali](#sequali) - Sequence quality metrics for short and long reads
@@ -119,6 +120,18 @@ This software is written in Python and developped by the GenomiqueENS core facil
 Includes functions to interleave and de-interleave FASTQ files, to rename sequences and to count and print statistics on sequence lengths.
 In this pipeline, the `seqfu stats` module is used to produce general quality metrics statistics.
 
+### BBMap Clumpify
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `clumped/[sample_id]/`
+  - `*.clumped.fastq.gz`: Deduplicated and compressed FASTQ files.
+
+</details>
+
+[BBMap Clumpify](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/clumpify-guide/) removes duplicates from sequencing data and creates smaller, faster gzipped FASTQ files. This is particularly useful for reducing file sizes while maintaining data quality.
+
 ### Seqtk
 
 <details markdown="1">

docs/usage.md

@@ -154,7 +154,7 @@ Be aware that the default tools will still be run. In order to ONLY run the sele
 --tools fastqscreen,rundirparser --tools_bundle null
 ```
 
-Currently the `tools` param can have the following values: fastqc, fastqscreen, picard_collecthsmetrics, picard_collectmultiplemetrics, rundirparser and seqfu_stats.
+Currently the `tools` param can have the following values: bbmap_clumpify, fastqc, fastqscreen, picard_collecthsmetrics, picard_collectmultiplemetrics, rundirparser and seqfu_stats.
 
 #### Skip specific tools
 
@@ -197,13 +197,15 @@ Requirements:
 
 Tools:
 
+- bbmap_clumpify
 - checkQC
 - fastqc
 - fastqscreen
 - picard_collecthsmetrics
 - picard_collectmultiplemetrics
 - rundirparser
 - seqfu_stats
+- sequali
 - toulligqc
 
 </details>

modules.json

@@ -5,6 +5,12 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
+                    "bbmap/clumpify": {
+                        "branch": "master",
+                        "git_sha": "f946047c97ed78d3cdcecdc64169c7f9faef99df",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/bbmap/clumpify/bbmap-clumpify.diff"
+                    },
                     "bwamem2/index": {
                         "branch": "master",
                         "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",

nextflow_schema.json

@@ -51,7 +51,7 @@
                 "tools": {
                     "type": "string",
                     "description": "Comma-separated string of tools to run",
-                    "pattern": "^((checkqc|fastp|fastqc|fastqe|fastqscreen|fq_lint|kraken2|multiqcsav|picard_collecthsmetrics|picard_collectmultiplemetrics|rundirparser|seqfu_stats|sequali|toulligqc)?,?)*(?<!,)$",
+                    "pattern": "^((bbmap_clumpify|checkqc|fastp|fastqc|fastqe|fastqscreen|fq_lint|kraken2|multiqcsav|picard_collecthsmetrics|picard_collectmultiplemetrics|rundirparser|seqfu_stats|sequali|toulligqc)?,?)*(?<!,)$",
                     "fa_icon": "fas fa-sort-amount-asc"
                 },
                 "tools_bundle": {
@@ -64,7 +64,7 @@
                 "skip_tools": {
                     "type": "string",
                     "description": "Comma-separated string of tools to skip - overrides any other means of tools selection",
-                    "pattern": "^((checkqc|fastp|fastqc|fastqe|fastqscreen|fq_lint|kraken2|multiqcsav|picard_collecthsmetrics|picard_collectmultiplemetrics|rundirparser|seqfu_stats|sequali|toulligqc)?,?)*(?<!,)$",
+                    "pattern": "^((bbmap_clumpify|checkqc|fastp|fastqc|fastqe|fastqscreen|fq_lint|kraken2|multiqcsav|picard_collecthsmetrics|picard_collectmultiplemetrics|rundirparser|seqfu_stats|sequali|toulligqc)?,?)*(?<!,)$",
                     "fa_icon": "fas fa-window-close "
                 }
             }

subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf

@@ -261,6 +261,7 @@ def genomeExistsError() {
 def toolCitationText() {
     def citation_text = [
         "Tools used in the workflow included:",
+        "BBMap (Bushnell 2014),",
         "BWAMEM2 (Vasimuddin et al. 2019)",
         "FastQC (Andrews 2010),",
         "FastQ Screen (Wingett & Andrews 2018)",
@@ -278,6 +279,7 @@ def toolCitationText() {
 
 def toolBibliographyText() {
     def reference_text = [
+        "<li>Bushnell B. BBTools: a collection of bioinformatics tools for processing short sequencing reads. https://jgi.doe.gov/data-and-tools/software-tools/bbtools/.</li>",
         "<li>Vasimuddin Md., Misra S., Li H, & Aluru S. (2019). Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems.</li>",
         "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.</li>",
         "<li>Wingett SW., & Andrews S. FastQ Screen: A tool for multi-genome mapping and quality control. F1000Res. 2018 Aug 24 [revised 2018 Jan 1];7:1338. doi: 10.12688/f1000research.15931.2. eCollection</li>",
@@ -343,6 +345,7 @@ def defineToolsList(input_bundle, input_tools, input_skip) {
     // please update the docs/usage.md section about tools selection when adding new tools here!
 
     if ('all' in bundle_list) {
+        tools_list << 'bbmap_clumpify'
         tools_list << 'checkqc'
         tools_list << 'fastqc'
         tools_list << 'fastqe'

tests/.nftignore

@@ -12,6 +12,7 @@ multiqc/{global_report,group_reports/*}/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,p
 multiqc/{global_report,group_reports/*}/multiqc_report.html
 pipeline_info/*.{html,json,txt,yml}
 references/R64-1-1.dict
+reports/bbmap/*/*.clumpify.log
 reports/fastp/*/*fastp.*
 reports/fastqc/*/*_fastqc.{html,zip}
 reports/fastqscreen/*/*_screen.html