nf-core · emmadizdarevic · Jun 10, 2026 · Jun 10, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,18 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## 3.1.0 - XXXXX [2026-XX-XX]
+
+### `Added`
+
+- FastDup module from nf-core and integrated it into the pipeline, as an alternative for Picard Markduplicates. #XXX
+
+### Parameters
+
+| Old parameter       | New parameter               |
+| ------------------- | --------------------------- |
+|                     | duplicates_marker           |
+
 ## 3.0.0 - Mario [2026-05-12]
 
 ### `Added`

diff --git a/conf/modules/align_bwa_bwamem2_bwameme.config b/conf/modules/align_bwa_bwamem2_bwameme.config
@@ -58,4 +58,9 @@ process {
         ext.args = "--TMP_DIR ."
         ext.prefix = { "${meta.id}_sorted_md" }
     }
-}
+
+    withName: '.*ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:FASTDUP' {
+        ext.args = "--create-index"
+        ext.prefix = { "${meta.id}_sorted_md" }
+    }
+}
diff --git a/docs/usage.md b/docs/usage.md
@@ -10,25 +10,25 @@ Table of contents:
   - [Run nf-core/raredisease with test data](#run-nf-coreraredisease-with-test-data)
     - [Updating the pipeline](#updating-the-pipeline)
   - [Run nf-core/raredisease with your data](#run-nf-coreraredisease-with-your-data)
-    - [Samplesheet](#samplesheet)
-      - [Samplesheet for BAM file input](#samplesheet-for-bam-file-input)
-    - [Reference files and parameters](#reference-files-and-parameters)
-      - [1. Alignment](#1-alignment)
-      - [2. QC stats from the alignment files](#2-qc-stats-from-the-alignment-files)
-      - [3. Repeat expansions](#3-repeat-expansions)
-      - [4. Variant calling - SNV](#4-variant-calling---snv)
-      - [5. Variant calling - Structural variants](#5-variant-calling---structural-variants)
-      - [6. Copy number variant calling](#6-copy-number-variant-calling)
-      - [7. SNV annotation \& Ranking](#7-snv-annotation--ranking)
-      - [8. SV annotation \& Ranking](#8-sv-annotation--ranking)
-      - [9. Mitochondrial annotation](#9-mitochondrial-annotation)
-      - [10. Mobile element calling](#10-mobile-element-calling)
-      - [11. Mobile element annotation](#11-mobile-element-annotation)
-      - [12. Variant evaluation](#12-variant-evaluation)
-      - [13. Prepare data for CNV visualisation in Gens](#13-prepare-data-for-cnv-visualisation-in-gens)
-    - [Run the pipeline](#run-the-pipeline)
-      - [Direct input in CLI](#direct-input-in-cli)
-      - [Import from a config file (recommended)](#import-from-a-config-file-recommended)
+      - [Samplesheet](#samplesheet)
+        - [Samplesheet for BAM file input](#samplesheet-for-bam-file-input)
+      - [Reference files and parameters](#reference-files-and-parameters)
+        - [1. Alignment](#1-alignment)
+        - [2. QC stats from the alignment files](#2-qc-stats-from-the-alignment-files)
+        - [3. Repeat expansions](#3-repeat-expansions)
+        - [4. Variant calling - SNV](#4-variant-calling---snv)
+        - [5. Variant calling - Structural variants](#5-variant-calling---structural-variants)
+        - [6. Copy number variant calling](#6-copy-number-variant-calling)
+        - [7. SNV annotation \& Ranking](#7-snv-annotation--ranking)
+        - [8. SV annotation \& Ranking](#8-sv-annotation--ranking)
+        - [9. Mitochondrial annotation](#9-mitochondrial-annotation)
+        - [10. Mobile element calling](#10-mobile-element-calling)
+        - [11. Mobile element annotation](#11-mobile-element-annotation)
+        - [12. Variant evaluation](#12-variant-evaluation)
+        - [13. Prepare data for CNV visualisation in Gens](#13-prepare-data-for-cnv-visualisation-in-gens)
+      - [Run the pipeline](#run-the-pipeline)
+        - [Direct input in CLI](#direct-input-in-cli)
+        - [Import from a config file (recommended)](#import-from-a-config-file-recommended)
   - [Best practices](#best-practices)
   - [Core Nextflow arguments](#core-nextflow-arguments)
     - [`-profile`](#-profile)
@@ -211,6 +211,7 @@ The mandatory and optional parameters for each category are tabulated below.
 |                                | extract_alignments              |
 |                                | restrict_to_contigs<sup>7</sup> |
 |                                | exclude_alt<sup>8</sup>         |
+|                                | duplicates_marker<sup>9</sup>   |
 
 <sup>1</sup>Default value is bwamem2. Other alternatives are bwa, bwameme and sentieon (requires valid Sentieon license ).<br />
 <sup>2</sup>Analysis set reference genome in fasta format, first 25 contigs need to be chromosome 1-22, X, Y and the mitochondria.<br />
@@ -220,6 +221,7 @@ The mandatory and optional parameters for each category are tabulated below.
 <sup>6</sup>Default value is 40. Used only by fastp.<br />
 <sup>7</sup>Used to limit your analysis to specific contigs. Can be used to remove alignments to unplaced contigs to minimize potential errors. This parameter should be used in conjunction with the `extract_alignments` parameter.<br />
 <sup>8</sup>When set to true, alignments to alt/unplaced contigs are removed after alignment using samtools view, retaining only primary chromosomes (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM). Note that this will affect all downstream variant calling, as variants will only be called on these primary chromosomes.<br />
+<sup>9</sup>Default value is "markduplicates". Other alternative is "fastdup".<br />
 
 ##### 2. QC stats from the alignment files
 

diff --git a/main.nf b/main.nf
@@ -52,6 +52,7 @@ workflow NFCORE_RAREDISEASE {
     val_call_interval
     val_concatenate_snv_calls
     val_skip_split_multiallelics
+    val_duplicates_marker
     val_exclude_alt
     val_extract_alignments
     val_fai
@@ -481,6 +482,7 @@ workflow NFCORE_RAREDISEASE {
         val_cadd_resources,
         val_concatenate_snv_calls,
         val_skip_split_multiallelics,
+        val_duplicates_marker,
         val_exclude_alt,
         val_extract_alignments,
         val_genome,
@@ -570,6 +572,7 @@ workflow {
         params.call_interval,
         params.concatenate_snv_calls,
         params.skip_split_multiallelics,
+        params.duplicates_marker,
         params.exclude_alt,
         params.extract_alignments,
         params.fai,

diff --git a/modules.json b/modules.json
@@ -146,6 +146,11 @@
                         "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de",
                         "installed_by": ["modules"]
                     },
+                    "fastdup": {
+                        "branch": "master",
+                        "git_sha": "4aab34a29f9ca1730e2f7d194261f5145f53d56d",
+                        "installed_by": ["modules"]
+                    },
                     "fastp": {
                         "branch": "master",
                         "git_sha": "a331ecfd1aa48b2b2298aab23bb4516c800e410b",

diff --git a/modules/nf-core/fastdup/environment.yml b/modules/nf-core/fastdup/environment.yml
diff --git a/modules/nf-core/fastdup/main.nf b/modules/nf-core/fastdup/main.nf
diff --git a/modules/nf-core/fastdup/meta.yml b/modules/nf-core/fastdup/meta.yml