Add support for fastp length_required

CHANGELOG.md

@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [1640](https://github.com/nf-core/sarek/pull/1620) - Add `lofreq` as a tumor-only variant caller.
 - [1642](https://github.com/nf-core/sarek/pull/1642) - Back to dev
+- [1660](https://github.com/nf-core/sarek/pull/1642) - Add `--length_required` for minimal reads length with `FASTP`
 
 ### Changed
 

conf/modules/trimming.config

@@ -23,7 +23,8 @@ process {
             params.three_prime_clip_r1 > 0 ? "--trim_tail1 ${params.three_prime_clip_r1}" : '', // Remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed
             params.three_prime_clip_r2 > 0 ? "--trim_tail2 ${params.three_prime_clip_r2}" : '', // Remove bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed
             params.trim_nextseq            ? '--trim_poly_g'                              : '', // Apply the --nextseq=X option, to trim based on quality after removing poly-G tails
-            params.split_fastq > 0         ? "--split_by_lines ${params.split_fastq * 4}" : ''
+            params.split_fastq > 0         ? "--split_by_lines ${params.split_fastq * 4}" : '', // Output by limiting lines of each file with this option
+            params.length_required > 0     ? "--length_required ${params.length_required}": '', // Reads shorter will be discarded
         ].join(' ').trim()
         publishDir = [
             [

conf/test/trimming.config

@@ -14,6 +14,7 @@ params {
     clip_r2             = 1
     three_prime_clip_r1 = 1
     three_prime_clip_r2 = 1
+    length_required     = 50
     tools               = null
     trim_fastq          = true
 }

docs/output.md

@@ -13,6 +13,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [Directory Structure](#directory-structure)
 - [Preprocessing](#preprocessing)
   - [Preparation of input files (FastQ or (u)BAM)](#preparation-of-input-files-fastq-or-ubam)
+    - [Clip and filter read length](#clip-and-filter-read-length)
     - [Trim adapters](#trim-adapters)
     - [Split FastQ files](#split-fastq-files)
     - [UMI consensus](#umi-consensus)
@@ -41,8 +42,8 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
       - [Sentieon DNAscope joint germline variant calling](#sentieon-dnascope-joint-germline-variant-calling)
     - [Sentieon Haplotyper](#sentieon-haplotyper)
       - [Sentieon Haplotyper joint germline variant calling](#sentieon-haplotyper-joint-germline-variant-calling)
-    - [Lofreq](#lofreq)
     - [Strelka](#strelka)
+    - [Lofreq](#lofreq)
   - [Structural Variants](#structural-variants)
     - [Manta](#manta)
     - [TIDDIT](#tiddit)
@@ -107,6 +108,10 @@ Sarek pre-processes raw FastQ files or unmapped BAM files, based on [GATK best p
 
 [FastP](https://github.com/OpenGene/fastp) is a tool designed to provide all-in-one preprocessing for FastQ files and as such is used for trimming and splitting. By default, these files are not published. However, if publishing is enabled, please be aware that these files are only published once, meaning if trimming and splitting is enabled, then the resulting files will be sharded FastQ files with trimmed reads. If only one of them is enabled then the files contain either trimmed or split reads, respectively.
 
+#### Clip and filter read length
+
+[FastP](https://github.com/OpenGene/fastp) enables efficient clipping of reads from either the 5' end (`--clip_r1`, `--clip_r2`) or the 3' end (`--three_prime_clip_r1`, `--three_prime_clip_r2`). Additionally, FastP allows the filtering of reads based on insert size by specifying a minimum required length with the `--length_required` parameter (default: 15bp). It is recommended to optimize these parameters according to the specific characteristics of your data.
+
 #### Trim adapters
 
 [FastP](https://github.com/OpenGene/fastp) supports global trimming, which means it trims all reads in the front or the tail. This function is useful since sometimes you want to drop some cycles of a sequencing run. In the current implementation in Sarek

nextflow.config

@@ -38,6 +38,7 @@ params {
     three_prime_clip_r1 = 0
     three_prime_clip_r2 = 0
     trim_nextseq        = 0
+    length_required     = 15 // Default in FastP
     save_trimmed        = false
     save_split_fastqs   = false
 

nextflow_schema.json

@@ -177,6 +177,14 @@
                     "help_text": "DetectS polyG in read tails and trim them. Corresponds to the FastP flag `--trim_poly_g`.",
                     "hidden": true
                 },
+                "length_required": {
+                    "type": "integer",
+                    "default": 15,
+                    "fa_icon": "fas fa-cut",
+                    "description": "Minimum length of reads to keep",
+                    "help_text": "This is the minimum length of reads to keep after trimming. Corresponds to the FastP flag `--length_required` (default in FastP is 15bp).",
+                    "hidden": true
+                },
                 "save_trimmed": {
                     "type": "boolean",
                     "fa_icon": "fas fa-save",

tests/test_fastp.yml

@@ -29,7 +29,7 @@
     - path: results/reports/fastp/test
     - path: results/reports/fastqc/test-test_L1
     - path: results/reports/markduplicates/test/test.md.cram.metrics
-      contains: ["test	16608	1860	160	1046616	12117	256	0	0.621261"]
+      contains: ["test	16608	1860	164	1046488	12097	254	0	0.620081	6174"]
     - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
     - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt