Simplify pipeline

CITATIONS.md

@@ -14,9 +14,7 @@
 
   > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
-- [fastp](https://www.ncbi.nlm.nih.gov/pubmed/30423086/)
-
-  > Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sep 1;34(17):i884-i890. doi: 10.1093/bioinformatics/bty560. PubMed PMID: 30423086; PubMed Central PMCID: PMC6129281.
+- [seqtk](https://github.com/lh3/seqtk)
 
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 

README.md

@@ -24,7 +24,7 @@
 ![nf-core/demo metro map](docs/images/nf-core-demo-subway.png)
 
 1. Read QC ([`FASTQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-2. Adapter and quality trimming ([`FASTP`](https://github.com/OpenGene/fastp))
+2. Adapter and quality trimming ([`SEQTK_TRIM`](https://github.com/lh3/seqtk))
 3. Present QC for raw reads ([`MULTIQC`](http://multiqc.info/))
 
 ## Usage

conf/modules.config

@@ -28,11 +28,11 @@ process {
     }
 
 
-    withName: 'FASTP' {
+    withName: 'SEQTK_TRIM' {
         publishDir = [
-            path: { "${params.outdir}/fastp/${meta.id}" },
+            path: { "${params.outdir}/fq/${meta.id}" },
             mode: params.publish_dir_mode,
-            pattern: "*.{html,json,log}"
+            pattern: "*.{fastq.gz}"
         ]
     }
 

conf/test.config

@@ -22,6 +22,4 @@ params {
     // Input data
     input  = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
 
-    // Genome references
-    genome = 'R64-1-1'
 }

conf/test_full.config

@@ -14,9 +14,7 @@ params {
     config_profile_name        = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'
 
-    // Input data for full size test
-    input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
+    // Input data
+    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
 
-    // Genome references
-    genome = 'R64-1-1'
 }

docs/output.md

@@ -11,7 +11,7 @@ The directories listed below will be created in the results directory after the
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
 - [FastQC](#fastqc) - Raw read QC
-- [fastp](#fastp) - Adapter and quality trimming
+- [seqtk](#seqtk) - Processing sequences in the FASTA or FASTQ format.
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
@@ -38,20 +38,17 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
 :::
 
-### fastp
+### seqtk
 
 <details markdown="1">
 <summary>Output files</summary>
 
 - `fastp/`
-  - `*.fastp.html`: Trimming report in html format.
-  - `*.fastp.json`: Trimming report in json format.
-  - `*.fastp.log`: Trimming log file.
-  - `*.fastq.gz`: If `--save_trimmed` is specified, FastQ files **after** adapter trimming will be placed in this directory.
+  - `*.fastq.gz`: Trimmed FASTQ files.
 
 </details>
 
-[fastp](https://github.com/OpenGene/fastp) is a tool designed to provide fast, all-in-one preprocessing for FastQ files. It has been developed in C++ with multithreading support to achieve higher performance. fastp can be used in this pipeline for standard adapter trimming and quality filtering.
+[seqtk](https://github.com/lh3/seqtk) is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.
 
 ### MultiQC
 

modules.json

@@ -5,11 +5,6 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
-                    "fastp": {
-                        "branch": "master",
-                        "git_sha": "95cf5fe0194c7bf5cb0e3027a2eb7e7c89385080",
-                        "installed_by": ["modules"]
-                    },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
@@ -19,6 +14,11 @@
                         "branch": "master",
                         "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
                         "installed_by": ["modules"]
+                    },
+                    "seqtk/trim": {
+                        "branch": "master",
+                        "git_sha": "71c669747731cbc360dc220069c9f83015558c07",
+                        "installed_by": ["modules"]
                     }
                 }
             },