Merge pull request #4 from nf-core/update-fq

Simplify pipeline

Author: christopher-hakkaart

CHANGELOG.md

@@ -3,14 +3,20 @@
 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).
 
-## v1.0dev - [date]
+## 1.0.0 2024-06-19
 
-Initial release of nf-core/demo, created with the [nf-core](https://nf-co.re/) template.
+### Credits
+
+Special thanks to the following for their reviews and assistance:
+
+- [Maxime Garcia](https://github.com/maxulysse)
+- [Friederike Hanssen](https://github.com/FriederikeHanssen)
 
 ### `Added`
 
-### `Fixed`
+- `nf-core/seqtk/trim` module
+- `skip_trim` parameter
 
-### `Dependencies`
+## v1.0dev - 2024-05-5
 
-### `Deprecated`
+Initial release of nf-core/demo, created with the [nf-core](https://nf-co.re/) template.

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

assets/nf-core-demo_logo_light.png

@@ -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/modules.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.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'
 }