Merge pull request #285 from jfy133/adapterremoval

Add alternative trimmer: AdapterRemoval

.github/workflows/ci.yml

@@ -55,7 +55,7 @@ jobs:
     strategy:
       matrix:
         # Run remaining test profiles with minimum nextflow version
-        profile: [test_host_rm, test_hybrid, test_hybrid_host_rm, test_busco_auto, test_ancient_dna]
+        profile: [test_host_rm, test_hybrid, test_hybrid_host_rm, test_busco_auto, test_ancient_dna, test_adapterremoval]
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2

CHANGELOG.md

@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#263](https://github.com/nf-core/mag/pull/263) - Restructure binning subworkflow in preparation for aDNA workflow and extended binning
 - [#247](https://github.com/nf-core/mag/pull/247) - Add ancient DNA subworkflow
 - [#263](https://github.com/nf-core/mag/pull/263) - Add MaxBin2 as second contig binning tool
+- [#284](https://github.com/nf-core/mag/pull/285) - Add AdapterRemoval2 as an alternative read trimmer
 
 ### `Changed`
 

assets/multiqc_config.yaml

@@ -17,6 +17,8 @@ top_modules:
     name: 'FastQC: raw reads'
     path_filters_exclude:
         - '*trimmed*'
+- 'fastp'
+- 'adapterRemoval':
 - custom_content
 - 'fastqc':
     name: 'FastQC: after preprocessing'
@@ -42,6 +44,9 @@ custom_data:
 sp:
     host_removal:
         fn: 'host_removal_metrics.tsv'
+    adapterRemoval:
+        fn: '*_ar2_*.log'
 
 extra_fn_clean_exts:
     - '.bowtie2'
+    - '_ar2'

conf/modules.config

@@ -34,7 +34,8 @@ process {
             "-q ${params.fastp_qualified_quality}",
             "--cut_front",
             "--cut_tail",
-            "--cut_mean_quality ${params.fastp_cut_mean_quality}"
+            "--cut_mean_quality ${params.fastp_cut_mean_quality}",
+            "--length_required ${params.reads_minlength}"
         ].join(' ').trim()
         publishDir = [
             path: { "${params.outdir}/QC_shortreads/fastp/${meta.id}" },
@@ -43,6 +44,36 @@ process {
         ]
     }
 
+    withName: ADAPTERREMOVAL_PE {
+        ext.args = [
+            "--minlength ${params.reads_minlength}",
+            "--adapter1 ${params.adapterremoval_adapter1} --adapter2 ${params.adapterremoval_adapter2}",
+            "--minquality ${params.adapterremoval_minquality} --trimns",
+            params.adapterremoval_trim_quality_stretch ? "--trim_qualities" : "--trimwindows 4"
+        ].join(' ').trim()
+        publishDir = [
+            path: { "${params.outdir}/QC_shortreads/adapterremoval/${meta.id}" },
+            mode: 'copy',
+            pattern: "*.{log}"
+        ]
+        ext.prefix = { "${meta.id}_ar2" }
+    }
+
+    withName: ADAPTERREMOVAL_SE {
+        ext.args = [
+            "--minlength ${params.reads_minlength}",
+            "--adapter1 ${params.adapterremoval_adapter1}",
+            "--minquality ${params.adapterremoval_minquality} --trimns",
+            params.adapterremoval_trim_quality_stretch ? "--trim_qualities" : "--trimwindows 4"
+        ].join(' ').trim()
+        publishDir = [
+            path: { "${params.outdir}/QC_shortreads/adapterremoval/${meta.id}" },
+            mode: 'copy',
+            pattern: "*.{log}"
+        ]
+        ext.prefix = { "${meta.id}_ar2" }
+    }
+
     withName: BOWTIE2_PHIX_REMOVAL_ALIGN {
         ext.suffix = "phix_removed"
         publishDir = [

conf/test_adapterremoval.config

@@ -0,0 +1,32 @@
+/*
+========================================================================================
+    Nextflow config file for running minimal tests
+========================================================================================
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/mag -profile test,<docker/singularity>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test profile for running with AdapterRemoval'
+    config_profile_description = 'Minimal test dataset to check pipeline function with AdapterRemoval data'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = '6.GB'
+    max_time   = '6.h'
+
+    // Input data
+    input                       = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.csv'
+    centrifuge_db               = "https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/minigut_cf.tar.gz"
+    kraken2_db                  = "https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/minigut_kraken.tgz"
+    skip_krona                  = true
+    min_length_unbinned_contigs = 1
+    max_unbinned_contigs        = 2
+    busco_reference             = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz"
+    gtdb                        = false
+    clip_tool                   = 'adapterremoval'
+}

docs/output.md

@@ -57,6 +57,18 @@ FastQC is run for visualising the general quality metrics of the sequencing runs
 
 </details>
 
+### AdapterRemoval2
+
+[AdapterRemoval](https://adapterremoval.readthedocs.io/en/stable/) searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. It is popular in the field of palaeogenomics. The output logs are stored in the results folder, and as a part of the MultiQC report.
+
+<details markdown="1">
+<summary>Output files</summary>
+
+* `QC_shortreads/adapterremoval/[sample]/`
+    * `[sample]_ar2.log`: AdapterRemoval log file (normally called `.settings` by AdapterRemoval.)
+
+</details>
+
 ### Remove PhiX sequences from short reads
 
 The pipeline uses bowtie2 to map the reads against PhiX and removes mapped reads.

modules.json

@@ -3,6 +3,9 @@
     "homePage": "https://github.com/nf-core/mag",
     "repos": {
         "nf-core/modules": {
+            "adapterremoval": {
+                "git_sha": "f0800157544a82ae222931764483331a81812012"
+            },
             "bcftools/consensus": {
                 "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
             },

modules/local/multiqc.nf

@@ -1,21 +1,21 @@
 process MULTIQC {
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::multiqc=1.11" : null)
+    conda (params.enable_conda ? "bioconda::multiqc=1.12" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' :
+        'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }"
 
     input:
     path multiqc_files
     path mqc_custom_config
     path 'fastqc_raw/*'
-    path 'fastp/*'
     path 'fastqc_trimmed/*'
     path host_removal
     path 'quast*/*'
     path 'bowtie2log/*'
     path short_summary
+    path additional
 
     output:
     path "*multiqc_report.html", emit: report

nextflow.config

@@ -14,11 +14,17 @@ params {
     single_end                           = false
 
     // short read preprocessing options
-    save_trimmed_fail                    = false
+    clip_tool                            = 'fastp'
+    reads_minlength                      = 15
+    fastp_save_trimmed_fail              = false
     fastp_qualified_quality              = 15
     fastp_cut_mean_quality               = 15
+    adapterremoval_minquality            = 2
+    adapterremoval_adapter1              = 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG'
+    adapterremoval_adapter2              = 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT'
+    adapterremoval_trim_quality_stretch  = false
     keep_phix                            = false
-    // phix_reference                     = "ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/viral/Enterobacteria_phage_phiX174_sensu_lato/all_assembly_versions/GCA_002596845.1_ASM259684v1/GCA_002596845.1_ASM259684v1_genomic.fna.gz"
+    // phix_reference                    = "ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/viral/Enterobacteria_phage_phiX174_sensu_lato/all_assembly_versions/GCA_002596845.1_ASM259684v1/GCA_002596845.1_ASM259684v1_genomic.fna.gz"
     phix_reference                       = "${baseDir}/assets/data/GCA_002596845.1_ASM259684v1_genomic.fna.gz"
     host_fasta                           = null
     host_genome                          = null
@@ -196,7 +202,9 @@ profiles {
     test_hybrid_host_rm { includeConfig 'conf/test_hybrid_host_rm.config' }
     test_busco_auto     { includeConfig 'conf/test_busco_auto.config'     }
     test_full           { includeConfig 'conf/test_full.config'           }
-    test_ancient_dna    { includeConfig 'conf/test_ancient_dna.config'   }
+    test_ancient_dna    { includeConfig 'conf/test_ancient_dna.config'    }
+    test_adapterremoval { includeConfig 'conf/test_adapterremoval.config' }
+
 }
 
 // Load igenomes.config if required