Dev

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## unreleased
+
+### Added
+
+- `bwa mem` as short-read mapper alternative, parameter: `--bwa`
+
 ## [v1.0.2] - 2024-05-17
 
 ### Added

CITATIONS.md

@@ -12,6 +12,10 @@
 
   > Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PubMed PMID: 20110278; PubMed Central PMCID: PMC2832824.
 
+- [BWA](https://arxiv.org/abs/1303.3997)
+
+  > Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v2 [q-bio.GN]
+
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
 - [Minimap2](https://pubmed.ncbi.nlm.nih.gov/29750242/)

clean.nf

@@ -10,7 +10,7 @@ Author: [email protected]
 
 // Parameters sanity checking
 
-Set valid_params = ['max_cores', 'cores', 'max_memory', 'memory', 'profile', 'help', 'input', 'input_type', 'list', 'host', 'own', 'control', 'keep', 'rm_rrna', 'bbduk', 'bbduk_kmer', 'bbduk_qin', 'reads_rna', 'min_clip', 'dcs_strict', 'output', 'multiqc_dir', 'nf_runinfo_dir', 'databases', 'cleanup_work_dir','condaCacheDir', 'singularityCacheDir', 'singularityCacheDir', 'cloudProcess', 'conda-cache-dir', 'singularity-cache-dir', 'cloud-process', 'publish_dir_mode', 'no_intermediate', 'skip_qc'] // don't ask me why there is also 'conda-cache-dir', 'singularity-cache-dir', 'cloud-process'
+Set valid_params = ['max_cores', 'cores', 'max_memory', 'memory', 'profile', 'help', 'input', 'input_type', 'list', 'host', 'own', 'control', 'keep', 'rm_rrna', 'bwa', 'bbduk', 'bbduk_kmer', 'bbduk_qin', 'reads_rna', 'min_clip', 'dcs_strict', 'output', 'multiqc_dir', 'nf_runinfo_dir', 'databases', 'cleanup_work_dir','condaCacheDir', 'singularityCacheDir', 'singularityCacheDir', 'cloudProcess', 'conda-cache-dir', 'singularity-cache-dir', 'cloud-process', 'publish_dir_mode', 'no_intermediate', 'skip_qc'] // don't ask me why there is also 'conda-cache-dir', 'singularity-cache-dir', 'cloud-process'
 def parameter_diff = params.keySet() - valid_params
 if (parameter_diff.size() != 0){
     exit 1, "ERROR: Parameter(s) $parameter_diff is/are not valid in the pipeline!\n"
@@ -275,6 +275,7 @@ def helpMSG() {
                                         Reads are assigned to a combined index for decontamination and keeping. The use of this parameter can prevent
                                         false positive hits and the accidental removal of reads due to (poor quality) mappings.
     ${c_green}--rm_rrna ${c_reset}      Clean your data from rRNA [default: $params.rm_rrna]
+    ${c_green}--bwa${c_reset}           Add this flag to use BAW MEM instead of minimap2 for decontamination of short reads [default: $params.bwa]
     ${c_green}--bbduk${c_reset}         Add this flag to use bbduk instead of minimap2 for decontamination of short reads [default: $params.bbduk]
     ${c_green}--bbduk_kmer${c_reset}    Set kmer for bbduk [default: $params.bbduk_kmer]
     ${c_green}--bbduk_qin${c_reset}     Set quality ASCII encoding for bbduk [default: $params.bbduk_qin; options are: 64, 33, auto]

configs/container.config

@@ -1,11 +1,12 @@
 process {
-    withLabel: smallTask {  container = 'nanozoo/samtools:1.14--d8fb865' }
-    withLabel: minimap2 {   container = 'nanozoo/minimap2:2.26--d9ef6b6' }
-    withLabel: bbmap {      container = 'nanozoo/bbmap:38.79--8e915d7' }
-    withLabel: multiqc {    container = 'nanozoo/multiqc:1.9--aba729b' }
-    withLabel: fastqc {     container = 'nanozoo/fastqc:0.11.9--f61b8b4' }
-    withLabel: nanoplot {   container = 'nanozoo/nanoplot:1.32.0--1ae6f5d' }
-    withLabel: quast {      container = 'nanozoo/quast:5.0.2--e7f0cfe' }
-    withLabel: bed_samtools {   container = 'nanozoo/bed_samtools:2.30.0--cc7d1b9' }
-    withLabel: seqkit   {   container = 'nanozoo/seqkit:2.6.1--022e008' }
+    withLabel: smallTask    { container = 'nanozoo/samtools:1.14--d8fb865' }
+    withLabel: minimap2     { container = 'nanozoo/minimap2:2.26--d9ef6b6' }
+    withLabel: bwa          { container = 'nanozoo/bwa:0.7.18--0eff897' }
+    withLabel: bbmap        { container = 'nanozoo/bbmap:38.79--8e915d7' }
+    withLabel: multiqc      { container = 'nanozoo/multiqc:1.9--aba729b' }
+    withLabel: fastqc       { container = 'nanozoo/fastqc:0.11.9--f61b8b4' }
+    withLabel: nanoplot     { container = 'nanozoo/nanoplot:1.32.0--1ae6f5d' }
+    withLabel: quast        { container = 'nanozoo/quast:5.0.2--e7f0cfe' }
+    withLabel: bed_samtools { container = 'nanozoo/bed_samtools:2.30.0--cc7d1b9' }
+    withLabel: seqkit       { container = 'nanozoo/seqkit:2.6.1--022e008' }
 }

configs/node.config

@@ -1,11 +1,12 @@
 process {
-    withLabel: minimap2 {   cpus = 24;  memory = 24.GB }
-    withLabel: bbmap {      cpus = 24;  memory = 24.GB }
-    withLabel: smallTask {  cpus = 1;   memory = 2.GB }
-    withLabel: pysam {      cpus = 2;   memory = 4.GB }
-    withLabel: fastqc { cpus = {2 * task.attempt}; memory = {4.GB * task.attempt } ; maxRetries = 3 ; errorStrategy = { task.exitStatus in 130..140 ? 'retry' : 'terminate' } }
-    withLabel: multiqc {    cpus = 4;   memory = 4.GB }
-    withLabel: nanoplot{    cpus = 8;   memory = 8.GB }
-    withLabel: quast{       cpus = 8;   memory = 8.GB }
+    withLabel: minimap2     { cpus = 24;  memory = {24.GB * task.attempt}; maxRetries = 4 ; errorStrategy = { task.exitStatus in 1 || 130..140 ? 'retry' : 'terminate' }; }
+    withLabel: bwa          { cpus = 24;  memory = {24.GB * task.attempt}; maxRetries = 3 ; errorStrategy = { task.exitStatus in 130..140 ? 'retry' : 'terminate' } }
+    withLabel: bbmap        { cpus = 24;  memory = {24.GB * task.attempt}; maxRetries = 6 ; errorStrategy = { task.exitStatus in 1 || 130..140 ? 'retry' : 'terminate' }; }
+    withLabel: smallTask    { cpus = 1;   memory = 2.GB }
+    withLabel: pysam        { cpus = 2;   memory = 4.GB }
+    withLabel: fastqc       { cpus = 2;   memory = {4.GB * task.attempt } ; maxRetries = 3 ; errorStrategy = { task.exitStatus in 130..140 ? 'retry' : 'terminate' }; }
+    withLabel: multiqc      { cpus = 4;   memory = 4.GB }
+    withLabel: nanoplot     { cpus = 8;   memory = 8.GB }
+    withLabel: quast        { cpus = 8;   memory = 8.GB }
 }
 

envs/bwa.yaml

@@ -0,0 +1,8 @@
+name: bwa
+channels:
+  - bioconda
+  - conda-forge
+dependencies: 
+  - bwa=0.7.18
+  - samtools=1.20
+  - htslib=1.20

modules/bwa.nf

@@ -0,0 +1,52 @@
+process bwa_index {
+  label 'bwa'
+
+  input:
+    path(fasta)
+
+  output:
+    path(bwa) , emit: index
+
+  script:
+  """
+  mkdir bwa
+  bwa \\
+    index \\
+    -p bwa/db \\
+    $fasta
+  """
+
+  stub:
+  """
+  mkdir bwa
+
+  touch bwa/db.{amb,ann,bwt,pac,sa}
+  """
+}
+
+process bwa {
+  label 'bwa'
+
+  input: 
+  tuple val(name), path(input)
+  path(db_index)
+  path(db)
+
+
+  output:
+  tuple val(name), val('raw'), path("${name}.bam"), emit: bam // input just for naming
+
+  script:
+  """
+  INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'`
+  bwa mem \\
+    -t $task.cpus \\
+    \$INDEX \\
+    $input \\
+    | samtools view -bhS -@ $task.cpus > ${name}.bam
+  """
+  stub:
+  """
+  touch ${name}.bam
+  """
+}

nextflow.config

@@ -24,6 +24,7 @@ params {
   control = false
   keep = false
   rm_rrna = false
+  bwa = false
   bbduk = false
   bbduk_kmer = 27
   bbduk_qin = 'auto'

tests/fasta/main.nf.test

@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../../clean.nf"
 
     test("Stub") {
+        tag "minimap2"
         options "-stub-run"
 
         when {

tests/illumina/main.nf.test

@@ -4,12 +4,13 @@ nextflow_pipeline {
     script "../../clean.nf"
 
     test("Stub paired-end") {
+        tag "minimap2"
         options "-stub-run"
 
         when {
             params {
-                input_type     = "illumina"
-                input      = "$projectDir/assets/EMPTY_FILE_{R1,R2}.fastq"
+                input_type = "illumina"
+                input = "$projectDir/assets/EMPTY_FILE_{R1,R2}.fastq"
                 own = "$projectDir/assets/EMPTY_FILE"
             }
         }
@@ -22,12 +23,13 @@ nextflow_pipeline {
     }
 
     test("Stub single-end") {
+        tag "minimap2"
         options "-stub-run"
 
         when {
             params {
-                input_type     = "illumina_single_end"
-                input      = "$projectDir/assets/EMPTY_FILE"
+                input_type = "illumina_single_end"
+                input = "$projectDir/assets/EMPTY_FILE"
                 own = "$projectDir/assets/EMPTY_FILE"
             }
         }
@@ -39,13 +41,54 @@ nextflow_pipeline {
         }
     }
 
+        test("Stub paired-end bwa") {
+        tag "bwa"
+        options "-stub-run"
+
+        when {
+            params {
+                input_type = "illumina"
+                input = "$projectDir/assets/EMPTY_FILE_{R1,R2}.fastq"
+                own = "$projectDir/assets/EMPTY_FILE"
+                bwa = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Stub single-end bwa") {
+        tag "bwa"
+        options "-stub-run"
+
+        when {
+            params {
+                input_type = "illumina_single_end"
+                input = "$projectDir/assets/EMPTY_FILE"
+                own = "$projectDir/assets/EMPTY_FILE"
+                bwa = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
     test("Stub paired-end bbduk") {
+        tag "bbduk"
         options "-stub-run"
 
         when {
             params {
-                input_type     = "illumina"
-                input      = "$projectDir/assets/EMPTY_FILE_{R1,R2}.fastq"
+                input_type = "illumina"
+                input = "$projectDir/assets/EMPTY_FILE_{R1,R2}.fastq"
                 own = "$projectDir/assets/EMPTY_FILE"
                 bbduk = true
             }
@@ -59,12 +102,13 @@ nextflow_pipeline {
     }
 
     test("Stub single-end bbduk") {
+        tag "bbduk"
         options "-stub-run"
 
         when {
             params {
-                input_type     = "illumina_single_end"
-                input      = "$projectDir/assets/EMPTY_FILE"
+                input_type = "illumina_single_end"
+                input = "$projectDir/assets/EMPTY_FILE"
                 own = "$projectDir/assets/EMPTY_FILE"
                 bbduk = true
             }

tests/nanopore/main.nf.test

@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../../clean.nf"
 
     test("Stub") {
+        tag "minimap2"
         options "-stub-run"
 
         when {

workflows/clean_wf.nf

@@ -1,4 +1,5 @@
 include { minimap2 } from '../modules/minimap2'
+include { bwa_index; bwa } from '../modules/bwa'
 include { bbduk } from '../modules/bbmap'
 include { bbduk_stats } from '../modules/utils'
 include { split_bam; fastq_from_bam ; idxstats_from_bam ; flagstats_from_bam ; index_bam as index_bam; index_bam as index_bam2; sort_bam ; filter_true_dcs_alignments ; merge_bam as merge_bam1 ; merge_bam as merge_bam2 ; merge_bam as merge_bam3 ; merge_bam as merge_bam4 ; filter_soft_clipped_alignments } from '../modules/alignment_processing'
@@ -22,11 +23,16 @@ workflow clean {
             out_reads = bbduk.out.cleaned_reads.concat(bbduk.out.contaminated_reads)
             bams_bai = Channel.empty()
             sort_bam_ch = Channel.empty()
-        } 
+        }
         else {
-            minimap2(input, contamination) | sort_bam | index_bam | ( idxstats_from_bam & flagstats_from_bam )
-
-            split_bam(minimap2.out.bam)
+            if ( params.bwa ) {
+                bwa_index(contamination)
+                bwa(input, bwa_index.out, contamination) | sort_bam | index_bam | ( idxstats_from_bam & flagstats_from_bam )
+                split_bam(bwa.out.bam)
+            } else {
+                minimap2(input, contamination) | sort_bam | index_bam | ( idxstats_from_bam & flagstats_from_bam )
+                split_bam(minimap2.out.bam)
+            }
             contamination_bam = split_bam.out.mapped
             cleaned_bam = split_bam.out.unmapped
             if ( params.control && 'dcs' in params.control.split(',') && params.dcs_strict ) {
@@ -51,7 +57,7 @@ workflow clean {
             idxstats = idxstats_from_bam.out
             flagstats = flagstats_from_bam.out
             out_reads = fastq_from_bam.out
-	        sort_bam_ch = sort_bam.out
+	          sort_bam_ch = sort_bam.out
         }
 
     emit:
@@ -60,5 +66,5 @@ workflow clean {
         flagstats
         out_reads
         bams_bai
-	    sort_bam_ch
+	      sort_bam_ch
 }