Merge pull request nf-core#600 from nf-core/mito-update

bwamem2 for mt

CHANGELOG.md

@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- A new parameter `mt_aligner` to control which aligner is used to align reads to mitochondria [#600](https://github.com/nf-core/raredisease/pull/600)
 - A new parameter `par_bed` to pass a PAR bed files to deepvariant [#598](https://github.com/nf-core/raredisease/pull/598)
 - A new functionality to pass gzipped resources to vcfanno_extra_resources [#589](https://github.com/nf-core/raredisease/pull/589)
 - A new parameter `vcfanno_extra_resources` to pass an extra resource to vcfanno [#588](https://github.com/nf-core/raredisease/pull/588)
@@ -20,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- bwameme can no longer be used to align mitochondrial reads [#600](https://github.com/nf-core/raredisease/pull/600)
 - Males' X and Y chromosomes will be treated as haploids during variant calling by deepvariant [#598](https://github.com/nf-core/raredisease/pull/598)
 - Acceptable type for lane field in the samplesheet from number to string [#597](https://github.com/nf-core/raredisease/pull/597)
 - Allow `0` as a valid value for `sex` in the samplesheet [#595](https://github.com/nf-core/raredisease/pull/595)
@@ -46,6 +48,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | Old parameter   | New parameter            |
 | --------------- | ------------------------ |
 |                 | mbuffer_mem              |
+|                 | mt_aligner               |
 |                 | samtools_sort_threads    |
 |                 | skip_repeat_calling      |
 |                 | skip_snv_calling         |

conf/modules/align_MT.config

@@ -23,12 +23,6 @@ process {
         ext.prefix = { "${meta.id}_sorted" }
     }
 
-    withName: '.*ALIGN_MT:BWAMEME_MEM_MT' {
-        ext.args = { "-7 -M -K 100000000 -R ${meta.read_group}" }
-        ext.args2 = { "-T ./samtools_sort_tmp" }
-        ext.prefix = { "${meta.id}_sorted" }
-    }
-
     withName: '.*ALIGN_MT:BWA_MEM_MT' {
         ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
         ext.args2 = { "-T ./samtools_sort_tmp" }
@@ -80,12 +74,6 @@ process {
         ext.prefix = { "${meta.id}_sorted_shifted" }
     }
 
-    withName: '.*ALIGN_MT_SHIFT:BWAMEME_MEM_MT' {
-        ext.args = { "-7 -M -K 100000000 -R ${meta.read_group}" }
-        ext.args2 = { "-T ./samtools_sort_tmp" }
-        ext.prefix = { "${meta.id}_sorted_shifted" }
-    }
-
     withName: '.*ALIGN_MT_SHIFT:SENTIEON_BWAMEM_MT' {
         ext.args = { "-M -K 10000000 -R ${meta.read_group}" }
         ext.args2 = { "-T ./samtools_sort_tmp" }

nextflow.config

@@ -53,6 +53,7 @@ params {
 
     // Alignment
     aligner                    = 'bwamem2'
+    mt_aligner                 = 'bwamem2'
     mbuffer_mem                = 3072
     samtools_sort_threads      = 4
     min_trimmed_length         = 40

nextflow_schema.json

@@ -632,6 +632,13 @@
                     "fa_icon": "fas fa-align-center",
                     "enum": ["bwa", "bwamem2", "bwameme", "sentieon"]
                 },
+                "mt_aligner": {
+                    "type": "string",
+                    "default": "bwamem2",
+                    "description": "Specifies the alignment algorithm to use - available options are 'bwamem2' and 'sentieon'.",
+                    "fa_icon": "fas fa-align-center",
+                    "enum": ["bwa", "bwamem2", "sentieon"]
+                },
                 "samtools_sort_threads": {
                     "type": "integer",
                     "default": 4,

subworkflows/local/align.nf

@@ -97,25 +97,19 @@ workflow ALIGN {
                 CONVERT_MT_BAM_TO_FASTQ.out.bam,
                 ch_genome_bwaindex,
                 ch_genome_bwamem2index,
-                ch_genome_bwamemeindex,
                 ch_genome_fasta,
                 ch_genome_dictionary,
-                ch_genome_fai,
-                val_mbuffer_mem,
-                val_sort_threads
+                ch_genome_fai
             )
 
             ALIGN_MT_SHIFT (
                 CONVERT_MT_BAM_TO_FASTQ.out.fastq,
                 CONVERT_MT_BAM_TO_FASTQ.out.bam,
                 ch_mtshift_bwaindex,
                 ch_mtshift_bwamem2index,
-                ch_mtshift_bwamemeindex,
                 ch_mtshift_fasta,
                 ch_mtshift_dictionary,
-                ch_mtshift_fai,
-                val_mbuffer_mem,
-                val_sort_threads
+                ch_mtshift_fai
             )
 
             ch_mt_marked_bam      = ALIGN_MT.out.marked_bam

subworkflows/local/alignment/align_MT.nf

@@ -5,7 +5,6 @@
 include { BWA_MEM as BWA_MEM_MT                                             } from '../../../modules/nf-core/bwa/mem/main'
 include { SENTIEON_BWAMEM as SENTIEON_BWAMEM_MT                             } from '../../../modules/nf-core/sentieon/bwamem/main'
 include { BWAMEM2_MEM as BWAMEM2_MEM_MT                                     } from '../../../modules/nf-core/bwamem2/mem/main'
-include { BWAMEME_MEM as BWAMEME_MEM_MT                                     } from '../../../modules/nf-core/bwameme/mem/main'
 include { GATK4_MERGEBAMALIGNMENT as GATK4_MERGEBAMALIGNMENT_MT             } from '../../../modules/nf-core/gatk4/mergebamalignment/main'
 include { PICARD_ADDORREPLACEREADGROUPS as PICARD_ADDORREPLACEREADGROUPS_MT } from '../../../modules/nf-core/picard/addorreplacereadgroups/main'
 include { PICARD_MARKDUPLICATES as PICARD_MARKDUPLICATES_MT                 } from '../../../modules/nf-core/picard/markduplicates/main'
@@ -18,32 +17,25 @@ workflow ALIGN_MT {
         ch_ubam          // channel: [mandatory] [ val(meta), path(bam) ]
         ch_bwaindex      // channel: [mandatory for sentieon] [ val(meta), path(index) ]
         ch_bwamem2index  // channel: [mandatory for bwamem2] [ val(meta), path(index) ]
-        ch_bwamemeindex  // channel: [mandatory for bwameme] [ val(meta), path(index) ]
         ch_fasta         // channel: [mandatory] [ val(meta), path(fasta) ]
         ch_dict          // channel: [mandatory] [ val(meta), path(dict) ]
         ch_fai           // channel: [mandatory] [ val(meta), path(fai) ]
-        val_mbuffer_mem  // integer: [mandatory] default: 3072
-        val_sort_threads // integer: [mandatory] default: 4
 
     main:
         ch_versions     = Channel.empty()
 
-        if (params.aligner.equals("bwamem2")) {
+        if (params.mt_aligner.equals("bwamem2")) {
             BWAMEM2_MEM_MT (ch_fastq, ch_bwamem2index, ch_fasta, true)
             ch_align       = BWAMEM2_MEM_MT.out.bam
             ch_versions    = ch_versions.mix(BWAMEM2_MEM_MT.out.versions.first())
-        } else if (params.aligner.equals("sentieon")) {
+        } else if (params.mt_aligner.equals("sentieon")) {
             SENTIEON_BWAMEM_MT ( ch_fastq, ch_bwaindex, ch_fasta, ch_fai )
             ch_align       = SENTIEON_BWAMEM_MT.out.bam_and_bai.map{ meta, bam, bai -> [meta, bam] }
             ch_versions    = ch_versions.mix(SENTIEON_BWAMEM_MT.out.versions.first())
-        } else if (params.aligner.equals("bwa")) {
+        } else if (params.mt_aligner.equals("bwa")) {
             BWA_MEM_MT ( ch_fastq, ch_bwaindex, ch_fasta, true )
             ch_align       = BWA_MEM_MT.out.bam
             ch_versions    = ch_versions.mix(BWA_MEM_MT.out.versions.first())
-        } else if (params.aligner.equals("bwameme")) {
-            BWAMEME_MEM_MT (ch_fastq, ch_bwamemeindex, ch_fasta, true, val_mbuffer_mem, val_sort_threads)
-            ch_align       = BWAMEME_MEM_MT.out.bam
-            ch_versions    = ch_versions.mix(BWAMEME_MEM_MT.out.versions.first())
         }
         ch_align
             .join(ch_ubam, failOnMismatch:true, failOnDuplicate:true)