Merge pull request #605 from nf-core/bugfix

Resolve issues that cropped up when aligner and mt_aligner were different
nf-core · Aug 27, 2024 · 92e0d64 · 92e0d64
2 parents d635171 + ca688e5
commit 92e0d64
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Showing 7 changed files with 12 additions and 23 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -37,6 +37,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- Issues that cropped up when `aligner` and `mt_aligner` were different [#605](https://github.com/nf-core/raredisease/pull/605)
 - Update docs to show 'vep_plugin_files' as a mandatory parameter for SNV annotation [#594](https://github.com/nf-core/raredisease/issues/593)
 - Error in SVDB merge when only a single SV caller is run [#586](https://github.com/nf-core/raredisease/pull/586)
 - Errors due to misplaced version statements [#578](https://github.com/nf-core/raredisease/pull/578)

diff --git a/conf/modules/prepare_references.config b/conf/modules/prepare_references.config
@@ -26,37 +26,32 @@ process {
     }
 
     withName: '.*PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME' {
-        ext.when = {!params.bwamem2 && params.aligner == "bwamem2"}
+        ext.when = {!params.bwamem2 && (params.aligner == "bwamem2" || params.mt_aligner == "bwamem2")}
     }
 
     withName: '.*PREPARE_REFERENCES:BWAMEME_INDEX_GENOME' {
         ext.args = '-a meme'
         ext.when = {!params.bwameme && params.aligner == "bwameme"}
     }
 
-    withName: '.*PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT' {
-        ext.when = { (params.analysis_type.equals("wgs") || params.run_mt_for_wes) && params.aligner == "bwamem2"}
+    withName: '.*PREPARE_REFERENCES:BWA_INDEX_GENOME' {
+        ext.when = {!params.bwa && (!(params.aligner == "sentieon") || params.mt_aligner == "bwa")}
     }
 
-    withName: '.*PREPARE_REFERENCES:BWAMEME_INDEX_MT_SHIFT' {
-        ext.args = '-a meme'
-        ext.when = { !(params.analysis_type == "wes") && params.aligner == "bwameme"}
+    withName: '.*PREPARE_REFERENCES:SENTIEON_BWAINDEX_GENOME' {
+        ext.when = {!params.bwa && (params.aligner == "sentieon" || params.mt_aligner == "sentieon")}
     }
 
-    withName: '.*PREPARE_REFERENCES:SENTIEON_BWAINDEX_GENOME' {
-        ext.when = {!params.bwa && params.aligner == "sentieon"}
+    withName: '.*PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT' {
+        ext.when = { (params.analysis_type.equals("wgs") || params.run_mt_for_wes) && params.mt_aligner == "bwamem2"}
     }
 
     withName: '.*PREPARE_REFERENCES:SENTIEON_BWAINDEX_MT_SHIFT' {
-        ext.when = { (params.analysis_type.equals("wgs") || params.run_mt_for_wes) && params.aligner == "sentieon"}
+        ext.when = { (params.analysis_type.equals("wgs") || params.run_mt_for_wes) && params.mt_aligner == "sentieon"}
     }
 
     withName: '.*PREPARE_REFERENCES:BWA_INDEX_MT_SHIFT' {
-        ext.when = { (params.analysis_type.equals("wgs") || params.run_mt_for_wes) && params.aligner == "bwa"}
-    }
-
-    withName: '.*PREPARE_REFERENCES:BWA_INDEX_GENOME' {
-        ext.when = {!params.bwa && (!(params.aligner == "sentieon") || params.aligner == "bwa")}
+        ext.when = { (params.analysis_type.equals("wgs") || params.run_mt_for_wes) && params.mt_aligner == "bwa"}
     }
 
     withName: '.*PREPARE_REFERENCES:SAMTOOLS_FAIDX_GENOME' {

diff --git a/subworkflows/local/align.nf b/subworkflows/local/align.nf
@@ -21,7 +21,6 @@ workflow ALIGN {
         ch_genome_dictionary     // channel: [mandatory] [ val(meta), path(dict) ]
         ch_mtshift_bwaindex      // channel: [mandatory] [ val(meta), path(index) ]
         ch_mtshift_bwamem2index  // channel: [mandatory] [ val(meta), path(index) ]
-        ch_mtshift_bwamemeindex  // channel: [mandatory] [ val(meta), path(index) ]
         ch_mtshift_fasta         // channel: [mandatory] [ val(meta), path(fasta) ]
         ch_mtshift_dictionary    // channel: [mandatory] [ val(meta), path(dict) ]
         ch_mtshift_fai           // channel: [mandatory] [ val(meta), path(fai) ]

diff --git a/subworkflows/local/alignment/align_bwa_bwamem2_bwameme.nf b/subworkflows/local/alignment/align_bwa_bwamem2_bwameme.nf
@@ -68,7 +68,7 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME {
         ch_align
             .map{ meta, bam ->
                     new_id   = meta.sample
-                    new_meta = meta + [id:new_id, read_group:"\'@RG\\tID:" + new_id + "_" + meta.lane + "\\tPL:" + val_platform + "\\tSM:" + new_id + "\'"] - meta.subMap('lane')
+                    new_meta = meta + [id:new_id, read_group:"\'@RG\\tID:" + new_id + "\\tPL:" + val_platform + "\\tSM:" + new_id + "\'"] - meta.subMap('lane')
                     [groupKey(new_meta, new_meta.num_lanes), bam]
                 }
             .groupTuple()

diff --git a/subworkflows/local/prepare_references.nf b/subworkflows/local/prepare_references.nf
@@ -7,7 +7,6 @@ include { BWA_INDEX as BWA_INDEX_MT_SHIFT                    } from '../../modul
 include { BWAMEM2_INDEX as BWAMEM2_INDEX_GENOME              } from '../../modules/nf-core/bwamem2/index/main'
 include { BWAMEM2_INDEX as BWAMEM2_INDEX_MT_SHIFT            } from '../../modules/nf-core/bwamem2/index/main'
 include { BWAMEME_INDEX as BWAMEME_INDEX_GENOME              } from '../../modules/nf-core/bwameme/index/main'
-include { BWAMEME_INDEX as BWAMEME_INDEX_MT_SHIFT            } from '../../modules/nf-core/bwameme/index/main'
 include { CAT_CAT as CAT_CAT_BAIT                            } from '../../modules/nf-core/cat/cat/main'
 include { GATK4_BEDTOINTERVALLIST as GATK_BILT               } from '../../modules/nf-core/gatk4/bedtointervallist/main'
 include { GATK4_CREATESEQUENCEDICTIONARY as GATK_SD          } from '../../modules/nf-core/gatk4/createsequencedictionary/main'
@@ -73,7 +72,6 @@ workflow PREPARE_REFERENCES {
 
         // MT alignment indices
         BWAMEM2_INDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa)
-        BWAMEME_INDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa)
         BWA_INDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa)
         SENTIEON_BWAINDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa)
         ch_bwa_mtshift = Channel.empty().mix(SENTIEON_BWAINDEX_MT_SHIFT.out.index, BWA_INDEX_MT_SHIFT.out.index).collect()
@@ -143,7 +141,6 @@ workflow PREPARE_REFERENCES {
         ch_versions = ch_versions.mix(SAMTOOLS_FAIDX_MT_SHIFT.out.versions)
         ch_versions = ch_versions.mix(GATK_SD_MT_SHIFT.out.versions)
         ch_versions = ch_versions.mix(GATK_SHIFTFASTA.out.versions)
-        ch_versions = ch_versions.mix(BWAMEME_INDEX_MT_SHIFT.out.versions)
         ch_versions = ch_versions.mix(BWAMEM2_INDEX_MT_SHIFT.out.versions)
         ch_versions = ch_versions.mix(BWA_INDEX_MT_SHIFT.out.versions)
         ch_versions = ch_versions.mix(SENTIEON_BWAINDEX_MT_SHIFT.out.versions)
@@ -175,7 +172,6 @@ workflow PREPARE_REFERENCES {
         mtshift_dict          = GATK_SHIFTFASTA.out.dict.collect()                               // channel: [ path(dict) ]
         mtshift_bwa_index     = ch_bwa_mtshift                                                   // channel: [ val(meta), path(index) ]
         mtshift_bwamem2_index = BWAMEM2_INDEX_MT_SHIFT.out.index.collect()                       // channel: [ val(meta), path(index) ]
-        mtshift_bwameme_index = BWAMEME_INDEX_MT_SHIFT.out.index.collect()                       // channel: [ val(meta), path(index) ]
 
         gnomad_af_idx         = TABIX_GNOMAD_AF.out.tbi.collect()                                // channel: [ val(meta), path(fasta) ]
         known_dbsnp_tbi       = TABIX_DBSNP.out.tbi.collect()                                    // channel: [ val(meta), path(fasta) ]

diff --git a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf
@@ -90,7 +90,7 @@ workflow PIPELINE_INITIALISATION {
         .combine( ch_original_input )
         .map { counts, meta, fastq1, fastq2 ->
             new_meta = meta + [num_lanes:counts[meta.id],
-                        read_group:"\'@RG\\tID:"+ fastq1.toString().split('/')[-1] + "\\tPL:" + params.platform.toUpperCase() + "\\tSM:" + meta.id + "\'"]
+                        read_group:"\'@RG\\tID:"+ fastq1.simpleName + "_" + meta.lane + "\\tPL:" + params.platform.toUpperCase() + "\\tSM:" + meta.id + "\'"]
             if (!fastq2) {
                 return [ new_meta + [ single_end:true ], [ fastq1 ] ]
             } else {

diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf
@@ -274,7 +274,6 @@ workflow RAREDISEASE {
     ch_mtshift_backchain        = ch_references.mtshift_backchain
     ch_mtshift_bwaindex         = ch_references.mtshift_bwa_index
     ch_mtshift_bwamem2index     = ch_references.mtshift_bwamem2_index
-    ch_mtshift_bwamemeindex     = ch_references.mtshift_bwameme_index
     ch_mtshift_dictionary       = ch_references.mtshift_dict
     ch_mtshift_fai              = ch_references.mtshift_fai
     ch_mtshift_fasta            = ch_references.mtshift_fasta
@@ -415,7 +414,6 @@ workflow RAREDISEASE {
         ch_genome_dictionary,
         ch_mtshift_bwaindex,
         ch_mtshift_bwamem2index,
-        ch_mtshift_bwamemeindex,
         ch_mtshift_fasta,
         ch_mtshift_dictionary,
         ch_mtshift_fai,