Refactor mitochondrial analysis workflow

conf/modules/align_and_call_MT.config → conf/modules/align_MT.config

@@ -12,115 +12,87 @@
 */
 
 //
-// ANALYSE_MT:ALIGN_AND_CALL_MT
+// Mitochondria alignment options
 //
 
 process {
 
-    withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT:BWAMEM2_MEM_MT' {
-        ext.when = { !params.skip_mt_analysis && !(params.analysis_type == "wes") && params.aligner == "bwamem2" }
+    withName: '.*ALIGN_MT:BWAMEM2_MEM_MT' {
+        ext.when = { !(params.analysis_type == "wes") && params.aligner == "bwamem2" }
         ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
     }
 
-    withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT:SENTIEON_BWAMEM_MT' {
+    withName: '.*ALIGN_MT:SENTIEON_BWAMEM_MT' {
         ext.args = { "-M -K 10000000 -R ${meta.read_group}" }
-        ext.when = { !params.skip_mt_analysis && !(params.analysis_type == "wes") && params.aligner == "sentieon" }
+        ext.when = { !(params.analysis_type == "wes") && params.aligner == "sentieon" }
         ext.prefix = { "${meta.id}.sorted" }
     }
 
-    withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT:GATK4_MERGEBAMALIGNMENT_MT' {
+    withName: '.*ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT' {
         ext.args = '--CREATE_INDEX true --MAX_GAPS -1  --SORT_ORDER queryname --INCLUDE_SECONDARY_ALIGNMENTS false --PAIRED_RUN false --VALIDATION_STRINGENCY LENIENT'
         ext.prefix = { "${meta.id}_merged" }
     }
 
-    withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT:PICARD_ADDORREPLACEREADGROUPS_MT' {
+    withName: '.*ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT' {
         ext.args = { [
             "--VALIDATION_STRINGENCY LENIENT",
             "--RGLB lib",
             "--RGPL ILLUMINA",
             "--RGPU barcode",
             "--RGSM ${meta.id}"
-        ].join(' ' ).trim() }
+        ].join(' ').trim() }
     }
 
-    withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT:PICARD_MARKDUPLICATES_MT' {
+    withName: '.*ALIGN_MT:PICARD_MARKDUPLICATES_MT' {
         ext.args = '--VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true'
         ext.prefix = { "${meta.id}_markduplicates" }
     }
 
-    withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT:SAMTOOLS_SORT_MT' {
+    withName: '.*ALIGN_MT:SAMTOOLS_SORT_MT' {
         ext.prefix = { "${meta.id}_sorted" }
     }
 
-    withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT:MT_DELETION' {
-        ext.args = '-s --insert-size 16000'
-        publishDir = [
-            path: { "${params.outdir}/mt_sv" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT:GATK4_MUTECT2_MT' {
-        ext.args = '--mitochondria-mode TRUE'
-    }
-
-    withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT:GATK4_FILTERMUTECTCALLS_MT' {
-        ext.prefix = { "${meta.id}_filtered" }
-    }
 }
 
 //
-// ANALYSE_MT:ALIGN_AND_CALL_MT_SHIFT
+// Shifted mitochondria alignment options
 //
 
 process {
 
-    withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT_SHIFT:BWAMEM2_MEM_MT' {
-        ext.when = { !params.skip_mt_analysis && !(params.analysis_type == "wes") && params.aligner == "bwamem2" }
+    withName: '.*ALIGN_MT_SHIFT:BWAMEM2_MEM_MT' {
+        ext.when = { !(params.analysis_type == "wes") && params.aligner == "bwamem2" }
         ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
     }
 
-    withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT_SHIFT:SENTIEON_BWAMEM_MT' {
+    withName: '.*ALIGN_MT_SHIFT:SENTIEON_BWAMEM_MT' {
         ext.args = { "-M -K 10000000 -R ${meta.read_group}" }
-        ext.when = { !params.skip_mt_analysis && !(params.analysis_type == "wes") && params.aligner == "sentieon" }
+        ext.when = { !(params.analysis_type == "wes") && params.aligner == "sentieon" }
         ext.prefix = { "${meta.id}.sorted" }
     }
 
-    withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT' {
+    withName: '.*ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT' {
         ext.args = '--CREATE_INDEX true --MAX_GAPS -1  --SORT_ORDER queryname --INCLUDE_SECONDARY_ALIGNMENTS false --PAIRED_RUN false --VALIDATION_STRINGENCY LENIENT'
         ext.prefix = { "${meta.id}_merged_shifted" }
     }
 
-    withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT' {
+    withName: '.*ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT' {
         ext.args =  { [
             "--VALIDATION_STRINGENCY LENIENT",
             "--RGLB lib",
             "--RGPL ${params.platform}",
             "--RGPU barcode",
             "--RGSM ${meta.id}"
-        ].join(' ' ).trim() }
+        ].join(' ').trim() }
     }
 
-    withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT_SHIFT:PICARD_MARKDUPLICATES_MT' {
+    withName: '.*ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT' {
         ext.args = '--VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true'
         ext.prefix = { "${meta.id}_markduplicates_shifted" }
     }
 
-    withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT_SHIFT:SAMTOOLS_SORT_MT' {
+    withName: '.*ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT' {
         ext.prefix = { "${meta.id}_sorted_shifted" }
     }
 
-    withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT_SHIFT:GATK4_MUTECT2_MT' {
-        ext.args = '--mitochondria-mode TRUE'
-    }
-
-    withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT_SHIFT:HAPLOCHECK_MT' {
-        ext.prefix = { "${meta.id}_shifted" }
-    }
-
-    withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT' {
-        ext.prefix = { "${meta.id}_filtered_shifted" }
-    }
-
 }

conf/modules/annotate_consequence_pli.config

@@ -21,15 +21,15 @@ process {
     }
 
     withName: '.*ANN_CSQ_PLI_SV:ADD_MOST_SEVERE_CSQ' {
-        ext.prefix = { "${meta.id}_vep_csq" }
+        ext.prefix = { "${meta.id}_genome_vep_csq" }
     }
 
     withName: '.*ANN_CSQ_PLI_SV:ADD_MOST_SEVERE_PLI' {
-        ext.prefix = { "${meta.id}_vep_csq_pli" }
+        ext.prefix = { "${meta.id}_genome_vep_csq_pli" }
     }
 
     withName: '.*ANN_CSQ_PLI_SV:TABIX_BGZIPTABIX' {
-        ext.prefix = { "${meta.id}_vep_csq_pli" }
+        ext.prefix = { "${meta.id}_genome_vep_csq_pli" }
         publishDir = [
             path: { "${params.outdir}/annotate_sv" },
             mode: params.publish_dir_mode,
@@ -58,7 +58,33 @@ process {
     withName: '.*ANN_CSQ_PLI_SNV:TABIX_BGZIPTABIX' {
         ext.prefix = { "${meta.id}_vep_csq_pli" }
         publishDir = [
-            path: { "${params.outdir}/annotate_snv" },
+            path: { "${params.outdir}/annotate_snv/genome" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+}
+
+process {
+    withName: '.*ANN_CSQ_PLI_MT:.*' {
+        ext.when = !params.skip_mt_annotation
+        publishDir = [
+            enabled: false
+        ]
+    }
+
+    withName: '.*ANN_CSQ_PLI_MT:ADD_MOST_SEVERE_CSQ' {
+        ext.prefix = { "${meta.id}_mt_vep_csq" }
+    }
+
+    withName: '.*ANN_CSQ_PLI_MT:ADD_MOST_SEVERE_PLI' {
+        ext.prefix = { "${meta.id}_mt_vep_csq_pli" }
+    }
+
+    withName: '.*ANN_CSQ_PLI_MT:TABIX_BGZIPTABIX' {
+        ext.prefix = { "${meta.id}_mt_vep_csq_pli" }
+        publishDir = [
+            path: { "${params.outdir}/annotate_snv/genome" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]

conf/modules/annotate_snvs.config → conf/modules/annotate_genome_snvs.config

@@ -16,75 +16,75 @@
 //
 
 process {
-    withName: '.*ANNOTATE_SNVS:.*' {
+    withName: '.*ANNOTATE_GENOME_SNVS:.*' {
         ext.when = !params.skip_snv_annotation
     }
 
-    withName: '.*ANNOTATE_SNVS:VCFANNO' {
+    withName: '.*ANNOTATE_GENOME_SNVS:VCFANNO' {
         ext.prefix = { "${meta.id}_vcfanno" }
         publishDir = [
             enabled: false
         ]
     }
 
-    withName: '.*ANNOTATE_SNVS:BCFTOOLS_ROH' {
+    withName: '.*ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH' {
         ext.args = { "--samples ${meta.probands.join(",")} --skip-indels " }
         ext.prefix = { "${meta.id}_roh" }
     }
 
-    withName: '.*ANNOTATE_SNVS:RHOCALL_ANNOTATE' {
+    withName: '.*ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE' {
         ext.args = { "--v14 " }
         ext.prefix = { "${meta.id}_rohann" }
     }
 
-    withName: '.*ANNOTATE_SNVS:VCFANNO' {
+    withName: '.*ANNOTATE_GENOME_SNVS:VCFANNO' {
         ext.prefix = { "${meta.id}_rohann_vcfanno" }
     }
 
-    withName: '.*ANNOTATE_SNVS:UPD_SITES' {
+    withName: '.*ANNOTATE_GENOME_SNVS:UPD_SITES' {
         ext.prefix = { "${meta.id}_rohann_vcfanno_upd_sites" }
         ext.args = {"--af-tag GNOMADAF --proband ${meta.upd_child} --mother ${meta.mother} --father ${meta.father} sites"}
     }
 
-    withName: '.*ANNOTATE_SNVS:UPD_REGIONS' {
+    withName: '.*ANNOTATE_GENOME_SNVS:UPD_REGIONS' {
         ext.prefix = { "${meta.id}_rohann_vcfanno_upd_regions" }
         ext.args = {"--af-tag GNOMADAF --proband ${meta.upd_child} --mother ${meta.mother} --father ${meta.father} regions --min-size 5 --min-sites 1"}
         ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample']).size() >= 1) || workflow.stubRun }
     }
 
-    withName: '.*ANNOTATE_SNVS:CHROMOGRAPH_SITES' {
+    withName: '.*ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES' {
         ext.prefix = { "${meta7.id}_rohann_vcfanno_upd_sites_chromograph" }
         ext.args = { "--euploid" }
         tag =  {"${meta7.id}"}
         publishDir = [
-            path: { "${params.outdir}/annotate_snv" },
+            path: { "${params.outdir}/annotate_snv/genome" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
-    withName: '.*ANNOTATE_SNVS:CHROMOGRAPH_REGIONS' {
+    withName: '.*ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS' {
         ext.prefix = { "${meta6.id}_rohann_vcfanno_upd_regions_chromograph" }
         ext.args = { '--euploid' }
         ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample']).size() >= 1) || workflow.stubRun }
         tag =  {"${meta6.id}"}
         publishDir = [
-            path: { "${params.outdir}/annotate_snv" },
+            path: { "${params.outdir}/annotate_snv/genome" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
-    withName: '.*ANNOTATE_SNVS:BCFTOOLS_VIEW' {
+    withName: '.*ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW' {
         ext.prefix = { "${meta.id}_rohann_vcfanno_filter" }
         ext.args = { '--output-type z --exclude "INFO/GNOMADAF > 0.70 | INFO/GNOMADAF_popmax > 0.70" ' }
     }
 
-    withName: '.*ANNOTATE_SNVS:GATK4_SELECTVARIANTS' {
+    withName: '.*ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS' {
         ext.prefix = { "${meta.id}_${intervals.simpleName}" }
     }
 
-    withName: '.*ANNOTATE_SNVS:ENSEMBLVEP_SNV' {
+    withName: '.*ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV' {
         ext.prefix = { "${vcf.simpleName}_rohann_vcfanno_filter_vep" }
         ext.args   = [
             '--dir_plugins vep_cache/Plugins',
@@ -103,18 +103,18 @@ process {
         ].join(' ')
     }
 
-    withName: '.*ANNOTATE_SNVS:BCFTOOLS_CONCAT' {
+    withName: '.*ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT' {
         ext.prefix = { "${meta.id}_rohann_vcfanno_filter_vep" }
         publishDir = [
-            path: { "${params.outdir}/annotate_snv" },
+            path: { "${params.outdir}/annotate_snv/genome" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
-    withName: '.*ANNOTATE_SNVS:TABIX_BCFTOOLS_CONCAT' {
+    withName: '.*ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT' {
         publishDir = [
-            path: { "${params.outdir}/annotate_snv" },
+            path: { "${params.outdir}/annotate_snv/genome" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]

conf/modules/merge_annotate_MT.config → conf/modules/annotate_mt_snvs.config

@@ -17,30 +17,8 @@
 
 process {
 
-    withName: '.*ANALYSE_MT:MERGE_ANNOTATE_MT:GATK4_MERGEVCFS_LIFT_UNLIFT_MT' {
-        ext.prefix = { "${meta.id}_merged" }
-    }
-
-    withName: '.*ANALYSE_MT:MERGE_ANNOTATE_MT:GATK4_VARIANTFILTRATION_MT' {
-        ext.prefix = { "${meta.id}_filt" }
-    }
-
-    withName: '.*ANALYSE_MT:MERGE_ANNOTATE_MT:SPLIT_MULTIALLELICS_MT' {
-        ext.args = '--output-type z --multiallelics -both'
-        ext.prefix = { "${meta.id}_split" }
-    }
-
-    withName: '.*ANALYSE_MT:MERGE_ANNOTATE_MT:REMOVE_DUPLICATES_MT' {
-        ext.args = '--output-type z --rm-dup none'
-        ext.prefix = { "${meta.id}_split_rmdup" }
-    }
-
-    withName: '.*ANALYSE_MT:MERGE_ANNOTATE_MT:BCFTOOLS_MERGE_MT' {
-        ext.args = '--output-type z'
-        ext.prefix = { "${meta.id}_merge_mt" }
-    }
 
-    withName: '.*ANALYSE_MT:MERGE_ANNOTATE_MT:ENSEMBLVEP_MT' {
+    withName: '.*ANNOTATE_MT_SNVS:ENSEMBLVEP_MT' {
         ext.args   = [
             '--dir_plugins vep_cache/Plugins',
             '--plugin LoFtool,vep_cache/LoFtool_scores.txt',
@@ -58,28 +36,28 @@ process {
         ].join(' ')
     }
 
-    withName: '.*ANALYSE_MT:MERGE_ANNOTATE_MT:ZIP_TABIX_HMTNOTE' {
+    withName: '.*ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE' {
         ext.prefix = { "${meta.id}_vep_vcfanno_hmtnote_mt" }
         publishDir = [
-            path: { "${params.outdir}/annotate_mt" },
+            path: { "${params.outdir}/annotate_snv/mitochondria" },
             mode: params.publish_dir_mode,
             pattern: "*{vcf.gz,vcf.gz.tbi}",
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
-    withName: '.*ANALYSE_MT:MERGE_ANNOTATE_MT:HMTNOTE_ANNOTATE' {
+    withName: '.*ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE' {
         ext.prefix = { "${meta.id}_vep_vcfanno_hmtnote_mt" }
         ext.args = '--offline'
         publishDir = [
             enabled: false
         ]
     }
 
-    withName: '.*ANALYSE_MT:MERGE_ANNOTATE_MT:HAPLOGREP2_CLASSIFY_MT' {
+    withName: '.*ANNOTATE_MT_SNVS:HAPLOGREP2_CLASSIFY_MT' {
         ext.prefix = { "${meta.id}_haplogrep" }
         publishDir = [
-            path: { "${params.outdir}/annotate_mt" },
+            path: { "${params.outdir}/annotate_snv/mitochondria" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]

conf/modules/call_snv.config

@@ -19,4 +19,14 @@ process {
         ]
     }
 
+    withName: '.*CALL_SNV:GATK4_SELECTVARIANTS' {
+        ext.args   = "--exclude-intervals ${params.mito_name}"
+        ext.prefix = { "${meta.id}_nomito" }
+        ext.when   = { !params.skip_snv_annotation }
+        publishDir = [
+            path: { "${params.outdir}/call_snv/genome" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 }