Refactoring + other issues with cadd and samtools merge

CHANGELOG.md

@@ -9,9 +9,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- Refactored config files [#538](https://github.com/nf-core/raredisease/pull/538)
+- Refactored mobile element annotation subworkflow files [#538](https://github.com/nf-core/raredisease/pull/538)
+
 ### `Fixed`
 
 - Include multiallelic indel sites in CADD scoring jobs [#545](https://github.com/nf-core/raredisease/pull/545)
+- Fixed issues with samtools merge not being run on samples sequenced over multiple lanes [#538](https://github.com/nf-core/raredisease/pull/538)
 
 ### Parameters
 
@@ -24,6 +28,12 @@ Parameter has been added if just the new parameter information is present.
 Parameter has been removed if new parameter information isn't present.
 :::
 
+## 2.0.1 - Asterix (Patch) [2024-03-25]
+
+### `Fixed`
+
+- Germlinecnvcaller subworkflow uses the output channel `casecalls` from germlinecnvcaller module instead of `calls` which was invalid. [#535](https://github.com/nf-core/raredisease/issues/535)
+
 ## 2.0.0 - Asterix [2024-03-18]
 
 ### `Added`

conf/base.config

@@ -57,4 +57,9 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
+    withName: 'NFCORE_RAREDISEASE:RAREDISEASE:.*' {
+        publishDir = [
+            enabled: false
+        ]
+    }
 }

conf/modules/align.config

@@ -12,36 +12,27 @@
 */
 
 process{
-    withName: '.*ALIGN:.*' {
+
+    withName: '.*ALIGN:FASTP' {
+        ext.args = { [
+            params.min_trimmed_length ? "--length_required ${params.min_trimmed_length}" : '',
+            '--correction',
+            '--overrepresentation_analysis'
+        ].join(' ').trim() }
         publishDir = [
-            enabled: false
+            path: { "${params.outdir}/trimming" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
-    if (!params.skip_fastp) {
-        withName: '.*ALIGN:FASTP' {
-            ext.args = { [
-                params.min_trimmed_length ? "--length_required ${params.min_trimmed_length}" : '',
-                '--correction',
-                '--overrepresentation_analysis'
-            ].join(' ').trim() }
-            publishDir = [
-                path: { "${params.outdir}/trimming" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-    }
-
-    if (params.save_mapped_as_cram) {
-        withName: '.*ALIGN:SAMTOOLS_VIEW' {
-            ext.args   = { '--output-fmt cram --write-index' }
-            ext.prefix = { "${meta.id}_sorted_md" }
-            publishDir = [
-                path: { "${params.outdir}/alignment" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
+    withName: '.*ALIGN:SAMTOOLS_VIEW' {
+        ext.args   = { '--output-fmt cram --write-index' }
+        ext.prefix = { "${meta.id}_sorted_md" }
+        publishDir = [
+            path: { "${params.outdir}/alignment" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
     }
 }

conf/modules/align_MT.config

@@ -17,28 +17,22 @@
 
 process {
 
-    if (params.aligner.equals("bwamem2")) {
-        withName: '.*ALIGN_MT:BWAMEM2_MEM_MT' {
-            ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
-            ext.when = { !(params.analysis_type.equals("wes")) }
-            ext.prefix = { "${meta.id}_sorted" }
-        }
+    withName: '.*ALIGN_MT:BWAMEM2_MEM_MT' {
+        ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
+        ext.when = { !(params.analysis_type.equals("wes")) }
+        ext.prefix = { "${meta.id}_sorted" }
     }
 
-    if (params.aligner.equals("bwa")) {
-        withName: '.*ALIGN_MT:BWA_MEM_MT' {
-            ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
-            ext.when = { !(params.analysis_type.equals("wes")) }
-            ext.prefix = { "${meta.id}_sorted" }
-        }
+    withName: '.*ALIGN_MT:BWA_MEM_MT' {
+        ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
+        ext.when = { !(params.analysis_type.equals("wes")) }
+        ext.prefix = { "${meta.id}_sorted" }
     }
 
-    if (params.aligner.equals("sentieon")) {
-        withName: '.*ALIGN_MT:SENTIEON_BWAMEM_MT' {
-            ext.args = { "-M -K 10000000 -R ${meta.read_group}" }
-            ext.when = { !(params.analysis_type.equals("wes"))}
-            ext.prefix = { "${meta.id}_sorted" }
-        }
+    withName: '.*ALIGN_MT:SENTIEON_BWAMEM_MT' {
+        ext.args = { "-M -K 10000000 -R ${meta.read_group}" }
+        ext.when = { !(params.analysis_type.equals("wes"))}
+        ext.prefix = { "${meta.id}_sorted" }
     }
 
     withName: '.*ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT' {
@@ -74,28 +68,22 @@ process {
 
 process {
 
-    if (params.aligner.equals("bwamem2")) {
-        withName: '.*ALIGN_MT_SHIFT:BWAMEM2_MEM_MT' {
-            ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
-            ext.when = { !(params.analysis_type.equals("wes")) }
-            ext.prefix = { "${meta.id}_sorted_shifted" }
-        }
+    withName: '.*ALIGN_MT_SHIFT:BWAMEM2_MEM_MT' {
+        ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
+        ext.when = { !(params.analysis_type.equals("wes")) }
+        ext.prefix = { "${meta.id}_sorted_shifted" }
     }
 
-    if (params.aligner.equals("sentieon")) {
-        withName: '.*ALIGN_MT_SHIFT:SENTIEON_BWAMEM_MT' {
-            ext.args = { "-M -K 10000000 -R ${meta.read_group}" }
-            ext.when = { !(params.analysis_type.equals("wes"))}
-            ext.prefix = { "${meta.id}_sorted_shifted" }
-        }
+    withName: '.*ALIGN_MT_SHIFT:SENTIEON_BWAMEM_MT' {
+        ext.args = { "-M -K 10000000 -R ${meta.read_group}" }
+        ext.when = { !(params.analysis_type.equals("wes"))}
+        ext.prefix = { "${meta.id}_sorted_shifted" }
     }
 
-    if (params.aligner.equals("bwa")) {
-        withName: '.*ALIGN_MT_SHIFT:BWA_MEM_MT' {
-            ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
-            ext.when = { !(params.analysis_type.equals("wes")) }
-            ext.prefix = { "${meta.id}_sorted_shifted" }
-        }
+    withName: '.*ALIGN_MT_SHIFT:BWA_MEM_MT' {
+        ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
+        ext.when = { !(params.analysis_type.equals("wes")) }
+        ext.prefix = { "${meta.id}_sorted_shifted" }
     }
 
     withName: '.*ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT' {

conf/modules/align_bwa_bwamem2.config

@@ -17,46 +17,45 @@
 
 process {
 
-    if (params.aligner.equals("bwamem2") || params.aligner.equals("bwa")) {
-
-        withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:BWAMEM2_MEM' {
-            ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
-            ext.prefix = { "${meta.id}_sorted" }
-            ext.when = { params.aligner.equals("bwamem2") }
-        }
-
-        withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:BWA_MEM' {
-            ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
-            ext.prefix = { "${meta.id}_sorted" }
-            ext.when = { params.aligner.equals("bwa") }
-        }
-
-        withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:SAMTOOLS_STATS' {
-            ext.args = '-s --remove-overlaps'
-        }
-
-        withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:SAMTOOLS_MERGE' {
-            ext.prefix = { "${meta.id}_sorted_merged" }
-        }
-
-        withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:MARKDUPLICATES' {
-            ext.args = "--TMP_DIR ."
-            ext.prefix = { "${meta.id}_sorted_md" }
-            publishDir = [
-                enabled: !params.save_mapped_as_cram,
-                path: { "${params.outdir}/alignment" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
-        withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:SAMTOOLS_INDEX_MARKDUP' {
-            publishDir = [
-                enabled: !params.save_mapped_as_cram,
-                path: { "${params.outdir}/alignment" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
+    withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:BWAMEM2_MEM' {
+        ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
+        ext.args2 = { "-T ./samtools_sort_tmp" }
+        ext.prefix = { "${meta.id}_sorted" }
+        ext.when = { params.aligner.equals("bwamem2") }
+    }
+
+    withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:BWA_MEM' {
+        ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
+        ext.args2 = { "-T ./samtools_sort_tmp" }
+        ext.prefix = { "${meta.id}_sorted" }
+        ext.when = { params.aligner.equals("bwa") }
+    }
+
+    withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:SAMTOOLS_STATS' {
+        ext.args = '-s --remove-overlaps'
+    }
+
+    withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:SAMTOOLS_MERGE' {
+        ext.prefix = { "${meta.id}_sorted_merged" }
+    }
+
+    withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:MARKDUPLICATES' {
+        ext.args = "--TMP_DIR ."
+        ext.prefix = { "${meta.id}_sorted_md" }
+        publishDir = [
+            enabled: !params.save_mapped_as_cram,
+            path: { "${params.outdir}/alignment" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:SAMTOOLS_INDEX_MARKDUP' {
+        publishDir = [
+            enabled: !params.save_mapped_as_cram,
+            path: { "${params.outdir}/alignment" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
     }
 }

conf/modules/align_sentieon.config

@@ -17,30 +17,28 @@
 
 process {
 
-    if (params.aligner.equals("sentieon")) {
-        withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_BWAMEM' {
-            ext.args = { "-M -K 10000000 -R ${meta.read_group} " }
-            ext.prefix = { "${meta.id}.sorted" }
-        }
+    withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_BWAMEM' {
+        ext.args = { "-M -K 10000000 -R ${meta.read_group} " }
+        ext.prefix = { "${meta.id}.sorted" }
+    }
 
-        withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_DATAMETRICS' {
-            ext.prefix = { "${meta.id}_datametrics" }
-        }
+    withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_DATAMETRICS' {
+        ext.prefix = { "${meta.id}_datametrics" }
+    }
 
-        withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_READWRITER' {
-            ext.prefix = { "${meta.id}_merged" }
-        }
+    withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_READWRITER' {
+        ext.prefix = { "${meta.id}_merged" }
+    }
 
-        withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_DEDUP' {
-            ext.args = { $params.rmdup ? "--rmdup" : '' }
-            ext.prefix = { "${meta.id}_dedup" }
-            ext.suffix = ".bam"
-            publishDir = [
-                enabled: !params.save_mapped_as_cram,
-                path: { "${params.outdir}/alignment" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
+    withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_DEDUP' {
+        ext.args = { $params.rmdup ? "--rmdup" : '' }
+        ext.prefix = { "${meta.id}_dedup" }
+        ext.suffix = ".bam"
+        publishDir = [
+            enabled: !params.save_mapped_as_cram,
+            path: { "${params.outdir}/alignment" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
     }
 }