Merge pull request #544 from FriederikeHanssen/fix_mutect2

Fix Mutect2
nf-core · May 16, 2022 · 5d0a0b9 · 5d0a0b9
2 parents 818e8e6 + 42d1506
commit 5d0a0b9
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Showing 36 changed files with 456 additions and 336 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -48,6 +48,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#520](https://github.com/nf-core/sarek/pull/520) - Improve annotation subworkflows
 - [#537](https://github.com/nf-core/sarek/pull/537) - Update workflow figure
 - [#539](https://github.com/nf-core/sarek/pull/539) - Update `CITATIONS.md`
+- [#544](https://github.com/nf-core/sarek/pull/544) - `Mutect2` is no longer compatible with `--no_intervals`
 
 ### Fixed
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -737,7 +737,8 @@ process{
     }
 
     //MUTECT2
-    withName: 'GATK4_CALCULATECONTAMINATION' {
+    withName: 'CALCULATECONTAMINATION' {
+        ext.args         = { "-tumor-segmentation ${meta.id}.segmentation.table" }
         publishDir        = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
@@ -747,7 +748,6 @@ process{
 
     withName: 'CONCAT_MUTECT2.*' {
         publishDir       = [
-            enabled: !params.no_intervals,
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
             pattern: "*{vcf.gz,vcf.gz.tbi}"
@@ -763,28 +763,50 @@ process{
         ]
     }
 
-    withName: 'GATHERPILEUPSUMMARIES.*' {
-        ext.prefix       = { "${meta.id}.table" }
-        ext.when         = { "${!params.no_intervals}"}
+    withName: 'GATHERPILEUPSUMMARIES' {
+        publishDir       = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: 'GATHERPILEUPSUMMARIES' {
         publishDir       = [
-            enabled: !params.no_intervals,
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
+    withName: 'GATHERPILEUPSUMMARIES_.*' {
+        publishDir       = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/${meta.tumor_id}_vs_${meta.normal_id}/mutect2" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: 'GETPILEUPSUMMARIES.*' {
         publishDir        = [
-            enabled: params.no_intervals,
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
+            pattern: "*.table",
+            saveAs: { meta.num_intervals > 1 ? null : it }
+        ]
+    }
+
+    withName: 'LEARNREADORIENTATIONMODEL'{
+        ext.prefix       = { "${meta.id}.artifactprior" }
+        publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
     withName: 'MERGEMUTECTSTATS' {
-        ext.prefix       = { "${meta.id}.vcf.gz" }
+        ext.prefix       = { "${meta.id}" }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
@@ -794,12 +816,12 @@ process{
 
     withName: 'MUTECT2'{
         ext.when         = { params.tools && params.tools.contains('mutect2') }
-        ext.args         = { params.ignore_soft_clipped_bases ? "--dont-use-soft-clipped-bases true" : "" }
+        ext.args         = { params.ignore_soft_clipped_bases ? "--dont-use-soft-clipped-bases true --f1r2-tar-gz ${meta.id}.f1r2.tar.gz" : "--f1r2-tar-gz ${meta.id}.f1r2.tar.gz" }
         publishDir       = [
-            enabled: params.no_intervals,
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
-            pattern: "*{gz,gz.tbi,stats}"
+            pattern: "*{vcf.gz,vcf.gz.tbi,stats}",
+            saveAs: { meta.num_intervals > 1 ? null : it }
         ]
     }
 
@@ -884,34 +906,11 @@ process{
     }
 
     //MUTECT2
-    withName: 'CALCULATECONTAMINATION' {
-        //ext.args         = { params.ignore_soft_clipped_bases ? "--dont-use-soft-clipped-bases true" : "" }
-        publishDir       = [
-            mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
 
-    withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING:GATHERPILEUPSUMMARIES.*' {
-        ext.prefix       = { "${meta.id}.table" }
-        publishDir       = [
-            enabled: !params.no_intervals,
-            mode: params.publish_dir_mode,
-            //use ${meta.tumor_id}_vs_${meta_normal_id} to publish in the same directory as the remainders of the
-            //somatic output whilst keeping the filename prefix identifiable for status type
-            path: { "${params.outdir}/variant_calling/${meta.tumor_id}_vs_${meta.normal_id}/mutect2" },
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: 'LEARNREADORIENTATIONMODEL' {
-        ext.prefix         = { "${meta.id}.learnreadorientationmodel" }
-        publishDir       = [
-            mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
+    withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING:MUTECT2' {
+        ext.args         = { params.ignore_soft_clipped_bases ?
+                            "--dont-use-soft-clipped-bases true --f1r2-tar-gz ${meta.id}.f1r2.tar.gz --normal-sample ${meta.patient}_${meta.normal_id}" :
+                            "--f1r2-tar-gz ${meta.id}.f1r2.tar.gz --normal-sample ${meta.patient}_${meta.normal_id}" }
     }
 
     //MSISENSORPRO

diff --git a/modules.json b/modules.json
@@ -79,70 +79,70 @@
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "gatk4/applybqsr": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/applybqsrspark": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/applyvqsr": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/baserecalibrator": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/baserecalibratorspark": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "fd7ee6799abf1bd5228b4b59ce541f3aeaa2280b"
             },
             "gatk4/calculatecontamination": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/createsequencedictionary": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/estimatelibrarycomplexity": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/filtermutectcalls": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/gatherbqsrreports": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/gatherpileupsummaries": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/genomicsdbimport": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/genotypegvcfs": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/getpileupsummaries": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "f40cfefc0899fd6bb6adc300142ca6c3a35573ff"
             },
             "gatk4/haplotypecaller": {
-                "git_sha": "68f1c27169946f931ea4318911de5681f88b2961"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/intervallisttobed": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/learnreadorientationmodel": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/markduplicates": {
-                "git_sha": "0511e7fbbfa4ba41940d33b687b1cc90227b4eb8"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/markduplicatesspark": {
                 "git_sha": "e04970b7d249365cafa5a52912f9a28840481c05"
             },
             "gatk4/mergemutectstats": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/mutect2": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/variantrecalibrator": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "manta/germline": {
                 "git_sha": "ffedf09b6e84b479c9c901274f74bb33f3777243"
@@ -172,7 +172,7 @@
                 "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
             },
             "samtools/bam2fq": {
-                "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
+                "git_sha": "5510ea39fe638594bc26ac34cadf4a84bf27d159"
             },
             "samtools/collatefastq": {
                 "git_sha": "705f8c9ac4dfdf07666e71abde28f267e2dfd5eb"
@@ -196,7 +196,7 @@
                 "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
             },
             "samtools/view": {
-                "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
+                "git_sha": "6b64f9cb6c3dd3577931cc3cd032d6fb730000ce"
             },
             "seqkit/split2": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"

diff --git a/modules/nf-core/modules/ascat/main.nf b/modules/nf-core/modules/ascat/main.nf
diff --git a/modules/nf-core/modules/gatk4/applybqsr/main.nf b/modules/nf-core/modules/gatk4/applybqsr/main.nf
diff --git a/modules/nf-core/modules/gatk4/applybqsrspark/main.nf b/modules/nf-core/modules/gatk4/applybqsrspark/main.nf
diff --git a/modules/nf-core/modules/gatk4/applyvqsr/main.nf b/modules/nf-core/modules/gatk4/applyvqsr/main.nf
diff --git a/modules/nf-core/modules/gatk4/baserecalibrator/main.nf b/modules/nf-core/modules/gatk4/baserecalibrator/main.nf
diff --git a/modules/nf-core/modules/gatk4/baserecalibratorspark/main.nf b/modules/nf-core/modules/gatk4/baserecalibratorspark/main.nf
diff --git a/modules/nf-core/modules/gatk4/calculatecontamination/main.nf b/modules/nf-core/modules/gatk4/calculatecontamination/main.nf
diff --git a/modules/nf-core/modules/gatk4/createsequencedictionary/main.nf b/modules/nf-core/modules/gatk4/createsequencedictionary/main.nf
diff --git a/modules/nf-core/modules/gatk4/estimatelibrarycomplexity/main.nf b/modules/nf-core/modules/gatk4/estimatelibrarycomplexity/main.nf
diff --git a/modules/nf-core/modules/gatk4/filtermutectcalls/main.nf b/modules/nf-core/modules/gatk4/filtermutectcalls/main.nf
diff --git a/modules/nf-core/modules/gatk4/gatherbqsrreports/main.nf b/modules/nf-core/modules/gatk4/gatherbqsrreports/main.nf