Merge pull request #581 from nf-core/bwamem_fix

bwamem_index fix

Author: eduard-watchmaker

.github/workflows/update-gpu-snapshot.yml

@@ -7,10 +7,10 @@ on:
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
-  NFT_VER: "0.9.2"
+  NFT_VER: "0.9.3"
   NXF_ANSI_LOG: false
   # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver
-  NXF_VER: "24.10.5"
+  NXF_VER: "25.04.0"
 
 jobs:
   update-gpu-snapshot:

.nf-core.yml

@@ -6,6 +6,7 @@ lint:
   files_unchanged:
     - docs/images/nf-core-methylseq_logo_light.png
     - docs/images/nf-core-methylseq_logo_dark.png
+    - assets/nf-core-methylseq_logo_light.png
   modules_config: false
 nf_core_version: 3.5.1
 repository_type: pipeline

CHANGELOG.md

@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Bug fixes & refactoring
 
 - 🐛 Fix error in `picard_bedtointervallist.config` [#566](https://github.com/nf-core/methylseq/pull/566)
+- 🐛 Fix error when using --aligner bwameth with samtools sort, the output bams will be labeled with prefix "${meta.id}.deduplicated.sorted" and published in the deduplication folder [#580](https://github.com/nf-core/methylseq/pull/581)
 - 🔧 Update Bismark to v0.25.1 [#569](https://github.com/nf-core/methylseq/pull/569)
 - 🔧 Update MultiQC module
 

README.md

@@ -1,7 +1,7 @@
 <h1>
   <picture>
-    <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-methylseq-dark.png">
-    <img alt="nf-core/methylseq" src="docs/images/nf-core-methylseq-light.png">
+    <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-methylseq_logo_dark.png">
+    <img alt="nf-core/methylseq" src="docs/images/nf-core-methylseq_logo_light.png">
   </picture>
 </h1>
 

assets/nf-core-methylseq_logo_light.png

@@ -0,0 +1,11 @@
+process {
+    withName: BWA_MEM {
+        ext.args = ''
+        publishDir = [
+                path: { "${params.outdir}/${params.aligner}/alignments" },
+                pattern: "*.bam",
+                mode: params.publish_dir_mode,
+                enabled: params.save_align_intermeds
+        ]
+    }
+}

conf/modules/bwamem_align.config

@@ -1,6 +1,5 @@
 process {
     withName: BWAMETH_ALIGN {
-        cache = 'lenient' // This is set because in the module command the index files are touched so as to have bwameth not complain
         ext.args = ''
         publishDir = [
                 path: { "${params.outdir}/${params.aligner}/alignments" },

conf/modules/bwameth_align.config

@@ -1,29 +1,12 @@
 process {
     withName: SAMTOOLS_SORT {
-        ext.prefix = params.skip_deduplication ? { "${meta.id}.sorted" } : { "${meta.id}.deduplicated.sorted" }
+        ext.prefix = { "${meta.id}.sorted" }
         publishDir = [
-            [
-                path: { "${params.outdir}/${params.aligner}/deduplicated/" },
-                mode: params.publish_dir_mode,
-                pattern: "*.deduplicated.sorted.bam"
-            ],
             [
                 path: { "${params.outdir}/${params.aligner}/alignments/" },
                 mode: params.publish_dir_mode,
                 pattern: "*.sorted.bam",
-                enabled: params.skip_deduplication
-            ],
-            [
-                path: { "${params.outdir}/${params.aligner}/deduplicated/" },
-                mode: params.publish_dir_mode,
-                pattern: "*markdup*.bam",
-                enabled: params.save_align_intermeds
-            ],
-            [
-                path: { "${params.outdir}/${params.aligner}/alignments/" },
-                mode: params.publish_dir_mode,
-                pattern: "*.bam",
-                enabled: params.save_align_intermeds
+                enabled: params.skip_deduplication || params.save_align_intermeds
             ]
         ]
     }

conf/modules/samtools_sort.config

@@ -6,3 +6,25 @@ includeConfig "../modules/bismark_methylationextractor.config"
 includeConfig "../modules/bismark_coverage2cytosine.config"
 includeConfig "../modules/bismark_report.config"
 includeConfig "../modules/bismark_summary.config"
+
+// Override SAMTOOLS_SORT for bismark workflow
+// In bismark, deduplication (BISMARK_DEDUPLICATE) happens BEFORE sorting,
+// so the BAM input to SAMTOOLS_SORT is already deduplicated when skip_deduplication is false
+process {
+    withName: SAMTOOLS_SORT {
+        ext.prefix = params.skip_deduplication ? { "${meta.id}.sorted" } : { "${meta.id}.deduplicated.sorted" }
+        publishDir = [
+            [
+                path: { "${params.outdir}/${params.aligner}/deduplicated/" },
+                mode: params.publish_dir_mode,
+                pattern: "*.deduplicated.sorted.bam"
+            ],
+            [
+                path: { "${params.outdir}/${params.aligner}/alignments/" },
+                mode: params.publish_dir_mode,
+                pattern: "*.sorted.bam",
+                enabled: params.skip_deduplication
+            ]
+        ]
+    }
+}

conf/subworkflows/fastq_align_dedup_bismark.config

@@ -1,2 +1,4 @@
+includeConfig "../modules/bwamem_align.config"
 includeConfig "../modules/picard_addorreplacereadgroups.config"
-includeConfig "../modules/picard_removeduplicates.config"
+includeConfig "../modules/picard_markduplicates.config"
+includeConfig "../modules/samtools_index.config"