bwamem_index fix

.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>
 

conf/modules/bwamem_align.config

@@ -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/bwameth_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/samtools_sort.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/subworkflows/fastq_align_dedup_bismark.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_bwamem.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"

modules.json

@@ -12,7 +12,7 @@
                     },
                     "bismark/align": {
                         "branch": "master",
-                        "git_sha": "107a3fb196ca4a174614d50d928739156a3c0f6c",
+                        "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
                         "installed_by": ["fastq_align_dedup_bismark"]
                     },
                     "bismark/coverage2cytosine": {
@@ -28,7 +28,7 @@
                     "bismark/genomepreparation": {
                         "branch": "master",
                         "git_sha": "107a3fb196ca4a174614d50d928739156a3c0f6c",
-                        "installed_by": ["fasta_index_bismark_bwameth"]
+                        "installed_by": ["fasta_index_bismark_bwameth", "fasta_index_methylseq"]
                     },
                     "bismark/methylationextractor": {
                         "branch": "master",
@@ -48,12 +48,12 @@
                     "bwa/index": {
                         "branch": "master",
                         "git_sha": "1c46359c837ef768b004519f535c30378e8289fc",
-                        "installed_by": ["modules"]
+                        "installed_by": ["fasta_index_methylseq"]
                     },
                     "bwa/mem": {
                         "branch": "master",
                         "git_sha": "1c46359c837ef768b004519f535c30378e8289fc",
-                        "installed_by": ["modules"]
+                        "installed_by": ["fastq_align_bwa"]
                     },
                     "bwameth/align": {
                         "branch": "master",
@@ -63,7 +63,7 @@
                     "bwameth/index": {
                         "branch": "master",
                         "git_sha": "79f1c3e487520405be6dd47ed7f196efd1e3b63e",
-                        "installed_by": ["fasta_index_bismark_bwameth"]
+                        "installed_by": ["fasta_index_bismark_bwameth", "fasta_index_methylseq"]
                     },
                     "cat/fastq": {
                         "branch": "master",
@@ -72,27 +72,27 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
                         "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
-                        "installed_by": ["fasta_index_bismark_bwameth"]
+                        "installed_by": ["fasta_index_bismark_bwameth", "fasta_index_methylseq"]
                     },
                     "methyldackel/extract": {
                         "branch": "master",
                         "git_sha": "c8df5757c72362907a43de49a6b20bd4998907a0",
-                        "installed_by": ["fastq_align_dedup_bwameth", "modules"]
+                        "installed_by": ["bam_methyldackel", "fastq_align_dedup_bwameth"]
                     },
                     "methyldackel/mbias": {
                         "branch": "master",
                         "git_sha": "c8df5757c72362907a43de49a6b20bd4998907a0",
-                        "installed_by": ["fastq_align_dedup_bwameth", "modules"]
+                        "installed_by": ["bam_methyldackel", "fastq_align_dedup_bwameth"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "8deffd6a402233ebf905c66dbf804bd4c2637946",
+                        "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
                         "installed_by": ["modules"]
                     },
                     "parabricks/fq2bammeth": {
@@ -103,7 +103,7 @@
                     "picard/addorreplacereadgroups": {
                         "branch": "master",
                         "git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
-                        "installed_by": ["modules"]
+                        "installed_by": ["fastq_align_dedup_bwamem"]
                     },
                     "picard/bedtointervallist": {
                         "branch": "master",
@@ -123,7 +123,7 @@
                     "picard/markduplicates": {
                         "branch": "master",
                         "git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
-                        "installed_by": ["fastq_align_dedup_bwameth"]
+                        "installed_by": ["fastq_align_dedup_bwamem", "fastq_align_dedup_bwameth"]
                     },
                     "preseq/lcextrap": {
                         "branch": "master",
@@ -143,52 +143,61 @@
                     "rastair/call": {
                         "branch": "master",
                         "git_sha": "20ff6c8d298d29bc00d3ef11cda614dac5f77ce8",
-                        "installed_by": ["modules"]
+                        "installed_by": ["bam_taps_conversion"]
                     },
                     "rastair/mbias": {
                         "branch": "master",
                         "git_sha": "20ff6c8d298d29bc00d3ef11cda614dac5f77ce8",
-                        "installed_by": ["modules"]
+                        "installed_by": ["bam_taps_conversion"]
                     },
                     "rastair/mbiasparser": {
                         "branch": "master",
                         "git_sha": "a4f1768a3026017b92a7e5d1c8b0fb9ac3efa3a9",
-                        "installed_by": ["modules"]
+                        "installed_by": ["bam_taps_conversion"]
                     },
                     "rastair/methylkit": {
                         "branch": "master",
                         "git_sha": "0dca361fb441760fb333467b3f5800d34490fb86",
-                        "installed_by": ["modules"]
+                        "installed_by": ["bam_taps_conversion"]
                     },
                     "samtools/faidx": {
                         "branch": "master",
                         "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
-                        "installed_by": ["fasta_index_bismark_bwameth"]
+                        "installed_by": ["fasta_index_bismark_bwameth", "fasta_index_methylseq"]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
                         "git_sha": "e334e12a1e985adc5ffc3fc78a68be1de711de45",
-                        "installed_by": ["fastq_align_dedup_bwameth"]
+                        "installed_by": ["bam_stats_samtools", "fastq_align_dedup_bwameth"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
                         "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
-                        "installed_by": ["modules"]
+                        "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/index": {
                         "branch": "master",
                         "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
-                        "installed_by": ["fastq_align_dedup_bismark", "fastq_align_dedup_bwameth"]
+                        "installed_by": [
+                            "bam_sort_stats_samtools",
+                            "fastq_align_dedup_bismark",
+                            "fastq_align_dedup_bwamem",
+                            "fastq_align_dedup_bwameth"
+                        ]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
-                        "installed_by": ["fastq_align_dedup_bismark", "fastq_align_dedup_bwameth"]
+                        "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
+                        "installed_by": [
+                            "bam_sort_stats_samtools",
+                            "fastq_align_dedup_bismark",
+                            "fastq_align_dedup_bwameth"
+                        ]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
-                        "installed_by": ["fastq_align_dedup_bwameth"]
+                        "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
+                        "installed_by": ["bam_stats_samtools", "fastq_align_dedup_bwameth"]
                     },
                     "trimgalore": {
                         "branch": "master",
@@ -198,25 +207,60 @@
                     "untar": {
                         "branch": "master",
                         "git_sha": "00ee87ebb541af0008596400ce6d5f66d79d5408",
-                        "installed_by": ["fasta_index_bismark_bwameth"]
+                        "installed_by": ["fasta_index_bismark_bwameth", "fasta_index_methylseq"]
                     }
                 }
             },
             "subworkflows": {
                 "nf-core": {
+                    "bam_methyldackel": {
+                        "branch": "master",
+                        "git_sha": "c8df5757c72362907a43de49a6b20bd4998907a0",
+                        "installed_by": ["subworkflows"]
+                    },
+                    "bam_sort_stats_samtools": {
+                        "branch": "master",
+                        "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
+                        "installed_by": ["fastq_align_bwa"]
+                    },
+                    "bam_stats_samtools": {
+                        "branch": "master",
+                        "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
+                        "installed_by": ["bam_sort_stats_samtools"]
+                    },
+                    "bam_taps_conversion": {
+                        "branch": "master",
+                        "git_sha": "a4f1768a3026017b92a7e5d1c8b0fb9ac3efa3a9",
+                        "installed_by": ["subworkflows"]
+                    },
                     "fasta_index_bismark_bwameth": {
                         "branch": "master",
                         "git_sha": "107a3fb196ca4a174614d50d928739156a3c0f6c",
                         "installed_by": ["subworkflows"]
                     },
+                    "fasta_index_methylseq": {
+                        "branch": "master",
+                        "git_sha": "654daca6c7d8a17479d1c56fb5fb8d1663f11428",
+                        "installed_by": ["subworkflows"]
+                    },
+                    "fastq_align_bwa": {
+                        "branch": "master",
+                        "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
+                        "installed_by": ["fastq_align_dedup_bwamem"]
+                    },
                     "fastq_align_dedup_bismark": {
                         "branch": "master",
-                        "git_sha": "107a3fb196ca4a174614d50d928739156a3c0f6c",
+                        "git_sha": "654daca6c7d8a17479d1c56fb5fb8d1663f11428",
+                        "installed_by": ["subworkflows"]
+                    },
+                    "fastq_align_dedup_bwamem": {
+                        "branch": "master",
+                        "git_sha": "654daca6c7d8a17479d1c56fb5fb8d1663f11428",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_align_dedup_bwameth": {
                         "branch": "master",
-                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
+                        "git_sha": "654daca6c7d8a17479d1c56fb5fb8d1663f11428",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {
@@ -226,7 +270,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2",
+                        "git_sha": "df4d1c8cdee98a1bbbed8fc51e82296568e0f9c1",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {