Merge branch 'dev' into bounlu-patch-1

.github/workflows/ci.yml

@@ -11,7 +11,7 @@ on:
 
 env:
   NXF_ANSI_LOG: false
-  NFT_VER: "0.9.1"
+  NFT_VER: "0.9.2"
   NFT_WORKDIR: "~"
   NFT_DIFF: "pdiff"
   NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"

CHANGELOG.md

@@ -1,5 +1,21 @@
 # nf-core/methylseq
 
+## [v2.8.0](https://github.com/nf-core/methylseq/releases/tag/2.8.0) - []
+
+### Bug fixes & refactoring
+
+- 🐛 fix fasta gunzip output [#462](https://github.com/nf-core/methylseq/pull/457)
+- 🐛 fix bismark/align not resuming from cache [#461](https://github.com/nf-core/methylseq/pull/457)
+
+### Pipeline Updates
+
+- 🔧 Install `fastq_align_dedup_bismark` subworkflow from nf-core/subworkflows [#453](https://github.com/nf-core/methylseq/pull/457)
+- 🔧 Install `fasta_index_bismark_bwameth` subworkflow from nf-core/subworkflows [#466](https://github.com/nf-core/methylseq/pull/468)
+- 🔧 Install `fastq_align_dedup_bwameth` subworkflow from nf-core/subworkflows [#467](https://github.com/nf-core/methylseq/pull/)
+- 🔧 reorg individual configs to `conf/modules/` named configs [#459](https://github.com/nf-core/methylseq/pull/469)
+- 🔧 `run_preseq` param + skip preseq/lcextrap module by default [#458](https://github.com/nf-core/methylseq/pull/470)
+- 🔧 `run_qualimap` param + skip qualimap module by default [#367](https://github.com/nf-core/methylseq/pull/471)
+
 ## [v2.7.1](https://github.com/nf-core/methylseq/releases/tag/2.7.1) - [2024-10-27]
 
 ### Bug fixes & refactoring

conf/base.config

@@ -59,6 +59,9 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
+    withName: PRESEQ_LCEXTRAP {
+        errorStrategy = 'ignore'
+    }
     withName: BISMARK_ALIGN {
         time = { 8.d * task.attempt }
     }
@@ -69,6 +72,7 @@ process {
         time = { 1.d * task.attempt }
     }
     withName: BWAMETH_ALIGN {
+        cache = 'lenient'
         time = { 6.d * task.attempt }
     }
 }

modules/nf-core/bismark/align/nextflow.config → conf/modules/bismark_align.config

@@ -35,4 +35,4 @@ process {
                 ]
             ]
         }
-}
+}

modules/nf-core/bismark/coverage2cytosine/nextflow.config → conf/modules/bismark_coverage2cytosine.config

@@ -19,4 +19,4 @@ process {
             ]
         ]
     }
-}
+}

modules/nf-core/bismark/deduplicate/nextflow.config → conf/modules/bismark_deduplicate.config

@@ -9,4 +9,4 @@ process {
             ]
         ]
     }
-}
+}

modules/nf-core/bismark/genomepreparation/nextflow.config → conf/modules/bismark_genomepreparation.config

@@ -11,4 +11,4 @@ process {
             enabled: params.save_reference
         ]
     }
-}
+}

modules/nf-core/bismark/methylationextractor/nextflow.config → conf/modules/bismark_methylationextractor.config

@@ -38,4 +38,4 @@ process {
             ]
         ]
     }
-}
+}

modules/nf-core/bismark/report/nextflow.config → conf/modules/bismark_report.config

@@ -7,4 +7,4 @@ process {
             pattern: "*.html"
         ]
     }
-}
+}

modules/nf-core/bismark/summary/nextflow.config → conf/modules/bismark_summary.config

@@ -7,4 +7,4 @@ process {
             pattern: "*.{html,txt}"
         ]
     }
-}
+}

modules/nf-core/bwameth/align/nextflow.config → conf/modules/bwameth_align.config

@@ -8,4 +8,4 @@ process {
                 enabled: params.save_align_intermeds
         ]
     }
-}
+}

modules/nf-core/bwameth/index/nextflow.config → conf/modules/bwameth_index.config

@@ -8,4 +8,4 @@ process {
             enabled: params.save_reference
         ]
     }
-}
+}

modules/nf-core/fastqc/nextflow.config → conf/modules/fastqc.config

@@ -14,4 +14,4 @@ process {
             ]
         ]
     }
-}
+}

modules/nf-core/methyldackel/extract/nextflow.config → conf/modules/methyldackel_extract.config

@@ -19,4 +19,4 @@ process {
             ]
         ]
     }
-}
+}

modules/nf-core/methyldackel/mbias/nextflow.config → conf/modules/methyldackel_mbias.config

@@ -12,4 +12,4 @@ process {
             ]
         ]
     }
-}
+}

modules/nf-core/multiqc/nextflow.config → conf/modules/multiqc.config

@@ -7,4 +7,4 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-}
+}

modules/nf-core/picard/markduplicates/nextflow.config → conf/modules/picard_markduplicates.config

@@ -15,4 +15,4 @@ process {
             ]
         ]
     }
-}
+}

modules/nf-core/preseq/lcextrap/nextflow.config → conf/modules/preseq_lcextrap.config

@@ -5,13 +5,15 @@ process {
             [
                 path: { "${params.outdir}/${params.aligner}/preseq" },
                 mode: params.publish_dir_mode,
-                pattern: "*.txt"
+                pattern: "*.txt",
+                enabled: params.run_preseq
             ],
             [
                 path: { "${params.outdir}/${params.aligner}/preseq/log" },
                 mode: params.publish_dir_mode,
-                pattern: "*.log"
+                pattern: "*.log",
+                enabled: params.run_preseq
             ]
         ]
     }
-}
+}

conf/modules/qualimap_bamqc.config

@@ -0,0 +1,16 @@
+process {
+    withName: QUALIMAP_BAMQC {
+        ext.args = [
+            params.genome.toString().startsWith('GRCh') ? '-gd HUMAN' : '',
+            params.genome.toString().startsWith('GRCm') ? '-gd MOUSE' : ''
+        ].join(" ").trim()
+        publishDir = [
+            [
+                path: { "${params.outdir}/${params.aligner}/qualimap/bamqc/" },
+                mode: params.publish_dir_mode,
+                pattern: "*",
+                enabled: params.run_qualimap
+            ]
+        ]
+    }
+}

modules/nf-core/samtools/faidx/nextflow.config → conf/modules/samtools_faidx.config

@@ -8,4 +8,4 @@ process {
             pattern: "*.fai"
         ]
     }
-}
+}

modules/nf-core/samtools/flagstat/nextflow.config → conf/modules/samtools_flagstat.config

@@ -8,4 +8,4 @@ process {
             ]
         ]
     }
-}
+}

modules/nf-core/samtools/sort/nextflow.config → conf/modules/samtools_index.config

@@ -1,19 +1,19 @@
 process {
-    withName: SAMTOOLS_SORT {
-        ext.prefix = { "${meta.id}.sorted" }
+    withName: SAMTOOLS_INDEX {
+        ext.prefix = ""
         publishDir = [
             [
                 path: { "${params.outdir}/${params.aligner}/deduplicated/" },
                 mode: params.publish_dir_mode,
-                pattern: "*markdup*.bam",
-                enabled: params.save_align_intermeds
+                pattern: "*.bai",
+                enabled: !params.skip_deduplication
             ],
             [
                 path: { "${params.outdir}/${params.aligner}/alignments/" },
                 mode: params.publish_dir_mode,
-                pattern: "*.bam",
-                enabled: params.save_align_intermeds
+                pattern: "*.bai",
+                enabled: params.skip_deduplication
             ]
         ]
     }
-}
+}

conf/modules/samtools_sort.config

@@ -0,0 +1,30 @@
+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
+            ],
+            [
+                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
+            ]
+        ]
+    }
+}

modules/nf-core/samtools/stats/nextflow.config → conf/modules/samtools_stats.config

@@ -8,4 +8,4 @@ process {
             ]
         ]
     }
-}
+}

modules/nf-core/trimgalore/nextflow.config → conf/modules/trimgalore.config

@@ -87,4 +87,4 @@ process {
             ]
         ]
     }
-}
+}

conf/test.config

@@ -18,7 +18,7 @@ params {
     input = "${projectDir}/assets/samplesheet.csv"
 
     // Genome references
-    fasta       = "${params.pipelines_testdata_base_path}/reference/genome.fa"
+    fasta       = "${params.pipelines_testdata_base_path}/reference/genome.fa.gz"
     fasta_index = "${params.pipelines_testdata_base_path}/reference/genome.fa.fai"
 }
 

main.nf

@@ -15,11 +15,11 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { METHYLSEQ               } from './workflows/methylseq/'
-include { PREPARE_GENOME          } from './subworkflows/local/prepare_genome/'
-include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_methylseq_pipeline'
-include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_methylseq_pipeline'
-include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_methylseq_pipeline'
+include { FASTA_INDEX_BISMARK_BWAMETH } from './subworkflows/nf-core/fasta_index_bismark_bwameth/main'
+include { METHYLSEQ                   } from './workflows/methylseq/'
+include { PIPELINE_INITIALISATION     } from './subworkflows/local/utils_nfcore_methylseq_pipeline'
+include { PIPELINE_COMPLETION         } from './subworkflows/local/utils_nfcore_methylseq_pipeline'
+include { getGenomeAttribute          } from './subworkflows/local/utils_nfcore_methylseq_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -52,13 +52,13 @@ workflow NFCORE_METHYLSEQ {
     //
     // SUBWORKFLOW: Prepare any required reference genome indices
     //
-    PREPARE_GENOME(
+    FASTA_INDEX_BISMARK_BWAMETH(
         params.fasta,
         params.fasta_index,
         params.bismark_index,
         params.bwameth_index,
     )
-    ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)
+    ch_versions = ch_versions.mix(FASTA_INDEX_BISMARK_BWAMETH.out.versions)
 
     //
     // WORKFLOW: Run pipeline
@@ -67,10 +67,10 @@ workflow NFCORE_METHYLSEQ {
     METHYLSEQ (
         samplesheet,
         ch_versions,
-        PREPARE_GENOME.out.fasta,
-        PREPARE_GENOME.out.fasta_index,
-        PREPARE_GENOME.out.bismark_index,
-        PREPARE_GENOME.out.bwameth_index,
+        FASTA_INDEX_BISMARK_BWAMETH.out.fasta,
+        FASTA_INDEX_BISMARK_BWAMETH.out.fasta_index,
+        FASTA_INDEX_BISMARK_BWAMETH.out.bismark_index,
+        FASTA_INDEX_BISMARK_BWAMETH.out.bwameth_index,
     )
     emit:
     multiqc_report = METHYLSEQ.out.multiqc_report // channel: /path/to/multiqc_report.html