Taps

.github/workflows/linting.yml

@@ -11,12 +11,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
 
-      - name: Set up Python 3.13
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - name: Set up Python 3.14
+        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -28,14 +28,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
           architecture: "x64"
 
       - name: read .nf-core.yml
@@ -71,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: linting-logs
           path: |

.github/workflows/linting_comment.yml

@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2
+        uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}

.prettierignore

@@ -10,5 +10,7 @@ testing/
 testing*
 *.pyc
 bin/
+.nf-test/
 ro-crate-metadata.json
-*.nf.test.snap
+modules/nf-core/
+subworkflows/nf-core/

CITATIONS.md

@@ -33,6 +33,10 @@
 
   > Felix Krueger, Simon R. Andrews, Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications, Bioinformatics, Volume 27, Issue 11, 1 June 2011, Pages 1571–1572, doi: [10.1093/bioinformatics/btr167](https://doi.org/10.1093/bioinformatics/btr167)
 
+- [BWA-MEM](https://arxiv.org/abs/1303.3997v2)
+
+  > Li H: Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv 2013. doi: 10.48550/arXiv.1303.3997
+
 - [bwa-meth](https://arxiv.org/abs/1401.1129)
 
   > Pedersen, Brent S. and Eyring, Kenneth and De, Subhajyoti and Yang, Ivana V. and Schwartz, David A. Fast and accurate alignment of long bisulfite-seq reads, arXiv:1401.1129, doi: [10.48550/arXiv.1401.1129](https://doi.org/10.48550/arXiv.1401.1129)
@@ -49,6 +53,8 @@
 
   > Daley, T., Smith, A. Predicting the molecular complexity of sequencing libraries. Nat Methods 10, 325–327 (2013). doi: [10.1038/nmeth.2375](https://doi.org/10.1038/nmeth.2375)
 
+- [rastair](https://bitbucket.org/bsblabludwig/rastair/src/master/)
+
 - [Samtools](https://doi.org/10.1093/gigascience/giab008)
 
   > Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li, Twelve years of SAMtools and BCFtools, GigaScience, Volume 10, Issue 2, February 2021, giab008, doi: [10.1093/gigascience/giab008](https://doi.org/10.1093/gigascience/giab008)

README.md

@@ -22,7 +22,7 @@
 
 **nf-core/methylseq** is a bioinformatics analysis pipeline used for Methylation (Bisulfite) sequencing data. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.
 
-![nf-core/methylseq metro map](docs/images/4.0.0_metromap.png)
+![nf-core/methylseq metro map](docs/images/taps_metromap.png)
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker / Singularity / Podman / Charliecloud / Apptainer containers making installation trivial and results highly reproducible.
 
@@ -32,26 +32,26 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 ## Pipeline Summary
 
-The pipeline allows you to choose between running either [Bismark](https://github.com/FelixKrueger/Bismark) or [bwa-meth](https://github.com/brentp/bwa-meth) / [MethylDackel](https://github.com/dpryan79/methyldackel).
+The pipeline allows you to choose between running either [Bismark](https://github.com/FelixKrueger/Bismark), [bwa-meth](https://github.com/brentp/bwa-meth) / [MethylDackel](https://github.com/dpryan79/methyldackel) or [BWA-Mem](https://github.com/lh3/bwa) plus [rastair](https://bitbucket.org/bsblabludwig/rastair/src/master/) for for TAPS data processing. rastair can also be used with bwa-meth aligned reads by setting the aligner to `--aligner bwameth` and adding the flag `--taps`.
 
-Choose between workflows by using `--aligner bismark` (default, uses bowtie2 for alignment), `--aligner bismark_hisat` or `--aligner bwameth`. For higher performance, the pipeline can leverage the [Parabricks implementation of bwa-meth (fq2bammeth)](https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam_meth.html), which implements the baseline tool `bwa-meth` in a performant method using fq2bam (BWA-MEM + GATK) as a backend for processing on GPU. To use this option, include the `gpu` profile along with `--aligner bwameth`.
+Choose between workflows by using `--aligner bismark` (default, uses bowtie2 for alignment), `--aligner bismark_hisat`, `--aligner bwameth` or `--aligner bwamem`. For higher performance, the pipeline can leverage the [Parabricks implementation of bwa-meth (fq2bammeth)](https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam_meth.html) and the [Parabricks implementation of bwa-mem (fq2bammemh)](https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam.html), which implement the baseline tools `bwa-meth` and `bwa-mem`. To use this option, include the `gpu` profile along with `--aligner bwameth` or `--aligner bwamem`.
 
 Note: For faster CPU runs with BWA-Meth, enable the BWA-MEM2 algorithm using `--use_mem2`. The GPU pathway (Parabricks) requires `-profile gpu` and a container runtime (Docker, Singularity, or Podman); Conda/Mamba are not supported for the GPU module.
 
-| Step                                         | Bismark workflow         | bwa-meth workflow     |
-| -------------------------------------------- | ------------------------ | --------------------- |
-| Generate Reference Genome Index _(optional)_ | Bismark                  | bwa-meth              |
-| Merge re-sequenced FastQ files               | cat                      | cat                   |
-| Raw data QC                                  | FastQC                   | FastQC                |
-| Adapter sequence trimming                    | Trim Galore!             | Trim Galore!          |
-| Align Reads                                  | Bismark (bowtie2/hisat2) | bwa-meth              |
-| Deduplicate Alignments                       | Bismark                  | Picard MarkDuplicates |
-| Extract methylation calls                    | Bismark                  | MethylDackel          |
-| Sample report                                | Bismark                  | -                     |
-| Summary Report                               | Bismark                  | -                     |
-| Alignment QC                                 | Qualimap _(optional)_    | Qualimap _(optional)_ |
-| Sample complexity                            | Preseq _(optional)_      | Preseq _(optional)_   |
-| Project Report                               | MultiQC                  | MultiQC               |
+| Step                                         | Bismark workflow         | bwa-meth workflow     | bwa-mem + TAPS workflow    |
+| -------------------------------------------- | ------------------------ | --------------------- | -------------------------- |
+| Generate Reference Genome Index _(optional)_ | Bismark                  | bwa-meth              | bwa index                  |
+| Merge re-sequenced FastQ files               | cat                      | cat                   | cat                        |
+| Raw data QC                                  | FastQC                   | FastQC                | FastQC                     |
+| Adapter sequence trimming                    | Trim Galore!             | Trim Galore!          | Trim Galore!               |
+| Align Reads                                  | Bismark (bowtie2/hisat2) | bwa-meth              | bwa mem                    |
+| Deduplicate Alignments                       | Bismark                  | Picard MarkDuplicates | Picard MarkDuplicates      |
+| Extract methylation calls                    | Bismark                  | MethylDackel          | TAPS subworkflow (rastair) |
+| Sample report                                | Bismark                  | -                     | -                          |
+| Summary Report                               | Bismark                  | -                     | -                          |
+| Alignment QC                                 | Qualimap _(optional)_    | Qualimap _(optional)_ | Qualimap _(optional)_      |
+| Sample complexity                            | Preseq _(optional)_      | Preseq _(optional)_   | Preseq _(optional)_        |
+| Project Report                               | MultiQC                  | MultiQC               | MultiQC                    |
 
 Optional targeted sequencing analysis is available via `--run_targeted_sequencing` and `--target_regions_file`; see the [usage documentation](https://nf-co.re/methylseq/usage) for details.
 

conf/base.config

@@ -81,4 +81,7 @@ process {
     withName: PARABRICKS_FQ2BAMMETH {
         memory = { 100.GB * task.attempt }
     }
+    withName: PARABRICKS_FQ2BAM {
+        memory = { 100.GB * task.attempt }
+    }
 }

conf/modules/gatk_removeduplicates.config

@@ -0,0 +1,5 @@
+process {
+    withName: GATK4_REMOVEDUPLICATES {
+        ext.args = "--REMOVE_DUPLICATES true --TAG_DUPLICATE_SET_MEMBERS true"
+    }
+}

conf/modules/picard_addorreplacereadgroups.config

@@ -0,0 +1,5 @@
+process {
+    withName: PICARD_ADDORREPLACEREADGROUPS {
+        ext.args = "--RGID 1 --RGLB lib1 --RGPL illumina --RGPU unit1 --RGSM sample1"
+    }
+}

conf/modules/picard_removeduplicates.config

@@ -0,0 +1,18 @@
+process {
+    withName: PICARD_REMOVEDUPLICATES {
+        ext.args = "--ASSUME_SORTED true --REMOVE_DUPLICATES true --VALIDATION_STRINGENCY LENIENT --PROGRAM_RECORD_ID 'null' --TMP_DIR tmp"
+        ext.prefix = { "${meta.id}.dedup.sorted" }
+        publishDir = [
+            [
+                path: { "${params.outdir}/${params.aligner}/deduplicated/picard_metrics" },
+                pattern: "*.metrics.txt",
+                mode: params.publish_dir_mode
+            ],
+            [
+                path: { "${params.outdir}/${params.aligner}/deduplicated" },
+                pattern: "*.bam",
+                mode: params.publish_dir_mode
+            ]
+        ]
+    }
+}

conf/modules/rastair_call.config

@@ -0,0 +1,20 @@
+process {
+    withName: RASTAIR_CALL {
+        ext.args = [
+            // Pending the resolution of the mbias_parse process
+            params.trim_OT ?: '0,0,10,0', // [r1_start, r1_end, r2_start, r2_end]
+            params.trim_OB ?: '0,0,10,0' // [r1_start, r1_end, r2_start, r2_end]
+        ].join(" ").trim()
+        publishDir = [
+            [
+                path: { "${params.outdir}/rastair/call" },
+                mode: params.publish_dir_mode,
+                pattern: "*.txt"
+            ], [
+                path: { "${params.outdir}/rastair/call" },
+                mode: params.publish_dir_mode,
+                pattern: "*.gz"
+            ]
+        ]
+    }
+}

conf/modules/rastair_mbias.config

@@ -0,0 +1,11 @@
+process {
+    withName: RASTAIR_MBIAS {
+        publishDir = [
+            [
+                path: { "${params.outdir}/rastair/mbias" },
+                mode: params.publish_dir_mode,
+                pattern: "*.txt"
+            ]
+        ]
+    }
+}

conf/modules/rastair_mbias_parser.config

@@ -0,0 +1,11 @@
+process {
+    withName: RASTAIR_MBIASPARSER {
+        publishDir = [
+            [
+                path: { "${params.outdir}/rastair/mbiasparser" },
+                mode: params.publish_dir_mode,
+                pattern: "*rastair_mbias_processed*"
+            ]
+        ]
+    }
+}

conf/modules/rastair_methylkit.config

@@ -0,0 +1,11 @@
+process {
+    withName: RASTAIR_METHYLKIT {
+        publishDir = [
+            [
+                path: { "${params.outdir}/rastair/methylkit" },
+                mode: params.publish_dir_mode,
+                pattern: "*.txt.gz"
+            ]
+        ]
+    }
+}

conf/subworkflows/bam_methyldackel.config

@@ -0,0 +1,2 @@
+includeConfig "../modules/methyldackel_extract.config"
+includeConfig "../modules/methyldackel_mbias.config"

conf/subworkflows/bam_taps_conversion.config

@@ -0,0 +1,4 @@
+includeConfig "../modules/rastair_call.config"
+includeConfig "../modules/rastair_mbias.config"
+includeConfig "../modules/rastair_mbias_parser.config"
+includeConfig "../modules/rastair_methylkit.config"

conf/subworkflows/fasta_index_methylseq.config

@@ -0,0 +1,4 @@
+includeConfig "../modules/gunzip.config"
+includeConfig "../modules/bismark_genomepreparation.config"
+includeConfig "../modules/samtools_faidx.config"
+includeConfig "../modules/bwameth_index.config"

conf/subworkflows/fastq_align_dedup_bwamem.config

@@ -0,0 +1,2 @@
+includeConfig "../modules/picard_addorreplacereadgroups.config"
+includeConfig "../modules/picard_removeduplicates.config"

conf/subworkflows/fastq_align_dedup_bwameth.config

@@ -5,8 +5,6 @@ includeConfig "../modules/samtools_sort.config"
 includeConfig "../modules/samtools_flagstat.config"
 includeConfig "../modules/samtools_stats.config"
 includeConfig "../modules/picard_markduplicates.config"
-includeConfig "../modules/methyldackel_extract.config"
-includeConfig "../modules/methyldackel_mbias.config"
 
 process {