FelixKrueger · FelixKrueger · Aug 8, 2026 · Aug 8, 2026 · Aug 8, 2026 · Aug 8, 2026
diff --git a/.dockerignore b/.dockerignore
@@ -3,6 +3,8 @@
 # and dev/plan artifacts that don't affect the build.
 rust/target/
 **/target/
+# Legacy Perl toolchain — nothing in it is consumed by the image build.
+legacy_perl/
 .git/
 .github/
 plans/

diff --git a/.gitattributes b/.gitattributes
@@ -6,10 +6,10 @@
 # are vendored third-party report assets, not Bismark source.
 
 # Vendored web assets (plot.ly bundle + embedded HTML report templates).
-*.ly               linguist-vendored
-plotly/**          linguist-vendored
-**/plotly/**       linguist-vendored
-*.html             linguist-vendored
+*.ly                  linguist-vendored
+legacy_perl/plotly/** linguist-vendored
+**/plotly/**          linguist-vendored
+*.html                linguist-vendored
 
 # Documentation (not counted as a language).
 Docs/**            linguist-documentation

diff --git a/.github/workflows/ci_tests.yml b/.github/workflows/ci_tests.yml
@@ -34,12 +34,12 @@ jobs:
 
       - name: Bismark help message
         shell: bash -l {0}
-        run: ./bismark --help
+        run: ./legacy_perl/bismark --help
 
       - name: software versions
         shell: bash -l {0}
         run: |
-          ./bismark --version
+          ./legacy_perl/bismark --version
           samtools --version
           bowtie2 --version
           hisat2 --version
@@ -48,85 +48,85 @@ jobs:
         shell: bash -l {0} # required: yes! see above
         run: |
           pwd
-          ./bismark_genome_preparation --verbose ./test_files/
-          ./bismark_genome_preparation --verbose --parallel 4 ./test_files/
+          ./legacy_perl/bismark_genome_preparation --verbose ./test_files/
+          ./legacy_perl/bismark_genome_preparation --verbose --parallel 4 ./test_files/
 
       - name: Bismark PE run
         shell: bash -l {0}
         run: |
-          ./bismark --genome ./test_files/ -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
-          ./deduplicate_bismark --bam test_R1_bismark_bt2_pe.bam
-          ./bismark_methylation_extractor test_R1_bismark_bt2_pe.bam --gzip --CX --bed --genome ./test_files/
-          ./bismark2report
-          ./bismark2summary
+          ./legacy_perl/bismark --genome ./test_files/ -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
+          ./legacy_perl/deduplicate_bismark --bam test_R1_bismark_bt2_pe.bam
+          ./legacy_perl/bismark_methylation_extractor test_R1_bismark_bt2_pe.bam --gzip --CX --bed --genome ./test_files/
+          ./legacy_perl/bismark2report
+          ./legacy_perl/bismark2summary
 
       - name: Bismark SE run
         shell: bash -l {0}
         run: |
-          ./bismark --genome ./test_files/ ./test_files/test_R1.fastq.gz
-          ./deduplicate_bismark --bam test_R1_bismark_bt2.bam
-          ./bismark_methylation_extractor test_R1_bismark_bt2.bam --gzip --CX --bed --genome ./test_files/
+          ./legacy_perl/bismark --genome ./test_files/ ./test_files/test_R1.fastq.gz
+          ./legacy_perl/deduplicate_bismark --bam test_R1_bismark_bt2.bam
+          ./legacy_perl/bismark_methylation_extractor test_R1_bismark_bt2.bam --gzip --CX --bed --genome ./test_files/
 
       - name: Bismark run with option ICPC
         shell: bash -l {0}
         run: |
-          ./bismark --bowtie2 --icpc ./test_files/ -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
-          ./bismark --bowtie2 --icpc ./test_files/ ./test_files/test_R1.fastq.gz
+          ./legacy_perl/bismark --bowtie2 --icpc ./test_files/ -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
+          ./legacy_perl/bismark --bowtie2 --icpc ./test_files/ ./test_files/test_R1.fastq.gz
 
       - name: Bismark run using HISAT2
         shell: bash -l {0}
         run: |
-          ./bismark_genome_preparation --hisat2 --verbose ./test_files/
-          ./bismark_genome_preparation --hisat2 --verbose --parallel 4 ./test_files/
-          ./bismark --genome ./test_files/ --hisat2 ./test_files/test_R1.fastq.gz
-          ./bismark --genome ./test_files/ --hisat2 -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
-          ./deduplicate_bismark --bam test_R1_bismark_hisat2.bam
-          ./bismark_methylation_extractor test_R1_bismark_hisat2.bam  --gzip --CX --bed --genome ./test_files/
-          ./bismark_methylation_extractor test_R1_bismark_hisat2_pe.bam  --gzip --CX --bed --genome ./test_files/
+          ./legacy_perl/bismark_genome_preparation --hisat2 --verbose ./test_files/
+          ./legacy_perl/bismark_genome_preparation --hisat2 --verbose --parallel 4 ./test_files/
+          ./legacy_perl/bismark --genome ./test_files/ --hisat2 ./test_files/test_R1.fastq.gz
+          ./legacy_perl/bismark --genome ./test_files/ --hisat2 -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
+          ./legacy_perl/deduplicate_bismark --bam test_R1_bismark_hisat2.bam
+          ./legacy_perl/bismark_methylation_extractor test_R1_bismark_hisat2.bam  --gzip --CX --bed --genome ./test_files/
+          ./legacy_perl/bismark_methylation_extractor test_R1_bismark_hisat2_pe.bam  --gzip --CX --bed --genome ./test_files/
 
       - name: Bismark run Multicore
         shell: bash -l {0}
         run: |
-          ./bismark --genome ./test_files/ --parallel 4 -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
-          ./bismark --genome ./test_files/ --hisat2 --parallel 4 -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
-          ./bismark_methylation_extractor test_R1_bismark_bt2_pe.bam --gzip --CX --bed --parallel 8 --genome ./test_files/
-          ./bismark_methylation_extractor test_R1_bismark_hisat2_pe.bam --gzip --CX --bed --parallel 8 --genome ./test_files/
+          ./legacy_perl/bismark --genome ./test_files/ --parallel 4 -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
+          ./legacy_perl/bismark --genome ./test_files/ --hisat2 --parallel 4 -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
+          ./legacy_perl/bismark_methylation_extractor test_R1_bismark_bt2_pe.bam --gzip --CX --bed --parallel 8 --genome ./test_files/
+          ./legacy_perl/bismark_methylation_extractor test_R1_bismark_hisat2_pe.bam --gzip --CX --bed --parallel 8 --genome ./test_files/
 
       - name: coverage2cytosine
         shell: bash -l {0}
         run: |
-          ./coverage2cytosine test_R1_bismark_bt2_pe.bismark.cov.gz --merge_CpG --genome ./test_files/ -o test.output
-          ./coverage2cytosine test_R1_bismark_bt2_pe.bismark.cov.gz --NOMe-seq --genome ./test_files/ -o test.output
+          ./legacy_perl/coverage2cytosine test_R1_bismark_bt2_pe.bismark.cov.gz --merge_CpG --genome ./test_files/ -o test.output
+          ./legacy_perl/coverage2cytosine test_R1_bismark_bt2_pe.bismark.cov.gz --NOMe-seq --genome ./test_files/ -o test.output
 
       - name: bam2nuc
         shell: bash -l {0}
         run: |
-          ./bam2nuc --genome_folder ./test_files/ --genomic_composition_only
-          ./bam2nuc --genome_folder ./test_files/ test_R1_bismark_bt2_pe.bam
-          ./bam2nuc --genome_folder ./test_files/ test_R1_bismark_hisat2_pe.bam
+          ./legacy_perl/bam2nuc --genome_folder ./test_files/ --genomic_composition_only
+          ./legacy_perl/bam2nuc --genome_folder ./test_files/ test_R1_bismark_bt2_pe.bam
+          ./legacy_perl/bam2nuc --genome_folder ./test_files/ test_R1_bismark_hisat2_pe.bam
 
       - name: Additional scenarios
         shell: bash -l {0}
         run: |
-          ./bismark --pbat --genome ./test_files/ -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
-          ./bismark --non_directional --genome ./test_files/ -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
-          ./bismark --hisat2 --pbat --genome ./test_files/ -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
-          ./bismark --hisat2 --non_directional --genome ./test_files/ -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
+          ./legacy_perl/bismark --pbat --genome ./test_files/ -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
+          ./legacy_perl/bismark --non_directional --genome ./test_files/ -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
+          ./legacy_perl/bismark --hisat2 --pbat --genome ./test_files/ -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
+          ./legacy_perl/bismark --hisat2 --non_directional --genome ./test_files/ -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
 
       - name: bismark2bedGraph
         shell: bash -l {0}
         run: |
-          ./bismark2bedGraph -o test.bedGraph --buffer 5G CpG_*
-          ./bismark2bedGraph -o test.bedGraph --ucsc --buffer 5G CpG_*
-          ./bismark2bedGraph -o test.bedGraph --CX --scaffolds CpG* CHG_* CHH_*
-          ./bismark2bedGraph -o test.bedGraph --CX --ample_memory --zero_based CpG* CHH_* CHG_*
+          ./legacy_perl/bismark2bedGraph -o test.bedGraph --buffer 5G CpG_*
+          ./legacy_perl/bismark2bedGraph -o test.bedGraph --ucsc --buffer 5G CpG_*
+          ./legacy_perl/bismark2bedGraph -o test.bedGraph --CX --scaffolds CpG* CHG_* CHH_*
+          ./legacy_perl/bismark2bedGraph -o test.bedGraph --CX --ample_memory --zero_based CpG* CHH_* CHG_*
 
       - name: Filte non-conversion
         shell: bash -l {0}
         run: |
-          ./filter_non_conversion test_R1_bismark_bt2_pe.bam
-          ./filter_non_conversion --consecutive --threshold 6 test_R1_bismark_bt2.bam
-          ./filter_non_conversion test_R1_bismark_hisat2_pe.bam
-          ./filter_non_conversion --consecutive --threshold 6 test_R1_bismark_hisat2.bam
-          ./filter_non_conversion --percentage_cutoff 66 --minimum_count 4 test_R1_bismark_bt2_pe.bam
-          ./filter_non_conversion --percentage_cutoff 66 --minimum_count 4 test_R1_bismark_hisat2_pe.bam
+          ./legacy_perl/filter_non_conversion test_R1_bismark_bt2_pe.bam
+          ./legacy_perl/filter_non_conversion --consecutive --threshold 6 test_R1_bismark_bt2.bam
+          ./legacy_perl/filter_non_conversion test_R1_bismark_hisat2_pe.bam
+          ./legacy_perl/filter_non_conversion --consecutive --threshold 6 test_R1_bismark_hisat2.bam
+          ./legacy_perl/filter_non_conversion --percentage_cutoff 66 --minimum_count 4 test_R1_bismark_bt2_pe.bam
+          ./legacy_perl/filter_non_conversion --percentage_cutoff 66 --minimum_count 4 test_R1_bismark_hisat2_pe.bam
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,10 @@
 
 ## Unreleased
 
+### Repository layout
+
+- **The legacy Perl toolchain moved from the repository root to [`legacy_perl/`](legacy_perl).** The 12 Perl scripts, their `plotly/` report assets, `test_data.fastq`, and the Perl-era release packager now live in `legacy_perl/`; the repository root is Rust-first. Nothing changes for any installed package — bioconda/Homebrew/containers build from `rust/` or from the immutable `v0.25.1` tag. Old `blob/master/<script>` deep links break (GitHub does not redirect file moves); use the [`v0.25.1` tag](https://github.com/FelixKrueger/Bismark/releases/tag/v0.25.1) for stable Perl references. If you run the Perl scripts from a clone on your `PATH`, point it at `legacy_perl/` (or check out `v0.25.1`).
+
 ### All tools
 
 - **Short options are accepted in either letter case again, matching Perl Bismark ([#1084](https://github.com/FelixKrueger/Bismark/issues/1084)).** Perl's `Getopt::Long` is case-insensitive by default, so Perl Bismark accepted `-N`/`-L` *and* `-n`/`-l` for the Bowtie 2 seed settings — and its own help documents the uppercase spellings (`-n`/`-l` are described there as retired Bowtie 1's flags). The Rust CLI copied Perl's lowercase declarations verbatim, but clap is case-sensitive, so `bismark -N 1 -L 20` — the form the documentation shows — was rejected. Both spellings now work, so existing command lines and scripts port unchanged. Likewise `-v` is accepted alongside `-V` for `--version` across the suite, as Perl accepted it via single-dash abbreviation. Reported by @alexg9010.

diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@
 > faithful default path, faster, and lower-memory — and this is the **supported default**. Get it via
 > [Installation](#installation) (`mamba install -c bioconda bismark`, cargo, container, or prebuilt binaries) and see the
 > **[Rust suite overview](https://felixkrueger.github.io/Bismark/rust/overview/)**.
-> The original **Perl `v0.25.x`** (the scripts at this repo root) is now **legacy / maintenance-freeze**
+> The original **Perl `v0.25.x`** (now in [`legacy_perl/`](legacy_perl)) is **legacy / maintenance-freeze**
 > (critical fixes only; tagged [`v0.25.1`](https://github.com/FelixKrueger/Bismark/releases/tag/v0.25.1)).
 > **New contributions should target the Rust suite** — see [CONTRIBUTING.md](CONTRIBUTING.md).
 
@@ -57,7 +57,7 @@ brew install bismark
 
 ### Legacy: the Perl Bismark (v0.25.x)
 
-The original Perl scripts remain at this repo root (maintenance-freeze). To use them, download the [`v0.25.1` release](https://github.com/FelixKrueger/Bismark/releases/tag/v0.25.1) (or `mamba install bismark=0.25.1`); they need [Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/)/[HISAT2](https://ccb.jhu.edu/software/hisat2/index.shtml)/[minimap2](https://lh3.github.io/minimap2/minimap2.html) **and** [Samtools](http://www.htslib.org/) on the `PATH`.
+The original Perl scripts live in [`legacy_perl/`](legacy_perl) (maintenance-freeze). To use them, download the [`v0.25.1` release](https://github.com/FelixKrueger/Bismark/releases/tag/v0.25.1) (or `mamba install bismark=0.25.1`); they need [Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/)/[HISAT2](https://ccb.jhu.edu/software/hisat2/index.shtml)/[minimap2](https://lh3.github.io/minimap2/minimap2.html) **and** [Samtools](http://www.htslib.org/) on the `PATH`.
 
 ## Links
 

diff --git a/NOMe_filtering → legacy_perl/NOMe_filtering b/NOMe_filtering → legacy_perl/NOMe_filtering
diff --git a/bam2nuc → legacy_perl/bam2nuc b/bam2nuc → legacy_perl/bam2nuc
diff --git a/bismark → legacy_perl/bismark b/bismark → legacy_perl/bismark
diff --git a/bismark2bedGraph → legacy_perl/bismark2bedGraph b/bismark2bedGraph → legacy_perl/bismark2bedGraph
diff --git a/bismark2report → legacy_perl/bismark2report b/bismark2report → legacy_perl/bismark2report
diff --git a/bismark2summary → legacy_perl/bismark2summary b/bismark2summary → legacy_perl/bismark2summary
diff --git a/bismark_genome_preparation → legacy_perl/bismark_genome_preparation b/bismark_genome_preparation → legacy_perl/bismark_genome_preparation
diff --git a/bismark_methylation_extractor → legacy_perl/bismark_methylation_extractor b/bismark_methylation_extractor → legacy_perl/bismark_methylation_extractor
diff --git a/copy_bismark_files_for_release.pl → ...cy_perl/copy_bismark_files_for_release.pl b/copy_bismark_files_for_release.pl → ...cy_perl/copy_bismark_files_for_release.pl
diff --git a/coverage2cytosine → legacy_perl/coverage2cytosine b/coverage2cytosine → legacy_perl/coverage2cytosine
diff --git a/deduplicate_bismark → legacy_perl/deduplicate_bismark b/deduplicate_bismark → legacy_perl/deduplicate_bismark
diff --git a/filter_non_conversion → legacy_perl/filter_non_conversion b/filter_non_conversion → legacy_perl/filter_non_conversion
diff --git a/methylation_consistency → legacy_perl/methylation_consistency b/methylation_consistency → legacy_perl/methylation_consistency
diff --git a/plotly/Bismark_Alignment_Stats_Summary.png → ...lotly/Bismark_Alignment_Stats_Summary.png b/plotly/Bismark_Alignment_Stats_Summary.png → ...lotly/Bismark_Alignment_Stats_Summary.png
diff --git a/plotly/bioinf.logo → legacy_perl/plotly/bioinf.logo b/plotly/bioinf.logo → legacy_perl/plotly/bioinf.logo
diff --git a/plotly/bismark.logo → legacy_perl/plotly/bismark.logo b/plotly/bismark.logo → legacy_perl/plotly/bismark.logo
diff --git a/plotly/bismark_bt2_PE_report.html → ...cy_perl/plotly/bismark_bt2_PE_report.html b/plotly/bismark_bt2_PE_report.html → ...cy_perl/plotly/bismark_bt2_PE_report.html
diff --git a/plotly/bismark_summary_RRBS.html → legacy_perl/plotly/bismark_summary_RRBS.html b/plotly/bismark_summary_RRBS.html → legacy_perl/plotly/bismark_summary_RRBS.html
diff --git a/plotly/bismark_summary_WGBS.html → legacy_perl/plotly/bismark_summary_WGBS.html b/plotly/bismark_summary_WGBS.html → legacy_perl/plotly/bismark_summary_WGBS.html
diff --git a/plotly/bismark_summary_single_cells.html → .../plotly/bismark_summary_single_cells.html b/plotly/bismark_summary_single_cells.html → .../plotly/bismark_summary_single_cells.html
diff --git a/plotly/bismark_summary_single_cells.txt → ...l/plotly/bismark_summary_single_cells.txt b/plotly/bismark_summary_single_cells.txt → ...l/plotly/bismark_summary_single_cells.txt
diff --git a/plotly/plot.ly → legacy_perl/plotly/plot.ly b/plotly/plot.ly → legacy_perl/plotly/plot.ly
diff --git a/plotly/plotly_template.tpl → legacy_perl/plotly/plotly_template.tpl b/plotly/plotly_template.tpl → legacy_perl/plotly/plotly_template.tpl
diff --git a/test_data.fastq → legacy_perl/test_data.fastq b/test_data.fastq → legacy_perl/test_data.fastq