From e72c52ecacb3cb1b6a859ddcca44f8baaef72628 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Miguel=20=C3=81lvarez=20Herrera?= <miguel.alvarez@uv.es>
Date: Thu, 5 Mar 2026 18:30:47 +0100
Subject: [PATCH 1/9] fix: mask sites before dN and dS calculation

---
 workflow/envs/bedtools.yaml              |  5 +++
 workflow/rules/evolution.smk             | 15 +++++++++
 workflow/scripts/calculate_dnds.R        | 16 ++++++++++
 workflow/scripts/n_s_sites_from_fasta.py | 40 ++++++++++++++++++++++--
 4 files changed, 73 insertions(+), 3 deletions(-)
 create mode 100644 workflow/envs/bedtools.yaml

diff --git a/workflow/envs/bedtools.yaml b/workflow/envs/bedtools.yaml
new file mode 100644
index 0000000..a76cc14
--- /dev/null
+++ b/workflow/envs/bedtools.yaml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bedtools==2.31.1
diff --git a/workflow/rules/evolution.smk b/workflow/rules/evolution.smk
index 0380940..ec53196 100644
--- a/workflow/rules/evolution.smk
+++ b/workflow/rules/evolution.smk
@@ -14,6 +14,19 @@ rule filter_genbank_features:
         "../scripts/filter_genbank_features.py"
 
 
+rule build_problematic_bed:
+    conda:
+        "../envs/bedtools.yaml"
+    input:
+        vcf = lambda wildcards: select_problematic_vcf(),
+    output:
+        bed = temp(OUTDIR / "sites_masked.bed"),
+    log:
+        LOGDIR / "build_problematic_bed" / "log.txt",
+    shell:
+        "bedtools merge -i {input.vcf} >{output.bed} 2>{log}"
+
+
 rule n_s_sites:
     threads: 1
     conda: "../envs/biopython.yaml"
@@ -21,6 +34,7 @@ rule n_s_sites:
         gb_qualifier_display = "gene",
     input:
         fasta = OUTDIR/f"{OUTPUT_NAME}.ancestor.fasta",
+        masked = OUTDIR / "sites_masked.bed",
         gb = OUTDIR/"reference.cds.gb",
         genetic_code = Path(config["GENETIC_CODE_JSON"]).resolve(),
     output:
@@ -35,6 +49,7 @@ rule calculate_dnds:
     conda: "../envs/renv.yaml"
     input: 
         n_s_sites = OUTDIR/f"{OUTPUT_NAME}.ancestor.n_s.sites.csv",
+        masked = OUTDIR / "sites_masked.bed",
         variants =  OUTDIR/f"{OUTPUT_NAME}.variants.tsv",
         metadata = config["METADATA"]
     output:
diff --git a/workflow/scripts/calculate_dnds.R b/workflow/scripts/calculate_dnds.R
index 4c34688..d600936 100644
--- a/workflow/scripts/calculate_dnds.R
+++ b/workflow/scripts/calculate_dnds.R
@@ -8,6 +8,7 @@ sink(log, type = "output")
 library(dplyr)
 library(readr)
 library(tidyr)
+library(purrr)
 library(logger)
 
 log_threshold(INFO)
@@ -37,6 +38,21 @@ metadata <- read_delim(snakemake@input[["metadata"]]) %>%
   select(ID, interval) %>%
   rename(SAMPLE = ID)
 
+log_info("Reading masked sites BED")
+masked <- read_tsv(
+  snakemake@input$masked,
+  col_names = c("chrom", "start", "end"),
+  col_types = "cii",
+  comment = "#"
+) %>%
+  mutate(POS = map2(start + 1, end, seq.int)) %>%
+  unnest(POS) %>%
+  pull(POS)
+
+log_info("Filtering variants on masked sites")
+variants <- variants %>%
+  filter(!POS %in% masked, !is.na(SYNONYMOUS))
+
 log_debug("Adding metadata to variants table")
 variants <- left_join(variants, metadata)
 
diff --git a/workflow/scripts/n_s_sites_from_fasta.py b/workflow/scripts/n_s_sites_from_fasta.py
index cb7fa6f..c0e37be 100644
--- a/workflow/scripts/n_s_sites_from_fasta.py
+++ b/workflow/scripts/n_s_sites_from_fasta.py
@@ -7,19 +7,50 @@
 
 import pandas as pd
 from Bio import SeqIO
-from Bio.SeqRecord import SeqRecord
+from Bio.SeqRecord import SeqRecord, SeqFeature
 from Bio.Seq import Seq
 
 
 NTS = ("A", "C", "G", "T")
+MASK_CHR = "N"
 
 
 def read_monofasta(path: str) -> SeqRecord:
     return SeqIO.read(path, format="fasta")
 
 
+def read_masked_positions(bed_path: str) -> set:
+    masked = set()
+    with open(bed_path) as fh:
+        for line in fh:
+            if line.startswith("#") or not line.strip():
+                continue
+            parts = line.strip().split("\t")
+            start, end = int(parts[1]), int(parts[2])
+            masked.update(range(start, end))
+    return masked
+
+
+def mask_feature(feature: SeqFeature, record: SeqRecord, masked_positions: set) -> SeqRecord:
+    extracted = feature.extract(record)
+    seq_chars = list(str(extracted.seq).upper())
+    # Handle reverse strand and compound locations
+    genomic_positions = []
+    for part in feature.location.parts:
+        positions = list(range(int(part.start), int(part.end)))
+        if part.strand == -1:
+            positions.reverse()
+        genomic_positions.extend(positions)
+    # Mask sites on sequence
+    for i, pos in enumerate(genomic_positions):
+        if seq_chars[i] not in NTS or pos in masked_positions:
+            seq_chars[i] = MASK_CHR
+    extracted.seq = Seq("".join(seq_chars))
+    return extracted
+
+
 def split_into_codons(seq: Seq) -> list:
-    """Split the complete CDS feature in to a list of codons"""
+    """Split the complete CDS feature in to a list of codons (if ACGT only)"""
     return [
         seq[i:i + 3] for i in range(0, len(seq)-2, 3) if all(char in NTS for char in seq[i:i + 3])
     ]
@@ -79,6 +110,9 @@ def main():
     with open(snakemake.input.genetic_code) as f:
         genetic_code = json.load(f)
 
+    logging.info("Reading masked sites BED")
+    masked = read_masked_positions(snakemake.input.masked)
+
     logging.info("Reading GenBank file")
     gb = SeqIO.read(snakemake.input.gb, format="gb")
 
@@ -95,7 +129,7 @@ def main():
             logging.warning(f"Identifier '{identifier}' is already among coding records and will not be replaced by feature at {feature.location}")
         else:
             logging.debug(f"Adding feature")
-            coding_records[identifier] = feature.extract(record)
+            coding_records[identifier] = mask_feature(feature, record, masked)
 
     logging.info(f"Splitting {len(coding_records)} records into codons")
     codons = get_feature_codons(coding_records)

From f16ffa9d27d28e8d0789f714f1d94bbb302d93f7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Miguel=20=C3=81lvarez=20Herrera?= <miguel.alvarez@uv.es>
Date: Thu, 5 Mar 2026 18:49:15 +0100
Subject: [PATCH 2/9] fix import

---
 workflow/scripts/n_s_sites_from_fasta.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/workflow/scripts/n_s_sites_from_fasta.py b/workflow/scripts/n_s_sites_from_fasta.py
index c0e37be..62cf6ed 100644
--- a/workflow/scripts/n_s_sites_from_fasta.py
+++ b/workflow/scripts/n_s_sites_from_fasta.py
@@ -7,7 +7,8 @@
 
 import pandas as pd
 from Bio import SeqIO
-from Bio.SeqRecord import SeqRecord, SeqFeature
+from Bio.SeqRecord import SeqRecord
+from Bio.SeqFeature import SeqFeature
 from Bio.Seq import Seq
 
 

From 40024594ada3eca1291e2cc1c6b750a2daeded74 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Miguel=20=C3=81lvarez=20Herrera?= <miguel.alvarez@uv.es>
Date: Thu, 5 Mar 2026 19:04:32 +0100
Subject: [PATCH 3/9] move and rename rule

---
 workflow/rules/evolution.smk | 13 -------------
 workflow/rules/sites.smk     | 13 +++++++++++++
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/workflow/rules/evolution.smk b/workflow/rules/evolution.smk
index ec53196..ef1895c 100644
--- a/workflow/rules/evolution.smk
+++ b/workflow/rules/evolution.smk
@@ -14,19 +14,6 @@ rule filter_genbank_features:
         "../scripts/filter_genbank_features.py"
 
 
-rule build_problematic_bed:
-    conda:
-        "../envs/bedtools.yaml"
-    input:
-        vcf = lambda wildcards: select_problematic_vcf(),
-    output:
-        bed = temp(OUTDIR / "sites_masked.bed"),
-    log:
-        LOGDIR / "build_problematic_bed" / "log.txt",
-    shell:
-        "bedtools merge -i {input.vcf} >{output.bed} 2>{log}"
-
-
 rule n_s_sites:
     threads: 1
     conda: "../envs/biopython.yaml"
diff --git a/workflow/rules/sites.smk b/workflow/rules/sites.smk
index 9ff7739..8cd74bc 100644
--- a/workflow/rules/sites.smk
+++ b/workflow/rules/sites.smk
@@ -1,3 +1,16 @@
+rule problematic_vcf_to_bed:
+    conda:
+        "../envs/bedtools.yaml"
+    input:
+        vcf = lambda wildcards: select_problematic_vcf(),
+    output:
+        bed = temp(OUTDIR / "sites_masked.bed"),
+    log:
+        LOGDIR / "build_problematic_bed" / "log.txt",
+    shell:
+        "bedtools merge -i {input.vcf} >{output.bed} 2>{log}"
+
+
 rule bcftools_mpileup_all_sites:
     threads: 1
     conda: "../envs/var_calling.yaml"

From a7a91f80508b44168eefdf08a1a5d27cc17e1bb7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Miguel=20=C3=81lvarez=20Herrera?= <miguel.alvarez@uv.es>
Date: Thu, 5 Mar 2026 19:19:23 +0100
Subject: [PATCH 4/9] update Dockerfile with bedtools environment

---
 Dockerfile | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 6c2556e..673a873 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,6 +1,6 @@
 FROM condaforge/miniforge3:latest
 LABEL io.github.snakemake.containerized="true"
-LABEL io.github.snakemake.conda_env_hash="ed26b44bdff1bc9f7a99d3830ae812bf262f78427b95a45fa1ac1ce255c5f054"
+LABEL io.github.snakemake.conda_env_hash="dac62e7daa260f58e83880b4ad266bb819917087f9c7baee7cbb1337b1603244"
 
 # Step 2: Retrieve conda environments
 
@@ -15,6 +15,17 @@ LABEL io.github.snakemake.conda_env_hash="ed26b44bdff1bc9f7a99d3830ae812bf262f78
 RUN mkdir -p /conda-envs/9c24a867826615972cc288081976e7fc
 COPY workflow/envs/afwdist.yaml /conda-envs/9c24a867826615972cc288081976e7fc/environment.yaml
 
+# Conda environment:
+#   source: workflow/envs/bedtools.yaml
+#   prefix: /conda-envs/cef13cdc1c388b3087761b0222ec0613
+#   channels:
+#     - conda-forge
+#     - bioconda
+#   dependencies:
+#     - bedtools==2.31.1
+RUN mkdir -p /conda-envs/cef13cdc1c388b3087761b0222ec0613
+COPY workflow/envs/bedtools.yaml /conda-envs/cef13cdc1c388b3087761b0222ec0613/environment.yaml
+
 # Conda environment:
 #   source: workflow/envs/biopython.yaml
 #   prefix: /conda-envs/162796cecea22d99c8702138f0c48e2f
@@ -165,6 +176,7 @@ COPY workflow/envs/var_calling.yaml /conda-envs/81e46c677a6cc0618c93963d57d17d3f
 # Step 3: Generate conda environments
 
 RUN conda env create --prefix /conda-envs/9c24a867826615972cc288081976e7fc --file /conda-envs/9c24a867826615972cc288081976e7fc/environment.yaml && \
+    conda env create --prefix /conda-envs/cef13cdc1c388b3087761b0222ec0613 --file /conda-envs/cef13cdc1c388b3087761b0222ec0613/environment.yaml && \
     conda env create --prefix /conda-envs/162796cecea22d99c8702138f0c48e2f --file /conda-envs/162796cecea22d99c8702138f0c48e2f/environment.yaml && \
     conda env create --prefix /conda-envs/9439457f932a4fbca3665c9ea1ac2f0a --file /conda-envs/9439457f932a4fbca3665c9ea1ac2f0a/environment.yaml && \
     conda env create --prefix /conda-envs/bb4c5f3a509433cc08861582fab4a705 --file /conda-envs/bb4c5f3a509433cc08861582fab4a705/environment.yaml && \

From a3b474226cb1051ba88ba75a9699651f2bd41079 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Miguel=20=C3=81lvarez=20Herrera?= <miguel.alvarez@uv.es>
Date: Fri, 6 Mar 2026 09:41:14 +0100
Subject: [PATCH 5/9] filter problematic sites

---
 workflow/rules/sites.smk | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/workflow/rules/sites.smk b/workflow/rules/sites.smk
index 8cd74bc..7b17d2c 100644
--- a/workflow/rules/sites.smk
+++ b/workflow/rules/sites.smk
@@ -1,8 +1,24 @@
+rule problematic_vcf_filter:
+    conda:
+        "../envs/bcftools.yaml"
+    params:
+        filters = ["mask"],
+    input:
+        vcf = lambda wildcards: select_problematic_vcf(),
+    output:
+        vcf = temp(OUTDIR / "sites_masked.vcf"),
+    log:
+        LOGDIR / "problematic_vcf_filter" / "log.txt"
+    shell:
+        """FILTER_STR=$(echo "{params.filters}" | tr ' ' ',') && """
+        """bcftools view -f "$FILTER_STR" {input.vcf} >{output.vcf} 2>{log}"""
+
+
 rule problematic_vcf_to_bed:
     conda:
         "../envs/bedtools.yaml"
     input:
-        vcf = lambda wildcards: select_problematic_vcf(),
+        vcf = OUTDIR / "sites_masked.vcf",
     output:
         bed = temp(OUTDIR / "sites_masked.bed"),
     log:

From 8c9cb629d2ea97b04d81eedc4d3a021a4991bf65 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Miguel=20=C3=81lvarez=20Herrera?= <miguel.alvarez@uv.es>
Date: Fri, 6 Mar 2026 10:04:04 +0100
Subject: [PATCH 6/9] merge rules to build BED

---
 workflow/envs/tools.yaml |  6 ++++++
 workflow/rules/sites.smk | 23 ++++++-----------------
 2 files changed, 12 insertions(+), 17 deletions(-)
 create mode 100644 workflow/envs/tools.yaml

diff --git a/workflow/envs/tools.yaml b/workflow/envs/tools.yaml
new file mode 100644
index 0000000..cc5ada1
--- /dev/null
+++ b/workflow/envs/tools.yaml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bedtools==2.31.1
+  - bcftools==1.23
diff --git a/workflow/rules/sites.smk b/workflow/rules/sites.smk
index 7b17d2c..9bbbd41 100644
--- a/workflow/rules/sites.smk
+++ b/workflow/rules/sites.smk
@@ -1,30 +1,19 @@
-rule problematic_vcf_filter:
+rule problematic_vcf_to_bed:
     conda:
-        "../envs/bcftools.yaml"
+        "../envs/tools.yaml"
     params:
         filters = ["mask"],
     input:
         vcf = lambda wildcards: select_problematic_vcf(),
     output:
         vcf = temp(OUTDIR / "sites_masked.vcf"),
-    log:
-        LOGDIR / "problematic_vcf_filter" / "log.txt"
-    shell:
-        """FILTER_STR=$(echo "{params.filters}" | tr ' ' ',') && """
-        """bcftools view -f "$FILTER_STR" {input.vcf} >{output.vcf} 2>{log}"""
-
-
-rule problematic_vcf_to_bed:
-    conda:
-        "../envs/bedtools.yaml"
-    input:
-        vcf = OUTDIR / "sites_masked.vcf",
-    output:
         bed = temp(OUTDIR / "sites_masked.bed"),
     log:
-        LOGDIR / "build_problematic_bed" / "log.txt",
+        LOGDIR / "problematic_vcf_to_bed" / "log.txt",
     shell:
-        "bedtools merge -i {input.vcf} >{output.bed} 2>{log}"
+        "FILTER_STR=$(echo \"{params.filters}\" | tr ' ' ',') && "
+        "bcftools view -f \"$FILTER_STR\" {input.vcf} >{output.vcf} 2>{log} && "
+        "bedtools merge -i {output.vcf} >{output.bed} 2>{log}"
 
 
 rule bcftools_mpileup_all_sites:

From b4fa480f01dcc64f0b4de85d54d14ffb8959c9a1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Miguel=20=C3=81lvarez=20Herrera?= <miguel.alvarez@uv.es>
Date: Fri, 6 Mar 2026 10:05:40 +0100
Subject: [PATCH 7/9] update Dockerfile

---
 Dockerfile | 27 ++++++++++++++-------------
 1 file changed, 14 insertions(+), 13 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 673a873..188459d 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,6 +1,6 @@
 FROM condaforge/miniforge3:latest
 LABEL io.github.snakemake.containerized="true"
-LABEL io.github.snakemake.conda_env_hash="dac62e7daa260f58e83880b4ad266bb819917087f9c7baee7cbb1337b1603244"
+LABEL io.github.snakemake.conda_env_hash="966286962ebc1e35e9809cc85e2904bfefb462e6a14ee09730b81ab69eb4d441"
 
 # Step 2: Retrieve conda environments
 
@@ -15,17 +15,6 @@ LABEL io.github.snakemake.conda_env_hash="dac62e7daa260f58e83880b4ad266bb8199170
 RUN mkdir -p /conda-envs/9c24a867826615972cc288081976e7fc
 COPY workflow/envs/afwdist.yaml /conda-envs/9c24a867826615972cc288081976e7fc/environment.yaml
 
-# Conda environment:
-#   source: workflow/envs/bedtools.yaml
-#   prefix: /conda-envs/cef13cdc1c388b3087761b0222ec0613
-#   channels:
-#     - conda-forge
-#     - bioconda
-#   dependencies:
-#     - bedtools==2.31.1
-RUN mkdir -p /conda-envs/cef13cdc1c388b3087761b0222ec0613
-COPY workflow/envs/bedtools.yaml /conda-envs/cef13cdc1c388b3087761b0222ec0613/environment.yaml
-
 # Conda environment:
 #   source: workflow/envs/biopython.yaml
 #   prefix: /conda-envs/162796cecea22d99c8702138f0c48e2f
@@ -160,6 +149,18 @@ COPY workflow/envs/renv.yaml /conda-envs/8ad6cdcf265d30289788da99d5bf9fff/enviro
 RUN mkdir -p /conda-envs/0adafb79cb1bec58ef4c77bf4cca4f95
 COPY workflow/envs/snpeff.yaml /conda-envs/0adafb79cb1bec58ef4c77bf4cca4f95/environment.yaml
 
+# Conda environment:
+#   source: workflow/envs/tools.yaml
+#   prefix: /conda-envs/1f283441022c3c9d97669994a3c5e8bb
+#   channels:
+#     - conda-forge
+#     - bioconda
+#   dependencies:
+#     - bedtools==2.31.1
+#     - bcftools==1.23
+RUN mkdir -p /conda-envs/1f283441022c3c9d97669994a3c5e8bb
+COPY workflow/envs/tools.yaml /conda-envs/1f283441022c3c9d97669994a3c5e8bb/environment.yaml
+
 # Conda environment:
 #   source: workflow/envs/var_calling.yaml
 #   prefix: /conda-envs/81e46c677a6cc0618c93963d57d17d3f
@@ -176,7 +177,6 @@ COPY workflow/envs/var_calling.yaml /conda-envs/81e46c677a6cc0618c93963d57d17d3f
 # Step 3: Generate conda environments
 
 RUN conda env create --prefix /conda-envs/9c24a867826615972cc288081976e7fc --file /conda-envs/9c24a867826615972cc288081976e7fc/environment.yaml && \
-    conda env create --prefix /conda-envs/cef13cdc1c388b3087761b0222ec0613 --file /conda-envs/cef13cdc1c388b3087761b0222ec0613/environment.yaml && \
     conda env create --prefix /conda-envs/162796cecea22d99c8702138f0c48e2f --file /conda-envs/162796cecea22d99c8702138f0c48e2f/environment.yaml && \
     conda env create --prefix /conda-envs/9439457f932a4fbca3665c9ea1ac2f0a --file /conda-envs/9439457f932a4fbca3665c9ea1ac2f0a/environment.yaml && \
     conda env create --prefix /conda-envs/bb4c5f3a509433cc08861582fab4a705 --file /conda-envs/bb4c5f3a509433cc08861582fab4a705/environment.yaml && \
@@ -187,6 +187,7 @@ RUN conda env create --prefix /conda-envs/9c24a867826615972cc288081976e7fc --fil
     conda env create --prefix /conda-envs/96f3c1cec4b3ce5d72f708992272e9c1 --file /conda-envs/96f3c1cec4b3ce5d72f708992272e9c1/environment.yaml && \
     conda env create --prefix /conda-envs/8ad6cdcf265d30289788da99d5bf9fff --file /conda-envs/8ad6cdcf265d30289788da99d5bf9fff/environment.yaml && \
     conda env create --prefix /conda-envs/0adafb79cb1bec58ef4c77bf4cca4f95 --file /conda-envs/0adafb79cb1bec58ef4c77bf4cca4f95/environment.yaml && \
+    conda env create --prefix /conda-envs/1f283441022c3c9d97669994a3c5e8bb --file /conda-envs/1f283441022c3c9d97669994a3c5e8bb/environment.yaml && \
     conda env create --prefix /conda-envs/81e46c677a6cc0618c93963d57d17d3f --file /conda-envs/81e46c677a6cc0618c93963d57d17d3f/environment.yaml && \
     conda clean --all -y
 

From a996935f9563b5caff3ab5d4feda3502b82857f7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Miguel=20=C3=81lvarez=20Herrera?= <miguel.alvarez@uv.es>
Date: Fri, 6 Mar 2026 13:12:10 +0100
Subject: [PATCH 8/9] update showtext dpi

equals the value in individual plots
---
 config/design_plots.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/design_plots.R b/config/design_plots.R
index 74e87d8..69f3540 100644
--- a/config/design_plots.R
+++ b/config/design_plots.R
@@ -5,7 +5,7 @@ library(showtext)
 
 # Ajustes ####
 showtext_auto(enable = FALSE)
-showtext_opts(dpi = 200)
+showtext_opts(dpi = 250)
 
 # Tema
 font_add_google("Noto Sans", "Noto Sans")

From eeb7d3c167945fd424d6eb5be23b3090c833c924 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Miguel=20=C3=81lvarez=20Herrera?= <miguel.alvarez@uv.es>
Date: Fri, 6 Mar 2026 14:35:24 +0100
Subject: [PATCH 9/9] avoid showtext dependency

ggplot falls back to the default font if Noto Sans is unavailable. showtext started causing a cryptic segfault
---
 Dockerfile              | 13 ++++++-------
 config/design_plots.R   | 20 ++++----------------
 workflow/envs/renv.yaml |  3 +--
 3 files changed, 11 insertions(+), 25 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 188459d..fbc2b93 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,6 +1,6 @@
 FROM condaforge/miniforge3:latest
 LABEL io.github.snakemake.containerized="true"
-LABEL io.github.snakemake.conda_env_hash="966286962ebc1e35e9809cc85e2904bfefb462e6a14ee09730b81ab69eb4d441"
+LABEL io.github.snakemake.conda_env_hash="fb2a04b98efa75d8b830a16722a8717eb91a3c66659e3c78b90b0cee3a50db69"
 
 # Step 2: Retrieve conda environments
 
@@ -117,12 +117,12 @@ COPY workflow/envs/quarto_render.yaml /conda-envs/96f3c1cec4b3ce5d72f708992272e9
 
 # Conda environment:
 #   source: workflow/envs/renv.yaml
-#   prefix: /conda-envs/8ad6cdcf265d30289788da99d5bf9fff
+#   prefix: /conda-envs/fe892aca096e6b2883923c8755f9ac77
 #   channels:
 #     - conda-forge
 #     - bioconda
 #   dependencies:
-#     - r-base=4.3.2
+#     - r-base=4.3.3
 #     - r-tidyverse==2.0.0
 #     - r-ggrepel==0.9.3
 #     - r-ggpubr==0.6.0
@@ -133,10 +133,9 @@ COPY workflow/envs/quarto_render.yaml /conda-envs/96f3c1cec4b3ce5d72f708992272e9
 #     - r-data.table==1.14.8
 #     - r-future.apply==1.11.0
 #     - r-scales==1.3.0
-#     - r-showtext==0.9_6
 #     - r-logger==0.2.2
-RUN mkdir -p /conda-envs/8ad6cdcf265d30289788da99d5bf9fff
-COPY workflow/envs/renv.yaml /conda-envs/8ad6cdcf265d30289788da99d5bf9fff/environment.yaml
+RUN mkdir -p /conda-envs/fe892aca096e6b2883923c8755f9ac77
+COPY workflow/envs/renv.yaml /conda-envs/fe892aca096e6b2883923c8755f9ac77/environment.yaml
 
 # Conda environment:
 #   source: workflow/envs/snpeff.yaml
@@ -185,7 +184,7 @@ RUN conda env create --prefix /conda-envs/9c24a867826615972cc288081976e7fc --fil
     conda env create --prefix /conda-envs/04a3347f94ddf7e21c34bc49e5246076 --file /conda-envs/04a3347f94ddf7e21c34bc49e5246076/environment.yaml && \
     conda env create --prefix /conda-envs/fb978640cd765c8a63bbcdc01f3a206b --file /conda-envs/fb978640cd765c8a63bbcdc01f3a206b/environment.yaml && \
     conda env create --prefix /conda-envs/96f3c1cec4b3ce5d72f708992272e9c1 --file /conda-envs/96f3c1cec4b3ce5d72f708992272e9c1/environment.yaml && \
-    conda env create --prefix /conda-envs/8ad6cdcf265d30289788da99d5bf9fff --file /conda-envs/8ad6cdcf265d30289788da99d5bf9fff/environment.yaml && \
+    conda env create --prefix /conda-envs/fe892aca096e6b2883923c8755f9ac77 --file /conda-envs/fe892aca096e6b2883923c8755f9ac77/environment.yaml && \
     conda env create --prefix /conda-envs/0adafb79cb1bec58ef4c77bf4cca4f95 --file /conda-envs/0adafb79cb1bec58ef4c77bf4cca4f95/environment.yaml && \
     conda env create --prefix /conda-envs/1f283441022c3c9d97669994a3c5e8bb --file /conda-envs/1f283441022c3c9d97669994a3c5e8bb/environment.yaml && \
     conda env create --prefix /conda-envs/81e46c677a6cc0618c93963d57d17d3f --file /conda-envs/81e46c677a6cc0618c93963d57d17d3f/environment.yaml && \
diff --git a/config/design_plots.R b/config/design_plots.R
index 69f3540..8952379 100644
--- a/config/design_plots.R
+++ b/config/design_plots.R
@@ -1,26 +1,14 @@
-# Jordi Sevilla
-
 library(ggplot2)
-library(showtext)
-
-# Ajustes ####
-showtext_auto(enable = FALSE)
-showtext_opts(dpi = 250)
-
-# Tema
-font_add_google("Noto Sans", "Noto Sans")
-showtext_auto()
 
+# Theme
 theme_set(theme_minimal())
-
 theme_update(
-  text = element_text(size = 16, family = "Noto Sans"),
-  axis.title = element_text(size = 16),
+  text = element_text(size = 10, family = "Noto Sans"),
+  axis.title = element_text(size = 12),
   axis.line = element_line(
     linewidth = 0.5,
     colour = "grey40",
-    linetype = 1,
-    arrow = arrow(length = unit(3, "mm"))
+    linetype = 1
   ),
   panel.grid = element_line(linewidth = 0.17, color = "lightgray")
 )
diff --git a/workflow/envs/renv.yaml b/workflow/envs/renv.yaml
index ceb6a99..9256d78 100644
--- a/workflow/envs/renv.yaml
+++ b/workflow/envs/renv.yaml
@@ -2,7 +2,7 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - r-base=4.3.2
+  - r-base=4.3.3
   - r-tidyverse==2.0.0
   - r-ggrepel==0.9.3
   - r-ggpubr==0.6.0
@@ -13,5 +13,4 @@ dependencies:
   - r-data.table==1.14.8
   - r-future.apply==1.11.0
   - r-scales==1.3.0
-  - r-showtext==0.9_6
   - r-logger==0.2.2