From 49813eb45643784e45d8f838ed6007a125c5ae1e Mon Sep 17 00:00:00 2001
From: Charlotte Soneson <charlottesoneson@gmail.com>
Date: Fri, 12 Jun 2026 19:19:35 +0200
Subject: [PATCH 01/14] Update tool versions

---
 envs/environment.yaml   | 22 +++++++++++-----------
 envs/environment_R.yaml | 14 +++++++-------
 2 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/envs/environment.yaml b/envs/environment.yaml
index 98b5f4d0..96350361 100755
--- a/envs/environment.yaml
+++ b/envs/environment.yaml
@@ -2,14 +2,14 @@ channels:
 - bioconda
 - conda-forge
 dependencies:
-- samtools=1.11
-- salmon=1.4.0
-- star=2.7.7a
-- fastqc=0.11.9
-- multiqc=1.9
-- trim-galore=0.6.6
-- cutadapt=3.2
-- bedtools=2.30.0
-- ucsc-bedgraphtobigwig=377
-- pandoc=2.11
-- tbb=2020.2
+- samtools=1.23.1
+- salmon=1.11.4
+- star=2.7.11b
+- fastqc=0.12.1
+- multiqc=1.35
+- trim-galore=2.2.0
+- cutadapt=5.2
+- bedtools=2.31.1
+- ucsc-bedgraphtobigwig=482
+- pandoc=3.10
+- tbb=2023.0.0
diff --git a/envs/environment_R.yaml b/envs/environment_R.yaml
index 8dec62d7..bfce6af3 100755
--- a/envs/environment_R.yaml
+++ b/envs/environment_R.yaml
@@ -1,11 +1,11 @@
 channels:
 - conda-forge
 dependencies:
-- r-base=4.4.1
+- r-base=4.6.0
 - pandoc=3.4
-- r-curl=5.2.1
-- r-rsqlite=2.3.7
-- r-xml2=1.3.6
-- r-httpuv=1.6.15
-- r-mass=7.3_60.0.1
-- r-matrix=1.6_5
+- r-curl=7.1.0
+- r-rsqlite=3.53.1
+- r-xml2=1.5.2
+- r-httpuv=1.6.17
+- r-mass=7.3_65
+- r-matrix=1.7_5

From 983c7eaa5e3e9fd2e9b05d8c3e7d36d79314e2ca Mon Sep 17 00:00:00 2001
From: Charlotte Soneson <charlottesoneson@gmail.com>
Date: Fri, 12 Jun 2026 19:27:49 +0200
Subject: [PATCH 02/14] Update environments

---
 .github/workflows/snakemake-run.yaml | 8 ++++----
 envs/environment_R.yaml              | 1 -
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/snakemake-run.yaml b/.github/workflows/snakemake-run.yaml
index d665fc7b..b778e0ad 100644
--- a/.github/workflows/snakemake-run.yaml
+++ b/.github/workflows/snakemake-run.yaml
@@ -18,12 +18,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [macos-15-intel, ubuntu-latest]
+        os: [macos-latest, ubuntu-latest]
         include:
-        - os: macos-15-intel
-          rversion: '4.5'
+        - os: macos-latest
+          rversion: '4.6'
         - os: ubuntu-latest
-          rversion: '4.5'
+          rversion: '4.6'
     steps:
       - name: Check out repository
         uses: actions/checkout@v2
diff --git a/envs/environment_R.yaml b/envs/environment_R.yaml
index bfce6af3..edd2c89d 100755
--- a/envs/environment_R.yaml
+++ b/envs/environment_R.yaml
@@ -4,7 +4,6 @@ dependencies:
 - r-base=4.6.0
 - pandoc=3.4
 - r-curl=7.1.0
-- r-rsqlite=3.53.1
 - r-xml2=1.5.2
 - r-httpuv=1.6.17
 - r-mass=7.3_65

From b2fe10649cd276bea2252a64cb460edac82a17c5 Mon Sep 17 00:00:00 2001
From: Charlotte Soneson <charlottesoneson@gmail.com>
Date: Fri, 12 Jun 2026 19:33:32 +0200
Subject: [PATCH 03/14] Update environments

---
 .github/workflows/snakemake-run.yaml | 4 ++--
 envs/environment.yaml                | 2 +-
 envs/environment_R.yaml              | 3 ++-
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/snakemake-run.yaml b/.github/workflows/snakemake-run.yaml
index b778e0ad..611878c0 100644
--- a/.github/workflows/snakemake-run.yaml
+++ b/.github/workflows/snakemake-run.yaml
@@ -21,9 +21,9 @@ jobs:
         os: [macos-latest, ubuntu-latest]
         include:
         - os: macos-latest
-          rversion: '4.6'
+          rversion: '4.5'
         - os: ubuntu-latest
-          rversion: '4.6'
+          rversion: '4.5'
     steps:
       - name: Check out repository
         uses: actions/checkout@v2
diff --git a/envs/environment.yaml b/envs/environment.yaml
index 96350361..d9f28561 100755
--- a/envs/environment.yaml
+++ b/envs/environment.yaml
@@ -2,7 +2,7 @@ channels:
 - bioconda
 - conda-forge
 dependencies:
-- samtools=1.23.1
+- samtools=1.21
 - salmon=1.11.4
 - star=2.7.11b
 - fastqc=0.12.1
diff --git a/envs/environment_R.yaml b/envs/environment_R.yaml
index edd2c89d..bd74b542 100755
--- a/envs/environment_R.yaml
+++ b/envs/environment_R.yaml
@@ -1,9 +1,10 @@
 channels:
 - conda-forge
 dependencies:
-- r-base=4.6.0
+- r-base=4.5.3
 - pandoc=3.4
 - r-curl=7.1.0
+- r-rsqlite=3.53.1
 - r-xml2=1.5.2
 - r-httpuv=1.6.17
 - r-mass=7.3_65

From a197735091bd03649f88d74cc2413660d54ac900 Mon Sep 17 00:00:00 2001
From: Charlotte Soneson <charlottesoneson@gmail.com>
Date: Fri, 12 Jun 2026 19:39:43 +0200
Subject: [PATCH 04/14] Update environments

---
 envs/environment.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/envs/environment.yaml b/envs/environment.yaml
index d9f28561..8cc2dc30 100755
--- a/envs/environment.yaml
+++ b/envs/environment.yaml
@@ -2,8 +2,8 @@ channels:
 - bioconda
 - conda-forge
 dependencies:
-- samtools=1.21
-- salmon=1.11.4
+- samtools=1.22
+- salmon=1.10.3
 - star=2.7.11b
 - fastqc=0.12.1
 - multiqc=1.35

From 64bc11f17a916bc13e112f426ff47db3298844ec Mon Sep 17 00:00:00 2001
From: Charlotte Soneson <charlottesoneson@gmail.com>
Date: Fri, 12 Jun 2026 22:05:17 +0200
Subject: [PATCH 05/14] Add gzip and zlib to environment

---
 Snakefile               | 2 +-
 envs/environment.yaml   | 1 +
 envs/environment_R.yaml | 1 +
 3 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/Snakefile b/Snakefile
index 4a6ebaab..574c7541 100755
--- a/Snakefile
+++ b/Snakefile
@@ -444,7 +444,7 @@ rule starSE:
 		"echo 'STAR version:\n' > {log}; STAR --version >> {log}; "
 		"STAR --genomeDir {params.STARindex} --readFilesIn {input.fastq} "
 		"--runThreadN {threads} --outFileNamePrefix {params.STARdir}/{wildcards.sample}/{wildcards.sample}_ "
-		"--outSAMtype BAM SortedByCoordinate --readFilesCommand gunzip -c "
+		"--outSAMtype BAM SortedByCoordinate --readFilesCommand zcat "
 		"{params.starextraparams}"
 
 rule starPE:
diff --git a/envs/environment.yaml b/envs/environment.yaml
index 8cc2dc30..538933d2 100755
--- a/envs/environment.yaml
+++ b/envs/environment.yaml
@@ -13,3 +13,4 @@ dependencies:
 - ucsc-bedgraphtobigwig=482
 - pandoc=3.10
 - tbb=2023.0.0
+- gzip=1.14
diff --git a/envs/environment_R.yaml b/envs/environment_R.yaml
index bd74b542..4f0a1a71 100755
--- a/envs/environment_R.yaml
+++ b/envs/environment_R.yaml
@@ -9,3 +9,4 @@ dependencies:
 - r-httpuv=1.6.17
 - r-mass=7.3_65
 - r-matrix=1.7_5
+- zlib=1.3.2

From add788958372db1d5ad063729ff70a09c67d99bc Mon Sep 17 00:00:00 2001
From: Charlotte Soneson <charlottesoneson@gmail.com>
Date: Sat, 13 Jun 2026 07:32:54 +0200
Subject: [PATCH 06/14] Update environments, use zcat instead of gunzip -c

---
 Snakefile               | 2 +-
 envs/environment_R.yaml | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/Snakefile b/Snakefile
index 574c7541..f8e5cc2e 100755
--- a/Snakefile
+++ b/Snakefile
@@ -470,7 +470,7 @@ rule starPE:
 		"echo 'STAR version:\n' > {log}; STAR --version >> {log}; "
 		"STAR --genomeDir {params.STARindex} --readFilesIn {input.fastq1} {input.fastq2} "
 		"--runThreadN {threads} --outFileNamePrefix {params.STARdir}/{wildcards.sample}/{wildcards.sample}_ "
-		"--outSAMtype BAM SortedByCoordinate --readFilesCommand gunzip -c "
+		"--outSAMtype BAM SortedByCoordinate --readFilesCommand zcat "
 		"{params.starextraparams}"
 
 ## Index bam files
diff --git a/envs/environment_R.yaml b/envs/environment_R.yaml
index 4f0a1a71..24fa528d 100755
--- a/envs/environment_R.yaml
+++ b/envs/environment_R.yaml
@@ -6,6 +6,7 @@ dependencies:
 - r-curl=7.1.0
 - r-rsqlite=3.53.1
 - r-xml2=1.5.2
+- r-rcurl=1.98_1.19
 - r-httpuv=1.6.17
 - r-mass=7.3_65
 - r-matrix=1.7_5

From b40dc38bc6be8f32769305ee3e976859a2d9e555 Mon Sep 17 00:00:00 2001
From: Charlotte Soneson <charlottesoneson@gmail.com>
Date: Sat, 13 Jun 2026 08:52:46 +0200
Subject: [PATCH 07/14] Update environments

---
 Snakefile               | 4 ++--
 envs/environment_R.yaml | 1 +
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/Snakefile b/Snakefile
index f8e5cc2e..d1a66506 100755
--- a/Snakefile
+++ b/Snakefile
@@ -444,7 +444,7 @@ rule starSE:
 		"echo 'STAR version:\n' > {log}; STAR --version >> {log}; "
 		"STAR --genomeDir {params.STARindex} --readFilesIn {input.fastq} "
 		"--runThreadN {threads} --outFileNamePrefix {params.STARdir}/{wildcards.sample}/{wildcards.sample}_ "
-		"--outSAMtype BAM SortedByCoordinate --readFilesCommand zcat "
+		"--outSAMtype BAM SortedByCoordinate --readFilesCommand gzip -d -c "
 		"{params.starextraparams}"
 
 rule starPE:
@@ -470,7 +470,7 @@ rule starPE:
 		"echo 'STAR version:\n' > {log}; STAR --version >> {log}; "
 		"STAR --genomeDir {params.STARindex} --readFilesIn {input.fastq1} {input.fastq2} "
 		"--runThreadN {threads} --outFileNamePrefix {params.STARdir}/{wildcards.sample}/{wildcards.sample}_ "
-		"--outSAMtype BAM SortedByCoordinate --readFilesCommand zcat "
+		"--outSAMtype BAM SortedByCoordinate --readFilesCommand gzip -d -c "
 		"{params.starextraparams}"
 
 ## Index bam files
diff --git a/envs/environment_R.yaml b/envs/environment_R.yaml
index 24fa528d..5e41c02a 100755
--- a/envs/environment_R.yaml
+++ b/envs/environment_R.yaml
@@ -11,3 +11,4 @@ dependencies:
 - r-mass=7.3_65
 - r-matrix=1.7_5
 - zlib=1.3.2
+- bioconductor-rhtslib=3.6.0

From 1ccbee38a853b0dbd60ce25cbb741e0838cea888 Mon Sep 17 00:00:00 2001
From: Charlotte Soneson <charlottesoneson@gmail.com>
Date: Sat, 13 Jun 2026 09:51:40 +0200
Subject: [PATCH 08/14] Update environments

---
 Snakefile               | 32 ++++++++++++++++++++++----------
 envs/environment_R.yaml |  1 +
 2 files changed, 23 insertions(+), 10 deletions(-)

diff --git a/Snakefile b/Snakefile
index d1a66506..211d23ab 100755
--- a/Snakefile
+++ b/Snakefile
@@ -441,11 +441,17 @@ rule starSE:
 	conda:
 		"envs/environment.yaml"
 	shell:
-		"echo 'STAR version:\n' > {log}; STAR --version >> {log}; "
-		"STAR --genomeDir {params.STARindex} --readFilesIn {input.fastq} "
-		"--runThreadN {threads} --outFileNamePrefix {params.STARdir}/{wildcards.sample}/{wildcards.sample}_ "
-		"--outSAMtype BAM SortedByCoordinate --readFilesCommand gzip -d -c "
-		"{params.starextraparams}"
+	    """
+		echo 'STAR version:\n' > {log}; 
+		STAR --version >> {log}; 
+		STAR --genomeDir {params.STARindex} \
+		     --readFilesIn {input.fastq} \
+		     --runThreadN {threads} \
+		     --outFileNamePrefix {params.STARdir}/{wildcards.sample}/{wildcards.sample}_ \
+		     --outSAMtype BAM SortedByCoordinate \
+		     --readFilesCommand "gunzip -c" \
+		     {params.starextraparams}
+		"""
 
 rule starPE:
 	input:
@@ -467,11 +473,17 @@ rule starPE:
 	conda:
 		"envs/environment.yaml"
 	shell:
-		"echo 'STAR version:\n' > {log}; STAR --version >> {log}; "
-		"STAR --genomeDir {params.STARindex} --readFilesIn {input.fastq1} {input.fastq2} "
-		"--runThreadN {threads} --outFileNamePrefix {params.STARdir}/{wildcards.sample}/{wildcards.sample}_ "
-		"--outSAMtype BAM SortedByCoordinate --readFilesCommand gzip -d -c "
-		"{params.starextraparams}"
+	    """
+		echo 'STAR version:\n' > {log}; 
+		STAR --version >> {log}; 
+		STAR --genomeDir {params.STARindex} \
+		     --readFilesIn {input.fastq1} {input.fastq2} \
+		     --runThreadN {threads} \
+		     --outFileNamePrefix {params.STARdir}/{wildcards.sample}/{wildcards.sample}_ \
+		     --outSAMtype BAM SortedByCoordinate \
+		     --readFilesCommand "gunzip -c" \
+		     {params.starextraparams}
+		"""
 
 ## Index bam files
 rule bamindex:
diff --git a/envs/environment_R.yaml b/envs/environment_R.yaml
index 5e41c02a..5e45900c 100755
--- a/envs/environment_R.yaml
+++ b/envs/environment_R.yaml
@@ -12,3 +12,4 @@ dependencies:
 - r-matrix=1.7_5
 - zlib=1.3.2
 - bioconductor-rhtslib=3.6.0
+- bioconductor-rsamtools=2.26.0

From 8b1c779c3308428e276cf58760825ee49fbe4ab6 Mon Sep 17 00:00:00 2001
From: Charlotte Soneson <charlottesoneson@gmail.com>
Date: Sat, 13 Jun 2026 10:33:44 +0200
Subject: [PATCH 09/14] Update environments

---
 Snakefile               | 4 ++--
 envs/environment_R.yaml | 1 +
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/Snakefile b/Snakefile
index 211d23ab..b781721d 100755
--- a/Snakefile
+++ b/Snakefile
@@ -449,7 +449,7 @@ rule starSE:
 		     --runThreadN {threads} \
 		     --outFileNamePrefix {params.STARdir}/{wildcards.sample}/{wildcards.sample}_ \
 		     --outSAMtype BAM SortedByCoordinate \
-		     --readFilesCommand "gunzip -c" \
+		     --readFilesCommand "gzip -d -c" \
 		     {params.starextraparams}
 		"""
 
@@ -481,7 +481,7 @@ rule starPE:
 		     --runThreadN {threads} \
 		     --outFileNamePrefix {params.STARdir}/{wildcards.sample}/{wildcards.sample}_ \
 		     --outSAMtype BAM SortedByCoordinate \
-		     --readFilesCommand "gunzip -c" \
+		     --readFilesCommand "gzip -d -c" \
 		     {params.starextraparams}
 		"""
 
diff --git a/envs/environment_R.yaml b/envs/environment_R.yaml
index 5e45900c..43974964 100755
--- a/envs/environment_R.yaml
+++ b/envs/environment_R.yaml
@@ -6,6 +6,7 @@ dependencies:
 - r-curl=7.1.0
 - r-rsqlite=3.53.1
 - r-xml2=1.5.2
+- r-xml=3.99_0.23
 - r-rcurl=1.98_1.19
 - r-httpuv=1.6.17
 - r-mass=7.3_65

From 262b98761a61dca7e477e87c37af8c505509fc62 Mon Sep 17 00:00:00 2001
From: Charlotte Soneson <charlottesoneson@gmail.com>
Date: Sat, 13 Jun 2026 10:48:41 +0200
Subject: [PATCH 10/14] Update environments

---
 Snakefile               | 4 ++--
 envs/environment.yaml   | 2 +-
 envs/environment_R.yaml | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/Snakefile b/Snakefile
index b781721d..211d23ab 100755
--- a/Snakefile
+++ b/Snakefile
@@ -449,7 +449,7 @@ rule starSE:
 		     --runThreadN {threads} \
 		     --outFileNamePrefix {params.STARdir}/{wildcards.sample}/{wildcards.sample}_ \
 		     --outSAMtype BAM SortedByCoordinate \
-		     --readFilesCommand "gzip -d -c" \
+		     --readFilesCommand "gunzip -c" \
 		     {params.starextraparams}
 		"""
 
@@ -481,7 +481,7 @@ rule starPE:
 		     --runThreadN {threads} \
 		     --outFileNamePrefix {params.STARdir}/{wildcards.sample}/{wildcards.sample}_ \
 		     --outSAMtype BAM SortedByCoordinate \
-		     --readFilesCommand "gzip -d -c" \
+		     --readFilesCommand "gunzip -c" \
 		     {params.starextraparams}
 		"""
 
diff --git a/envs/environment.yaml b/envs/environment.yaml
index 538933d2..2dd69c61 100755
--- a/envs/environment.yaml
+++ b/envs/environment.yaml
@@ -4,7 +4,7 @@ channels:
 dependencies:
 - samtools=1.22
 - salmon=1.10.3
-- star=2.7.11b
+- star=2.7.10b
 - fastqc=0.12.1
 - multiqc=1.35
 - trim-galore=2.2.0
diff --git a/envs/environment_R.yaml b/envs/environment_R.yaml
index 43974964..b7925314 100755
--- a/envs/environment_R.yaml
+++ b/envs/environment_R.yaml
@@ -6,7 +6,7 @@ dependencies:
 - r-curl=7.1.0
 - r-rsqlite=3.53.1
 - r-xml2=1.5.2
-- r-xml=3.99_0.23
+- r-xml=3.99_0.22
 - r-rcurl=1.98_1.19
 - r-httpuv=1.6.17
 - r-mass=7.3_65

From e38a4c07747e68c0a6178db0f25f1851bc6fff62 Mon Sep 17 00:00:00 2001
From: Charlotte Soneson <charlottesoneson@gmail.com>
Date: Sat, 13 Jun 2026 11:31:26 +0200
Subject: [PATCH 11/14] Change GitHub runner

---
 .github/workflows/snakemake-run.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/snakemake-run.yaml b/.github/workflows/snakemake-run.yaml
index 611878c0..d665fc7b 100644
--- a/.github/workflows/snakemake-run.yaml
+++ b/.github/workflows/snakemake-run.yaml
@@ -18,9 +18,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [macos-latest, ubuntu-latest]
+        os: [macos-15-intel, ubuntu-latest]
         include:
-        - os: macos-latest
+        - os: macos-15-intel
           rversion: '4.5'
         - os: ubuntu-latest
           rversion: '4.5'

From 8b7f94ce323cd08eb8b23dd76843c42189056b74 Mon Sep 17 00:00:00 2001
From: Charlotte Soneson <charlottesoneson@gmail.com>
Date: Sat, 13 Jun 2026 12:54:22 +0200
Subject: [PATCH 12/14] Try older trim-galore

---
 envs/environment.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/envs/environment.yaml b/envs/environment.yaml
index 2dd69c61..c11a3a23 100755
--- a/envs/environment.yaml
+++ b/envs/environment.yaml
@@ -7,7 +7,7 @@ dependencies:
 - star=2.7.10b
 - fastqc=0.12.1
 - multiqc=1.35
-- trim-galore=2.2.0
+- trim-galore=0.6.11
 - cutadapt=5.2
 - bedtools=2.31.1
 - ucsc-bedgraphtobigwig=482

From 4cbc74fde8f302a2aad1f9658b443808693c618a Mon Sep 17 00:00:00 2001
From: Charlotte Soneson <charlottesoneson@gmail.com>
Date: Sat, 13 Jun 2026 17:01:38 +0200
Subject: [PATCH 13/14] Bump version

---
 NEWS    | 4 ++++
 version | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/NEWS b/NEWS
index 2f363784..173b0d06 100755
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,7 @@
+v1.5.11
+======
+o Update tool versions in conda environments
+
 v1.5.10
 ======
 o Update R to v4.4.1
diff --git a/version b/version
index 1615c9f5..f81fd1d8 100755
--- a/version
+++ b/version
@@ -1 +1 @@
-1.5.10 (2024-09-21)
+1.5.11 (2026-06-13)

From 15aa47dfe3b566cce404a8fb21320dabd7917e83 Mon Sep 17 00:00:00 2001
From: Charlotte Soneson <charlottesoneson@gmail.com>
Date: Sat, 13 Jun 2026 19:06:25 +0200
Subject: [PATCH 14/14] Add bioconda channel to R environment yaml

---
 envs/environment_R.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/envs/environment_R.yaml b/envs/environment_R.yaml
index b7925314..9c5ca54c 100755
--- a/envs/environment_R.yaml
+++ b/envs/environment_R.yaml
@@ -1,4 +1,5 @@
 channels:
+- bioconda
 - conda-forge
 dependencies:
 - r-base=4.5.3