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Merged
csoneson merged 14 commits into from
Jun 13, 2026
Merged

Update tools #121

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49813eb
Update tool versions
csoneson Jun 12, 2026
983c7ea
Update environments
csoneson Jun 12, 2026
b2fe106
Update environments
csoneson Jun 12, 2026
a197735
Update environments
csoneson Jun 12, 2026
64bc11f
Add gzip and zlib to environment
csoneson Jun 12, 2026
add7889
Update environments, use zcat instead of gunzip -c
csoneson Jun 13, 2026
b40dc38
Update environments
csoneson Jun 13, 2026
1ccbee3
Update environments
csoneson Jun 13, 2026
8b1c779
Update environments
csoneson Jun 13, 2026
262b987
Update environments
csoneson Jun 13, 2026
e38a4c0
Change GitHub runner
csoneson Jun 13, 2026
8b7f94c
Try older trim-galore
csoneson Jun 13, 2026
4cbc74f
Bump version
csoneson Jun 13, 2026
15aa47d
Add bioconda channel to R environment yaml
csoneson Jun 13, 2026
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4 changes: 4 additions & 0 deletions NEWS
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Original file line number Diff line number Diff line change
@@ -1,3 +1,7 @@
v1.5.11
======
o Update tool versions in conda environments

v1.5.10
======
o Update R to v4.4.1
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32 changes: 22 additions & 10 deletions Snakefile
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Expand Up @@ -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 gunzip -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:
Expand All @@ -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 gunzip -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:
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23 changes: 12 additions & 11 deletions envs/environment.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,14 +2,15 @@ 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=1.22
- salmon=1.10.3
- star=2.7.10b
- fastqc=0.12.1
- multiqc=1.35
- trim-galore=0.6.11
- cutadapt=5.2
- bedtools=2.31.1
- ucsc-bedgraphtobigwig=482
- pandoc=3.10
- tbb=2023.0.0
- gzip=1.14
20 changes: 13 additions & 7 deletions envs/environment_R.yaml
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Original file line number Diff line number Diff line change
@@ -1,11 +1,17 @@
channels:
- bioconda
- conda-forge
dependencies:
- r-base=4.4.1
- r-base=4.5.3
- 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-xml=3.99_0.22
- r-rcurl=1.98_1.19
- r-httpuv=1.6.17
- r-mass=7.3_65
- r-matrix=1.7_5
- zlib=1.3.2
- bioconductor-rhtslib=3.6.0
- bioconductor-rsamtools=2.26.0
2 changes: 1 addition & 1 deletion version
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
1.5.10 (2024-09-21)
1.5.11 (2026-06-13)
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