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Kallisto options #58

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Merged
MareikeJaniak merged 2 commits into from
Oct 23, 2025
Merged

Kallisto options #58

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5c058b8
add other options to kallisto to allow parameter setting via ini
MareikeJaniak Oct 10, 2025
790173e
add other_options to kallisto ini section
MareikeJaniak Oct 10, 2025
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10 changes: 6 additions & 4 deletions genpipes/bfx/kallisto.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,8 @@ def quant(
inputs,
output_dir,
transcriptome,
parameters
parameters,
ini_section="kallisto"
):
"""
Call to kalliso quant
Expand All @@ -43,18 +44,19 @@ def quant(
os.path.join(output_dir, "abundance.h5")
],
[
['kallisto', 'module_kallisto']
[ini_section, 'module_kallisto']
],
command="""\
kallisto quant \\
kallisto quant {other_options} \\
{parameters} \\
-t {threads} \\
-i {transcriptome} \\
-o {output_dir} \\
{infiles} \\
2> {output_dir}/kallisto_quant.log""".format(
other_options=global_conf.global_get(ini_section, 'other_options'),
parameters=parameters,
threads=global_conf.global_get('kallisto', 'threads'),
threads=global_conf.global_get(ini_section, 'threads'),
transcriptome=transcriptome,
output_dir=output_dir,
infiles=" \\\n ".join(inputs),
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1 change: 1 addition & 0 deletions genpipes/pipelines/rnaseq_light/rnaseq_light.base.ini
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Expand Up @@ -94,6 +94,7 @@ java_other_options = -XX:ParallelGCThreads=5 -Dsamjdk.buffer_size=1048576

[kallisto]
module_R=mugqic/R_Bioconductor/3.5.0_3.7
other_options=
# note that kallisto indexes on cvmfs should contain the name of the kallisto version. Any versions without this naming structure are retained on cvmfs only for legacy reasons
transcriptome_idx = %(annotation_dir)s/cdna_kallisto_index/%(scientific_name)s.%(assembly)s.%(source)s%(version)s.kallisto-%(kallisto_version)s.cdna.fa.idx
transcript2genes = %(annotation_dir)s/cdna_kallisto_index/%(scientific_name)s.%(assembly)s.%(source)s%(version)s.tx2gene
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