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use new rulegraph snippet #26

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Merged
cokelaer merged 2 commits into from
Mar 20, 2026
Merged

use new rulegraph snippet #26

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9a25c55
use new rulegraph snippet
cokelaer Mar 20, 2026
4e83984
fix multiqc rule
cokelaer Mar 20, 2026
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2 changes: 0 additions & 2 deletions sequana_pipelines/mapper/config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,8 +6,6 @@
# If input_directory provided, use it otherwise if input_pattern provided,
# use it, otherwise use input_samples.
# ============================================================================
sequana_wrappers: v24.8.29

input_directory:
input_readtag: _R[12]_
input_pattern: '*fastq.gz'
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8 changes: 4 additions & 4 deletions sequana_pipelines/mapper/main.py
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Expand Up @@ -124,11 +124,11 @@ def main(**options):

# seems to be a hardcoded values in bwa according to the documentation
if N >= 2000000000:
cfg["bwa"]["index_algorithm"] = "bwtsw"
cfg["bwa_split"]["index_algorithm"] = "bwtsw"
cfg.bwa.index_algorithm = "bwtsw"
cfg.bwa_split.index_algorithm = "bwtsw"
else:
cfg["bwa"]["index_algorithm"] = "is"
cfg["bwa_split"]["index_algorithm"] = "is"
cfg.bwa.index_algorithm = "is"
cfg.bwa_split.index_algorithm = "is"

# finalise the command and save it; copy the snakemake. update the config
# file and save it.
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13 changes: 5 additions & 8 deletions sequana_pipelines/mapper/mapper.rules
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Expand Up @@ -370,18 +370,15 @@ if config["general"]["create_bigwig"]:

# ========================================================== multiqc

multiqc_params_options = config['multiqc']['options']
if manager.config.multiqc.config_file:
multiqc_params_options += f" -c {manager.config.multiqc.config_file}"

rule multiqc:
input:
get_multiqc_inputs()
output:
"multiqc/multiqc_report.html"
params:
options=multiqc_params_options,
options=config['multiqc']['options'],
input_directory=config['multiqc']['input_directory'],
config_file=config['multiqc']['config_file'],
modules=config['multiqc']['modules']
log:
"multiqc/multiqc.log"
Expand All @@ -400,8 +397,8 @@ rule rulegraph:
params:
mapper = {"multiqc": "../multiqc/multiqc_report.html"},
configname = "config.yaml"
wrapper:
f"{manager.wrappers}/wrappers/rulegraph"
run:
manager.get_run("rulegraph/run", "v1")(input, output, params)


rule dot2svg:
Expand All @@ -412,7 +409,7 @@ rule dot2svg:
container:
config['apptainers']['graphviz']
shell:
"""dot -Tsvg {input} -o {output}"""
manager.get_shell("graphviz/dot2svg", "v1")


# Those rules takes a couple of seconds so no need for a cluster
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3 changes: 0 additions & 3 deletions sequana_pipelines/mapper/schema.yaml
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Expand Up @@ -3,9 +3,6 @@

type: map
mapping:
"sequana_wrappers":
type: str
required: true
"input_directory":
type: str
required: True
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