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fusionfusionの新フィルタに対応するためのアップデート #14

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fusionfusionの新フィルタに対応するためのアップデート #14

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3 changes: 2 additions & 1 deletion genomon_pipeline_cloud/script/fusionfusion.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -3,13 +3,14 @@
set -o errexit
set -o xtrace

INPUT_PREF=${INPUT_DIR}/${SAMPLE}
OUTPUT_PREF=${OUTPUT_DIR}/${SAMPLE}
mkdir -p ${OUTPUT_DIR}

if [ "_${MERGED_COUNT_DIR}" != "_" ]; then
OPTION="${OPTION} --pooled_control_file ${MERGED_COUNT_DIR}/${PANEL_NAME}.merged.Chimeric.count"
fi
/usr/local/bin/fusionfusion --star ${INPUT} --out ${OUTPUT_DIR} --reference_genome ${REFERENCE} ${OPTION}
/usr/local/bin/fusionfusion --star ${INPUT_PREF} --out ${OUTPUT_DIR} --reference_genome ${REFERENCE} ${OPTION}

mv ${OUTPUT_DIR}/star.fusion.result.txt ${OUTPUT_DIR}/${SAMPLE}.star.fusion.result.txt
mv ${OUTPUT_DIR}/fusion_fusion.result.txt ${OUTPUT_DIR}/${SAMPLE}.genomonFusion.result.txt
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4 changes: 2 additions & 2 deletions genomon_pipeline_cloud/tasks/fusionfusion.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ def task_file_generation(self, output_dir, task_dir, sample_conf, param_conf, ru
with open(task_file, 'w') as hout:

hout.write('\t'.join(["--env SAMPLE",
"--input INPUT",
"--input-recursive INPUT_DIR",
"--output-recursive OUTPUT_DIR",
"--env OPTION",
"--env FILT_OPTION",
Expand All @@ -41,7 +41,7 @@ def task_file_generation(self, output_dir, task_dir, sample_conf, param_conf, ru
bam_dir = os.path.dirname(bam)

record = [sample,
bam_dir +"/"+ sample + ".Chimeric.out.sam",
bam_dir,
output_dir + "/fusion/" + sample,
param_conf.get("fusionfusion", "fusionfusion_option"),
param_conf.get("fusionfusion", "filt_option"),
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