File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/8e894066db6243b4e35a1ac7673cd9/.command.sh
Size
740 bytes
Task
SOMATIC_CNV_CALLING:SOMA_CNV_EXPORT_VIEWER (1029_11H)
Attempt

Content

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#!/bin/bash -Ceuo pipefail
mkdir -p normalized/1029_11H baf
ln -s $(pwd)/1029_11H-T1-TDNA-1_B23KFCWLT4_1_normalized.parquet normalized/1029_11H/1029_11H-T1-TDNA-1_B23KFCWLT4_1.parquet
ln -s $(pwd)/1029_11H-N1-BDNA-1_B23KGCJLT4_1_normalized.parquet normalized/1029_11H/1029_11H-N1-BDNA-1_B23KGCJLT4_1.parquet
zcat 1029_11H-T1-TDNA-1_B23KFCWLT4_1_alleles.tsv.gz > baf/1029_11H-T1-TDNA-1_B23KFCWLT4_1.tsv
zcat 1029_11H-N1-BDNA-1_B23KGCJLT4_1_alleles.tsv.gz > baf/1029_11H-N1-BDNA-1_B23KGCJLT4_1.tsv

python /usr/local/bin/export_viewer.py \
    --normalized-dir normalized \
    --pairs test_pairs.tsv \
    --segments 1029_11H_segments.tsv \
    --output-dir viewer \
    --baf baf \
    --specimens-file <(echo "1029_11H") \
    --workers 4