File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/3dbc6c2b95405d8e40dda8d28bf4a8/.command.sh
Size
1020 bytes
Task
NFCORE_RNAFUSION:RNAFUSION:KALLISTO_QUANT (aih-tih-sc-01c779-R1_A23YTGFLT4_1)
Attempt

Content

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#!/bin/bash -euo pipefail
mkdir -p aih-tih-sc-01c779-R1_A23YTGFLT4_1 && kallisto quant \
        --threads 4 \
        --index kallisto \
        --gtf Homo_sapiens.GRCh38.102.gtf \
         \
         \
         \
        --seed 1 \
        -o aih-tih-sc-01c779-R1_A23YTGFLT4_1 \
        aih-tih-sc-01c779-R1_A23YTGFLT4_1_1.fastp.fastq.gz aih-tih-sc-01c779-R1_A23YTGFLT4_1_2.fastp.fastq.gz 2> >(tee -a aih-tih-sc-01c779-R1_A23YTGFLT4_1/kallisto_quant.log >&2)

cp aih-tih-sc-01c779-R1_A23YTGFLT4_1/kallisto_quant.log aih-tih-sc-01c779-R1_A23YTGFLT4_1.log
cp aih-tih-sc-01c779-R1_A23YTGFLT4_1/abundance.h5 aih-tih-sc-01c779-R1_A23YTGFLT4_1.abundance.h5
cp aih-tih-sc-01c779-R1_A23YTGFLT4_1/abundance.tsv aih-tih-sc-01c779-R1_A23YTGFLT4_1.abundance.tsv
cp aih-tih-sc-01c779-R1_A23YTGFLT4_1/run_info.json aih-tih-sc-01c779-R1_A23YTGFLT4_1.run_info.json

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:RNAFUSION:KALLISTO_QUANT":
    kallisto: $(echo $(kallisto version) | sed "s/kallisto, version //g" )
END_VERSIONS