.command.sh - Workdir - DAQ:CONTROL_METRICS:NEGATIVE_SOMATIC_METRICS:TMB (negative_somatic_control_4)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/e2a58c423b5b240e89119047fe872d/.command.sh
Size: 567 bytes
Task: DAQ:CONTROL_METRICS:NEGATIVE_SOMATIC_METRICS:TMB (negative_somatic_control_4)
Attempt

Content

#!/bin/bash -Ceuo pipefail
awk -F, '
    $3 == "Filtered Nonsyn Variant Count" { printf "non_synonymous_count\t%s\n",         $4 }
    $3 == "Eligible Region (MB)"          { printf "effective_coding_region_size\t%s\n", $4 }
    $3 == "Nonsyn TMB"                    { printf "score\t%s\n",                        $4 }
' negative_somatic_control_4.snv_indel.tmb.csv > negative_somatic_control_4.tmb.tsv

cat <<-END_VERSIONS > versions.yml
"DAQ:CONTROL_METRICS:NEGATIVE_SOMATIC_METRICS:TMB":
    gawk: $(awk -W version 2>&1 | head -n1 | awk '{print $3}')
END_VERSIONS