.command.sh - Workdir - NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:SEQTOOL_QC (659_b4x-T1-TRNA-1_B23MHV2LT4_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/ca318f4a77f5bfc72c827961063111/.command.sh
Size: 921 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:SEQTOOL_QC (659_b4x-T1-TRNA-1_B23MHV2LT4_1)
Attempt

Content

#!/bin/bash -euo pipefail
set -euxo pipefail

mkdir 659_b4x-T1-TRNA-1_B23MHV2LT4_1

all_qc \
-bam "659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bam" \
-beds Twist_rna_exome_AND_fusion_hg38.bed \
-dbsnp_vcf "Homo_sapiens_assembly38.dbsnp138.vcf.gz" \
-contamination_bed "dbsnp_hg38_contam_sites.bed" \
-output_folder 659_b4x-T1-TRNA-1_B23MHV2LT4_1 \
-reference "ref_genome.fa" \
-region 'chr20'

merge_qc -folders 659_b4x-T1-TRNA-1_B23MHV2LT4_1/* -output 659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv

head -n1 659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv > 659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-T1-TRNA-1_B23MHV2LT4_1_basic_stats.tsv
grep -e "$(basename Twist_rna_exome_AND_fusion_hg38.bed)" 659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv >> 659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-T1-TRNA-1_B23MHV2LT4_1_basic_stats.tsv