File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/85b424364998a84b02b361fb1710a7/.command.sh
Size
572 bytes
Task
NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_INNERDISTANCE (BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1)
Attempt

Content

View in new tab 
#!/bin/bash -euo pipefail
inner_distance.py \
    -i BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai \
    -r ref_annot.bed \
    -o BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1 \
     \
    > stdout.txt
head -n 2 stdout.txt > BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.inner_distance_mean.txt

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_INNERDISTANCE":
    rseqc: $(inner_distance.py --version | sed -e "s/inner_distance.py //g")
END_VERSIONS