Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/2407ee9d805bd78492ebfcd9a62694/custom_Sig_18_tumor_normal.strelka.somatic_snvs.bcftools_stats.txt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/8d16d7d0df71a82a11e39ac5e16a92/custom_Sig_18_tumor_normal.tnseq.filtered_snpEff.ann.tmb.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/1b84916310daf5d10f9c3f55367517/HCC1395_BL.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/a451a095f48106cfc5c341e46a2d31/Sig_18_tissue_vs_Sig_18_Blood.conpair.contamination.txt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/3fa0f0abfd1b940088332d62089007/custom_Sig_18_tumor_normal.strelka.somatic_indels.bcftools_stats.txt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/d382ac389db5807e52b462bbbde150/Sig_18_Blood.deconfliction_audit.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/7c24ea296a11437e22e7c312dc4b46/HCC1395_tumor_vs_HCC1395_BL.tnseq.filtered_snpEff.ann.tmb.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/3f97a72e9491ae2d0df1f142415595/HCC1395_tumor_vs_HCC1395_BL.conpair.contamination.txt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/0e84f931a9d392188e7e496ef83f94/ngscheckmate_all.txt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/8ddb3075f0d712d255fbcaf5cd4f99/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels.bcftools_stats.txt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/ff71096e4853bf9a9ea82820bf2bdc/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs.bcftools_stats.txt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/f50e5d23b7880a538c6b3f697f07a4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/8cea654bac0439d443e20dc6c9baec/Sig_18_Blood.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/f50e5d23b7880a538c6b3f697f07a4/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/4beeef7561e559a12847bcd3f66452/HCC1395_BL.deconfliction_audit.tsv
==> STAGING COMPLETE (15 inputs)

Variant QC aggregation complete: 3 pairs, 2 samples
Output: variant_qc.json