Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/401b3d6bf67198e539149454137a44/HCC1395_tumor_vs_HCC1395_BL.conpair.contamination.txt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/9133ba710b70be66a46311393abc6c/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs.bcftools_stats.txt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/045ae03d25ba174a8d467990d6fa62/custom_Sig_18_tumor_normal.tnseq.filtered_snpEff.ann.tmb.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/4871fb298b779d647ef3012db89ec6/Sig_18_tissue_vs_Sig_18_Blood.conpair.contamination.txt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/62b211d7a00ca1835990508483246f/custom_Sig_18_tumor_normal.strelka.somatic_indels.bcftools_stats.txt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/4c5ce0c53717415c8e7f59332eaf81/Sig_18_Blood.deconfliction_audit.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/44a0ab698296fc5dd1e13c23cc0c8b/HCC1395_tumor_vs_HCC1395_BL.tnseq.filtered_snpEff.ann.tmb.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/ef74380b66c90c3a83a5d0a3cf9268/Sig_18_Blood.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/2db506627b730e68c0d1efd157990c/custom_Sig_18_tumor_normal.strelka.somatic_snvs.bcftools_stats.txt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/16c5d963d3504a1b6f6d751bf3d371/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/7958f0e7b805d430e93af135ef4102/ngscheckmate_all.txt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/a79a42778c19fc661d37f0e78020b6/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels.bcftools_stats.txt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/16c5d963d3504a1b6f6d751bf3d371/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/b45bb5c68a1af6f1d8fa3755af9d6d/HCC1395_BL.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/53095a184b1f0ac0e59d9ddd3e7977/HCC1395_BL.deconfliction_audit.tsv
==> STAGING COMPLETE (15 inputs)

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