Fixed some variable names

genome · Jan 14, 2021 · ffe0551 · ffe0551
1 parent 8c4f8a8
commit ffe0551
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/definitions/pipelines/immuno.cwl b/definitions/pipelines/immuno.cwl
@@ -860,7 +860,7 @@ steps:
             somalier_vcf: somalier_vcf
             tumor_sample_name: tumor_sample_name
             normal_sample_name: normal_sample_name
-            cle_variants: cle_variants
+            validated_variants: validated_variants
         out:
             [tumor_cram,tumor_mark_duplicates_metrics,tumor_insert_size_metrics,tumor_alignment_summary_metrics,tumor_hs_metrics,tumor_per_target_coverage_metrics,tumor_per_target_hs_metrics,tumor_per_base_coverage_metrics,tumor_per_base_hs_metrics,tumor_summary_hs_metrics,tumor_flagstats,tumor_verify_bam_id_metrics,tumor_verify_bam_id_depth,normal_cram,normal_mark_duplicates_metrics,normal_insert_size_metrics,normal_alignment_summary_metrics,normal_hs_metrics,normal_per_target_coverage_metrics,normal_per_target_hs_metrics,normal_per_base_coverage_metrics,normal_per_base_hs_metrics,normal_summary_hs_metrics,normal_flagstats,normal_verify_bam_id_metrics,normal_verify_bam_id_depth,mutect_unfiltered_vcf,mutect_filtered_vcf,strelka_unfiltered_vcf,strelka_filtered_vcf,varscan_unfiltered_vcf,varscan_filtered_vcf,pindel_unfiltered_vcf,pindel_filtered_vcf,docm_filtered_vcf,final_vcf,final_filtered_vcf,final_tsv,vep_summary,tumor_snv_bam_readcount_tsv,tumor_indel_bam_readcount_tsv,normal_snv_bam_readcount_tsv,normal_indel_bam_readcount_tsv,intervals_antitarget,intervals_target,normal_antitarget_coverage,normal_target_coverage,reference_coverage,cn_diagram,cn_scatter_plot,tumor_antitarget_coverage,tumor_target_coverage,tumor_bin_level_ratios,tumor_segmented_ratios,diploid_variants,somatic_variants,all_candidates,small_candidates,tumor_only_variants,somalier_concordance_metrics,somalier_concordance_statistics]
     germline:

diff --git a/definitions/pipelines/somatic_wgs.cwl b/definitions/pipelines/somatic_wgs.cwl
@@ -432,7 +432,7 @@ steps:
             tumor_sample_name: tumor_sample_name
             normal_sample_name: normal_sample_name
             vep_custom_annotations: vep_custom_annotations
-            cle_variants: cle_variants
+            validated_variants: validated_variants
         out:
             [mutect_unfiltered_vcf, mutect_filtered_vcf, strelka_unfiltered_vcf, strelka_filtered_vcf, varscan_unfiltered_vcf, varscan_filtered_vcf, docm_filtered_vcf, final_vcf, final_filtered_vcf, final_tsv, vep_summary, tumor_snv_bam_readcount_tsv, tumor_indel_bam_readcount_tsv, normal_snv_bam_readcount_tsv, normal_indel_bam_readcount_tsv]
     manta: