From 55077e9339f06018dc8684c759b2192ead0b7c0b Mon Sep 17 00:00:00 2001 From: Nikhil Kumar Date: Tue, 4 Feb 2020 14:02:00 -0500 Subject: [PATCH] Removed cutadapt_summary input --- setup/cwl/tools/roslin-qc/qc-merge-and-hotspots.cwl | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/setup/cwl/tools/roslin-qc/qc-merge-and-hotspots.cwl b/setup/cwl/tools/roslin-qc/qc-merge-and-hotspots.cwl index 9337374e4..86d3969b1 100644 --- a/setup/cwl/tools/roslin-qc/qc-merge-and-hotspots.cwl +++ b/setup/cwl/tools/roslin-qc/qc-merge-and-hotspots.cwl @@ -142,11 +142,7 @@ outputs: qual_files_o: type: File outputSource: qc_merge/qual_files_o - - cutadapt_summary: - type: File - outputSource: qc_merge/cutadapt_summary - + hs_portal_fillout: type: File outputSource: hotspots_fillout/portal_fillout @@ -180,7 +176,7 @@ steps: fp_genotypes: fp_genotypes grouping_file: grouping_file pairing_file: pairing_file - out: [ merged_mdmetrics, merged_hsmetrics, merged_hstmetrics, merged_insert_size_histograms, fingerprints_output, fingerprint_summary, minor_contam_output, qual_files_r, qual_files_o, cutadapt_summary ] + out: [ merged_mdmetrics, merged_hsmetrics, merged_hstmetrics, merged_insert_size_histograms, fingerprints_output, fingerprint_summary, minor_contam_output, qual_files_r, qual_files_o ] hotspots_fillout: run: ../cmo-fillout/1.2.2/cmo-fillout.cwl @@ -217,7 +213,7 @@ steps: run: ../consolidate-files/consolidate-files.cwl in: files: - source: [ qc_merge/merged_mdmetrics, qc_merge/merged_hsmetrics, qc_merge/merged_hstmetrics, qc_merge/merged_insert_size_histograms, qc_merge/fingerprint_summary, qc_merge/minor_contam_output, qc_merge/qual_files_r, qc_merge/qual_files_o, qc_merge/cutadapt_summary, run_hotspots_in_normals/hs_in_normals, run_minor_contam_binlist/minor_contam_freqlist, qc_merge/fingerprints_output ] + source: [ qc_merge/merged_mdmetrics, qc_merge/merged_hsmetrics, qc_merge/merged_hstmetrics, qc_merge/merged_insert_size_histograms, qc_merge/fingerprint_summary, qc_merge/minor_contam_output, qc_merge/qual_files_r, qc_merge/qual_files_o, run_hotspots_in_normals/hs_in_normals, run_minor_contam_binlist/minor_contam_freqlist, qc_merge/fingerprints_output ] linkMerge: merge_flattened output_directory_name: valueFrom: ${ return "qc_merged_directory"; }