add bbmap log file to output

803f0c97 · Nijsse, Bart · eeae5fef · 803f0c97
Commit 803f0c97 authored Apr 18, 2022 by Nijsse, Bart
--- a/cwl/workflows/workflow_illumina_quality.cwl
+++ b/cwl/workflows/workflow_illumina_quality.cwl
@@ -285,7 +285,7 @@ steps:
    run: ../expressions/files_to_folder.cwl
    in:
      files: 
-        source: [fastqc_illumina_before/html_files, fastqc_illumina_before/zip_files, fastqc_illumina_after/html_files, fastqc_illumina_after/zip_files, fastp/html_report, fastp/json_report, reference_filter_illumina/stats, reference_filter_illumina/covstats, illumina_quality_kraken2/sample_report, illumina_quality_kraken2_krona/krona_html, phix_filter/summary, rrna_filter/summary]
+        source: [fastqc_illumina_before/html_files, fastqc_illumina_before/zip_files, fastqc_illumina_after/html_files, fastqc_illumina_after/zip_files, fastp/html_report, fastp/json_report, reference_filter_illumina/stats, reference_filter_illumina/covstats, reference_filter_illumina/log, illumina_quality_kraken2/sample_report, illumina_quality_kraken2_krona/krona_html, phix_filter/summary, rrna_filter/summary]
        linkMerge: merge_flattened
        pickValue: all_non_null
      step: step