Commit cbe7c460 authored by Nijsse, Bart's avatar Nijsse, Bart
Browse files

add bdduk stats file for multiqc report

parent 0f2f8e09
......@@ -190,8 +190,8 @@ steps:
reference:
valueFrom: "/unlock/references/databases/riboKmers.fa.gz"
threads: threads
memory: memory
out: [out_forward_reads, out_reverse_reads, summary]
memory: memory
out: [out_forward_reads, out_reverse_reads, summary, stats_file]
#############################################
#### Filter PhiX
......@@ -217,7 +217,7 @@ steps:
valueFrom: "/unlock/references/databases/phix.fasta"
threads: threads
memory: memory
out: [out_forward_reads, out_reverse_reads, summary]
out: [out_forward_reads, out_reverse_reads, summary, stats_file]
#############################################
#### Kraken2
......@@ -308,7 +308,7 @@ 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, reference_filter_illumina/log, 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, phix_filter/stats_file, rrna_filter/summary, rrna_filter/stats_file]
linkMerge: merge_flattened
pickValue: all_non_null
step: step
......
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