diff --git a/pipes/WDL/workflows/demux_metag.wdl b/pipes/WDL/workflows/demux_metag.wdl index f69c2b2a6..7ff1ae27a 100644 --- a/pipes/WDL/workflows/demux_metag.wdl +++ b/pipes/WDL/workflows/demux_metag.wdl @@ -18,7 +18,7 @@ workflow demux_metag { File kraken2_db_tgz File krona_taxonomy_db_kraken2_tgz - File blast_db_tgz + #File blast_db_tgz File krona_taxonomy_db_blast_tgz } @@ -53,12 +53,12 @@ workflow demux_metag { kraken2_db_tgz = kraken2_db_tgz, krona_taxonomy_db_tgz = krona_taxonomy_db_kraken2_tgz } - call metagenomics.blastx as blastx { - input: - contigs_fasta = spades.contigs_fasta, - blast_db_tgz = blast_db_tgz, - krona_taxonomy_db_tgz = krona_taxonomy_db_blast_tgz - } + #call metagenomics.blastx as blastx { + # input: + # contigs_fasta = spades.contigs_fasta, + # blast_db_tgz = blast_db_tgz, + # krona_taxonomy_db_tgz = krona_taxonomy_db_blast_tgz + #} } call reports.MultiQC as multiqc_raw { @@ -95,11 +95,11 @@ workflow demux_metag { out_basename = "merged-kraken2.krona.html" } - call metagenomics.krona_merge as krona_merge_blastx { - input: - krona_reports = blastx.krona_report_html, - out_basename = "merged-spades-blastx.krona.html" - } + #call metagenomics.krona_merge as krona_merge_blastx { + # input: + # krona_reports = blastx.krona_report_html, + # out_basename = "merged-spades-blastx.krona.html" + #} output { Array[File] raw_reads_unaligned_bams = illumina_demux.raw_reads_unaligned_bams @@ -124,12 +124,12 @@ workflow demux_metag { File spikein_counts = spike_summary.count_summary File kraken2_merged_krona = krona_merge_kraken2.krona_report_html File kraken2_summary = metag_summary_report.krakenuniq_aggregate_taxlevel_summary - File blastx_merged_krona = krona_merge_blastx.krona_report_html + #File blastx_merged_krona = krona_merge_blastx.krona_report_html Array[File] kraken2_summary_reports = kraken2.kraken2_summary_report Array[File] kraken2_krona_by_sample = kraken2.krona_report_html - Array[File] blastx_report_by_sample = blastx.blast_report - Array[File] blastx_krona_by_sample = blastx.krona_report_html + #Array[File] blastx_report_by_sample = blastx.blast_report + #Array[File] blastx_krona_by_sample = blastx.krona_report_html String demux_viral_core_version = illumina_demux.viralngs_version String kraken2_viral_classify_version = kraken2.viralngs_version[0] diff --git a/pipes/WDL/workflows/demux_only.wdl b/pipes/WDL/workflows/demux_only.wdl index 1ce9c86a6..4bdb24aac 100644 --- a/pipes/WDL/workflows/demux_only.wdl +++ b/pipes/WDL/workflows/demux_only.wdl @@ -28,7 +28,19 @@ workflow demux_only { File demux_commonBarcodes = illumina_demux.commonBarcodes File demux_outlierBarcodes = illumina_demux.outlierBarcodes File multiqc_report_raw = MultiQC.multiqc_report + + String run_date = illumina_demux.run_info['run_start_date'] + Map[String,String] run_info = illumina_demux.run_info + File run_info_json = illumina_demux.run_info_json + String run_id = illumina_demux.run_info['run_id'] + String run_lane_count = illumina_demux.flowcell_lane_count + String instrument_model_inferred = select_first(flatten([[instrument_model_user_specified],[illumina_demux.run_info['sequencer_model']]])) String demux_viral_core_version = illumina_demux.viralngs_version + + Map[String,Map[String,String]] meta_by_filename = illumina_demux.meta_by_filename + Map[String,Map[String,String]] meta_by_sample = illumina_demux.meta_by_sample + File meta_by_filename_json = illumina_demux.meta_by_filename_json + File meta_by_sample_json = illumina_demux.meta_by_sample_json } }