diff --git a/myco_raw.wdl b/myco_raw.wdl index ab0089c..aa17b2a 100644 --- a/myco_raw.wdl +++ b/myco_raw.wdl @@ -6,7 +6,7 @@ import "https://raw.githubusercontent.com/aofarrel/SRANWRP/v1.1.17/tasks/process import "https://raw.githubusercontent.com/aofarrel/tree_nine/0.0.11/tree_nine.wdl" as build_treesWF import "https://raw.githubusercontent.com/aofarrel/parsevcf/1.2.0/vcf_to_diff.wdl" as diff import "https://raw.githubusercontent.com/aofarrel/tb_profiler/0.2.2/tbprofiler_tasks.wdl" as profiler -import "https://raw.githubusercontent.com/aofarrel/TBfastProfiler/0.0.12/neoTBfastProfiler.wdl" as qc_fastqsWF # aka earlyQC +import "https://raw.githubusercontent.com/aofarrel/tb_profiler/main/thiagen_tbprofiler.wdl" as qc_fastqsWF # aka earlyQC import "https://raw.githubusercontent.com/aofarrel/goleft-wdl/0.1.2/goleft_functions.wdl" as goleft workflow myco { @@ -101,20 +101,17 @@ workflow myco { } if(!earlyQC_skip_entirely) { - call qc_fastqsWF.TBfastProfiler as qc_fastqs { + call qc_fastqsWF.ThiagenTBProfiler as qc_fastqs { input: fastq1 = real_decontaminated_fastq_1, fastq2 = real_decontaminated_fastq_2, - minimum_q30_rate = earlyQC_min_q30_rate, - average_qual = earlyQC_trim_qual_below, - use_fastps_cleaned_fastqs = !(earlyQC_skip_trimming), soft_all_qc = earlyQC_skip_QC, minimum_pct_mapped = tbprofilerQC_min_pct_mapped } # if this sample passes fastp, or if earlyQC_skip_QC is true... if(qc_fastqs.status_code == pass) { - File possibly_fastp_cleaned_fastq1=select_first([qc_fastqs.cleaned_fastq1, real_decontaminated_fastq_1]) - File possibly_fastp_cleaned_fastq2=select_first([qc_fastqs.cleaned_fastq2, real_decontaminated_fastq_2]) + File possibly_fastp_cleaned_fastq1=select_first([decontam_each_sample.decontaminated_fastq_1, real_decontaminated_fastq_1]) + File possibly_fastp_cleaned_fastq2=select_first([decontam_each_sample.decontaminated_fastq_1, real_decontaminated_fastq_2]) call clckwrk_var_call.variant_call_one_sample_ref_included as variant_call_after_earlyQC { input: reads_files = [possibly_fastp_cleaned_fastq1, possibly_fastp_cleaned_fastq2], @@ -464,7 +461,7 @@ workflow myco { "reads_is_contam": select_first([decontam_each_sample.reads_is_contam[0], "NA"]), # decontamination "reads_reference": select_first([decontam_each_sample.reads_reference[0], "NA"]), # decontamination "reads_unmapped": select_first([decontam_each_sample.reads_unmapped[0], "NA"]), # decontamination - "pct_above_q30": select_first([qc_fastqs.pct_above_q30[0], "NA"]), # fastp + "pct_above_q30": select_first([decontam_each_sample.dcntmd_pct_above_q30[0], "NA"]), # fastp "median_coverage": select_first([qc_fastqs.median_coverage[0], "NA"]), # thiagen!TBProfiler "genome_pct_coverage": select_first([qc_fastqs.pct_genome_covered[0], "NA"]), # thiagen!TBProfiler "mean_coverage": select_first([meanCoverage, "NA"]) # covstats @@ -491,7 +488,6 @@ workflow myco { # metadata Array[File?] covstats_reports = covstats.covstatsOutfile Array[File?] diff_reports = real_reports - Array[File?] fastp_reports = qc_fastqs.fastp_txt Array[File?] tbprof_bam_jsons = profile_bam.tbprofiler_json Array[File?] tbprof_bam_summaries = profile_bam.tbprofiler_txt Array[File?] tbprof_fq_jsons = qc_fastqs.tbprofiler_json