diff --git a/tasks/task_sample_metrics.wdl b/tasks/task_sample_metrics.wdl index e0cfafb..9350eb4 100644 --- a/tasks/task_sample_metrics.wdl +++ b/tasks/task_sample_metrics.wdl @@ -92,7 +92,6 @@ task sample_metrics { Float primer_trimmed_read_percent Float? kraken_human Float? kraken_sc2 - Int variant_num Int number_N Int number_ATCG Int number_Degenerate @@ -101,7 +100,6 @@ task sample_metrics { Float meanmapq_trim Float coverage_trim Float depth_trim - Int amp_fail Float? coverage_threshold = 95.00 Float? meanbaseq_threshold = 30.00 Float? meanmapq_threshold = 30.00 @@ -121,7 +119,7 @@ task sample_metrics { ~{nextclade_clade},~{nextclade_aa_subs},~{nextclade_aa_dels},\ ~{fastqc_raw_pairs},~{fastqc_clean_pairs},~{primer_trimmed_read_percent},\ ~{depth_trim},~{coverage_trim},\ - ~{kraken_human},~{kraken_sc2},~{amp_fail},~{variant_num},\ + ~{kraken_human},~{kraken_sc2},\ ~{number_N},~{number_Degenerate},~{number_ATCG},~{number_Total},\ ~{meanbaseq_trim},~{meanmapq_trim}," + assembly_status @@ -157,7 +155,7 @@ task merge_metrics { nextclade_lineage,nextclade_aaSubstitutions,nextclade_aaDeletions,\ raw_pairs,cleaned_pairs,primer_trimmed_read_percent,\ depth_after_trimming,coverage_after_trimming,\ - %_human_reads,%_SARS-COV-2_reads,num_failed_amplicons,num_variants,\ + %_human_reads,%_SARS-COV-2_reads,\ num_N,num_degenerate,num_ACTG,num_total,\ meanbaseq_trim,meanmapq_trim,assembly_status" >> run_results.csv diff --git a/workflows/wf_viral_pipeline_local.wdl b/workflows/wf_viral_pipeline_local.wdl index 1a89f3d..fba00c7 100644 --- a/workflows/wf_viral_pipeline_local.wdl +++ b/workflows/wf_viral_pipeline_local.wdl @@ -49,23 +49,16 @@ workflow nCoV19_pipeline { nextclade_clade = viral_refbased_assembly.nextclade_clade, nextclade_aa_subs = viral_refbased_assembly.nextclade_aa_subs, nextclade_aa_dels = viral_refbased_assembly.nextclade_aa_dels, -# fastqc_raw_pairs = viral_refbased_assembly.fastqc_raw_pairs, -# seqy_pairs = viral_refbased_assembly.seqy_pairs, -# seqy_percent = viral_refbased_assembly.seqy_percent, kraken_human = viral_refbased_assembly.kraken_human, kraken_sc2 = viral_refbased_assembly.kraken_sc2, - variant_num = viral_refbased_assembly.variant_num, number_N = viral_refbased_assembly.number_N, number_ATCG = viral_refbased_assembly.assembly_length_unambiguous, number_Degenerate = viral_refbased_assembly.number_Degenerate, number_Total = viral_refbased_assembly.number_Total, -# coverage = viral_refbased_assembly.coverage, -# depth = viral_refbased_assembly.depth, meanbaseq_trim = viral_refbased_assembly.meanbaseq_trim, meanmapq_trim = viral_refbased_assembly.meanmapq_trim, coverage_trim = viral_refbased_assembly.coverage_trim, - depth_trim = viral_refbased_assembly.depth_trim, - amp_fail = viral_refbased_assembly.amp_fail + depth_trim = viral_refbased_assembly.depth_trim } call submission.SC2_submission_files { @@ -111,7 +104,7 @@ workflow nCoV19_pipeline { Array[File] cov_stats = viral_refbased_assembly.cov_stats Array[File] samtools_flagstat = viral_refbased_assembly.consensus_flagstat Array[File] pango_lineage_report = viral_refbased_assembly.pango_lineage_report - Array[File] amp_coverage = viral_refbased_assembly.amp_coverage +# Array[File] amp_coverage = viral_refbased_assembly.amp_coverage File merged_metrics = merge_metrics.run_results Array[File?] read1_submission = SC2_submission_files.read1_submission diff --git a/workflows/wf_viral_refbased_assembly.wdl b/workflows/wf_viral_refbased_assembly.wdl index 8201b7a..93dc33b 100644 --- a/workflows/wf_viral_refbased_assembly.wdl +++ b/workflows/wf_viral_refbased_assembly.wdl @@ -48,19 +48,6 @@ workflow viral_refbased_assembly { file_URL = select_first([primer_PCR_BED_URL]) } } - # call ops_utils.get_ref_files { - # input: - # ref_genome_URL = ref_genome_URL, - # ref_gff_URL = ref_gff_URL - # } - # call ops_utils.get_single_file as primer_BEDf { - # input: - # file_URL = primer_BED_URL - # } - # call ops_utils.get_single_file as primer_PCR_BED { - # input: - # file_URL = primer_PCR_BED_URL - # } call read_qc.read_QC_trim { input: samplename = samplename, @@ -103,28 +90,11 @@ workflow viral_refbased_assembly { samplename = samplename, bamfile = primer_trim.trim_sorted_bam } - # call taxon_ID.pangolin2 { - # input: - # samplename = samplename, - # fasta = consensus.consensus_seq - # } - # call taxon_ID.nextclade_one_sample { - # input: - # genome_fasta = consensus.consensus_seq - # } call SC2_identification.sc2_variantID { input: samplename = samplename, fasta = consensus.consensus_seq } - - call amplicon_metrics.bedtools_cov { - input: - samplename = samplename, - bamfile = bwa.sorted_bam, - baifile = bwa.sorted_bai, - primer_bed = select_first([primer_PCR_BEDfile, primer_PCR_BED.outfile]) - } call ncbi.vadr { input: genome_fasta = consensus.consensus_seq, @@ -157,10 +127,8 @@ workflow viral_refbased_assembly { File aligned_bai = primer_trim.trim_sorted_bai Float primer_trimmed_read_percent = primer_trim.primer_trimmed_read_percent String ivar_version_primtrim = primer_trim.ivar_version - String samtools_version_primtrim = primer_trim.samtools_version File ivar_tsv = variant_call.sample_variants - Int variant_num = variant_call.variant_num String ivar_version_variants = variant_call.ivar_version String samtools_version_variants = variant_call.samtools_version @@ -200,10 +168,5 @@ workflow viral_refbased_assembly { File vadr_alerts_list = vadr.alerts_list Int vadr_num_alerts = vadr.num_alerts - - Int amp_fail = bedtools_cov.amp_fail - File amp_coverage = bedtools_cov.amp_coverage - String bedtools_version = bedtools_cov.version - } }