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removed bedtools step. Removed variant num output
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@AndrewLangvt
AndrewLangvt committed May 13, 2021
1 parent 36ce316 commit c158745
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Showing 3 changed files with 4 additions and 50 deletions.
6 changes: 2 additions & 4 deletions tasks/task_sample_metrics.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -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
Expand Down
11 changes: 2 additions & 9 deletions workflows/wf_viral_pipeline_local.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -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 {
Expand Down Expand Up @@ -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
Expand Down
37 changes: 0 additions & 37 deletions workflows/wf_viral_refbased_assembly.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

}
}

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