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Merge pull request #30 from aofarrel/cleanup-and-clarify
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Cleanup and clarify
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@aofarrel
aofarrel authored Jul 15, 2023
2 parents c89d92f + 19c68a7 commit 74deaaf
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144 changes: 106 additions & 38 deletions myco_raw.wdl
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Expand Up @@ -6,29 +6,39 @@ import "https://raw.githubusercontent.com/aofarrel/SRANWRP/v1.1.12/tasks/process
import "https://raw.githubusercontent.com/aofarrel/tree_nine/0.0.10/tree_nine.wdl" as build_treesWF
import "https://raw.githubusercontent.com/aofarrel/parsevcf/1.1.9/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/0.0.2/TBfastProfiler.wdl" as earlyQC
import "https://raw.githubusercontent.com/aofarrel/TBfastProfiler/0.0.4/TBfastProfiler.wdl" as earlyQC

workflow myco {
input {
Array[Array[File]] paired_fastq_sets

Boolean decorate_tree = false
Boolean early_qc_apply_cutoffs = false
Float early_qc_cutoff_q30 = 0.90
Boolean early_qc_skip_entirely = false
Boolean fastqc_on_timeout = false
Boolean force_diff = false
Boolean decorate_tree = false
Boolean early_qc_apply_cutoffs = false
Float early_qc_cutoff_q30 = 0.90
Boolean early_qc_skip_entirely = false
Boolean fastqc_on_timeout = false
Boolean force_diff = false
File? input_tree
Float max_low_coverage_sites = 0.05
Int min_coverage_per_site = 10
Float max_low_coverage_sites = 0.05
Int min_coverage_per_site = 10
Int quick_tasks_disk_size = 10
File? ref_genome_for_tree_building
Int subsample_cutoff = 450
Int subsample_seed = 1965
Boolean tbprofiler_on_bam = false
Int timeout_decontam_part1 = 0
Int timeout_decontam_part2 = 0
Int timeout_variant_caller = 0
Int subsample_cutoff = 450
Int subsample_seed = 1965
Boolean tbprofiler_on_bam = false
Int timeout_decontam_part1 = 0
Int timeout_decontam_part2 = 0
Int timeout_variant_caller = 0
File? typical_tb_masked_regions
Int variantcalling_addl_disk = 100
Boolean variantcalling_crash_on_error = false
Boolean variantcalling_crash_on_timeout = false
Int variantcalling_cpu = 16
Int? variantcalling_mem_height
Int variantcalling_memory = 32
Int variantcalling_preemptibles = 1
Int variantcalling_retries = 1
Boolean variantcalling_ssd = true
}

parameter_meta {
Expand Down Expand Up @@ -81,7 +91,7 @@ workflow myco {
File real_decontaminated_fastq_2=select_first([decontam_each_sample.decontaminated_fastq_2, paired_fastqs[0]])

if(!early_qc_skip_entirely) {
call earlyQC.TBfastProfiler as check_fastqs {
call earlyQC.TBfastProfiler as qc_fastqs {
input:
fastq1 = real_decontaminated_fastq_1,
fastq2 = real_decontaminated_fastq_2,
Expand All @@ -90,24 +100,42 @@ workflow myco {

# if we are filtering out samples via earlyQC...
if(early_qc_apply_cutoffs) {
if(check_fastqs.did_this_sample_pass) {
File possibly_fastp_cleaned_fastq1_passed=select_first([check_fastqs.cleaned_fastq1, real_decontaminated_fastq_1])
File possibly_fastp_cleaned_fastq2_passed=select_first([check_fastqs.cleaned_fastq2, real_decontaminated_fastq_2])
if(qc_fastqs.did_this_sample_pass) {
File possibly_fastp_cleaned_fastq1_passed=select_first([qc_fastqs.cleaned_fastq1, real_decontaminated_fastq_1])
File possibly_fastp_cleaned_fastq2_passed=select_first([qc_fastqs.cleaned_fastq2, real_decontaminated_fastq_2])
call clckwrk_var_call.variant_call_one_sample_ref_included as variant_call_after_earlyQC_filtering {
input:
reads_files = [possibly_fastp_cleaned_fastq1_passed, possibly_fastp_cleaned_fastq2_passed],
addldisk = variantcalling_addl_disk,
cpu = variantcalling_cpu,
crash_on_error = variantcalling_crash_on_error,
crash_on_timeout = variantcalling_crash_on_timeout,
mem_height = variantcalling_mem_height,
memory = variantcalling_memory,
preempt = variantcalling_preemptibles,
retries = variantcalling_retries,
ssd = variantcalling_ssd,
timeout = timeout_variant_caller
}
}
}

# if we are not filtering out samples via the early qc step (but ran earlyQC anyway)...
if(!early_qc_apply_cutoffs) {
File possibly_fastp_cleaned_fastq1=select_first([check_fastqs.cleaned_fastq1, real_decontaminated_fastq_1])
File possibly_fastp_cleaned_fastq2=select_first([check_fastqs.cleaned_fastq2, real_decontaminated_fastq_2])
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])
call clckwrk_var_call.variant_call_one_sample_ref_included as variant_call_after_earlyQC_but_not_filtering_samples {
input:
reads_files = [possibly_fastp_cleaned_fastq1, possibly_fastp_cleaned_fastq2],
addldisk = variantcalling_addl_disk,
cpu = variantcalling_cpu,
crash_on_error = variantcalling_crash_on_error,
crash_on_timeout = variantcalling_crash_on_timeout,
mem_height = variantcalling_mem_height,
memory = variantcalling_memory,
preempt = variantcalling_preemptibles,
retries = variantcalling_retries,
ssd = variantcalling_ssd,
timeout = timeout_variant_caller
}
}
Expand All @@ -118,6 +146,15 @@ workflow myco {
call clckwrk_var_call.variant_call_one_sample_ref_included as variant_call_without_earlyQC {
input:
reads_files = [real_decontaminated_fastq_1, real_decontaminated_fastq_2],
addldisk = variantcalling_addl_disk,
cpu = variantcalling_cpu,
crash_on_error = variantcalling_crash_on_error,
crash_on_timeout = variantcalling_crash_on_timeout,
mem_height = variantcalling_mem_height,
memory = variantcalling_memory,
preempt = variantcalling_preemptibles,
retries = variantcalling_retries,
ssd = variantcalling_ssd,
timeout = timeout_variant_caller
}
}
Expand Down Expand Up @@ -149,34 +186,58 @@ workflow myco {
}

if(tbprofiler_on_bam) {
call profiler.tb_profiler_bam as profile {
call profiler.tb_profiler_bam as profile_bam {
input:
bam = vcfs_and_bams.left
}
}
}

if(defined(profile.strain)) {
Array[String] coerced_strains=select_all(profile.strain)
Array[String] coerced_resistance=select_all(profile.resistance)
Array[String] coerced_depth=select_all(profile.median_depth)
# pull TBProfiler information, if we ran TBProfiler on bams
if(defined(profile_bam.strain)) {
Array[String] coerced_bam_strains=select_all(profile_bam.strain)
Array[String] coerced_bam_resistance=select_all(profile_bam.resistance)
Array[String] coerced_bam_depth=select_all(profile_bam.median_depth)

call sranwrp_processing.cat_strings as collate_strains {
call sranwrp_processing.cat_strings as collate_bam_strains {
input:
strings = coerced_strains,
out = "strain_reports.txt"
strings = coerced_bam_strains,
out = "strain_reports.txt",
disk_size = quick_tasks_disk_size
}

call sranwrp_processing.cat_strings as collate_resistance {
call sranwrp_processing.cat_strings as collate_bam_resistance {
input:
strings = coerced_resistance,
out = "resistance_reports.txt"
strings = coerced_bam_resistance,
out = "resistance_reports.txt",
disk_size = quick_tasks_disk_size
}

call sranwrp_processing.cat_strings as collate_depth {
call sranwrp_processing.cat_strings as collate_bam_depth {
input:
strings = coerced_depth,
out = "depth_reports.txt"
strings = coerced_bam_depth,
out = "depth_reports.txt",
disk_size = quick_tasks_disk_size
}
}

# pull TBProfiler information, if we ran TBProfiler on fastqs
if(defined(qc_fastqs.samp_strain)) {
Array[String] coerced_fq_strains=select_all(qc_fastqs.samp_strain)
Array[String] coerced_fq_resistance=select_all(qc_fastqs.samp_resistance)

call sranwrp_processing.cat_strings as collate_fq_strains {
input:
strings = coerced_fq_strains,
out = "strain_reports.txt",
disk_size = quick_tasks_disk_size
}

call sranwrp_processing.cat_strings as collate_fq_resistance {
input:
strings = coerced_fq_resistance,
out = "resistance_reports.txt",
disk_size = quick_tasks_disk_size
}
}

Expand All @@ -202,9 +263,16 @@ workflow myco {
Array[File] vcfs = minos_vcfs

# metadata
File? depth_report = collate_depth.outfile
File? strain_report = collate_strains.outfile
File? resistance_report = collate_resistance.outfile
Array[File?]? fastp_reports = qc_fastqs.fastp_txt
File? tbprof_bam_depths = collate_bam_depth.outfile
Array[File?]? tbprof_bam_jsons = profile_bam.tbprofiler_json
File? tbprof_bam_strains = collate_bam_strains.outfile
Array[File?]? tbprof_bam_summaries = profile_bam.tbprofiler_txt
File? tbprof_bam_resistances = collate_bam_resistance.outfile
Array[File?]? tbprof_fq_jsons = qc_fastqs.tbprofiler_json
File? tbprof_fq_strains = collate_fq_strains.outfile
Array[File?]? tbprof_fq_summaries = qc_fastqs.tbprofiler_txt
File? tbprof_fq_resistances = collate_fq_resistance.outfile

# tree nine
File? tree_nwk = trees.tree_nwk
Expand Down
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