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Update clockwork to v0.12.5 #51

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Update clockwork to v0.12.5 #51

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3034f25
Test updated tbprofiler and clockwork
aofarrel Aug 23, 2024
76edc7e
Revert to older TBProfiler
aofarrel Aug 23, 2024
527efb3
Update decontam docker properly and tsv columns
aofarrel Aug 23, 2024
08751d8
Merge branch 'main' into update-prereqs
aofarrel Aug 23, 2024
25e052c
Update myco_raw.wdl
aofarrel Aug 23, 2024
72ef6f8
Revert tbprofiler update for myco_raw
aofarrel Aug 23, 2024
02e56ff
Update default cryptic image for myco raw
aofarrel Aug 23, 2024
19a2f85
TEMPORARILY avoid using CDC varpipe reference
aofarrel Aug 23, 2024
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10 changes: 4 additions & 6 deletions myco_raw.wdl
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
version 1.0

import "https://raw.githubusercontent.com/aofarrel/clockwork-wdl/2.12.2/tasks/combined_decontamination.wdl" as clckwrk_combonation
import "https://raw.githubusercontent.com/aofarrel/clockwork-wdl/2.12.2/tasks/variant_call_one_sample.wdl" as clckwrk_var_call
import "https://raw.githubusercontent.com/aofarrel/clockwork-wdl/2.14.0/tasks/combined_decontamination.wdl" as clckwrk_combonation
import "https://raw.githubusercontent.com/aofarrel/clockwork-wdl/2.14.0/tasks/variant_call_one_sample.wdl" as clckwrk_var_call
import "https://raw.githubusercontent.com/aofarrel/SRANWRP/v1.1.24/tasks/processing_tasks.wdl" as sranwrp_processing
import "https://raw.githubusercontent.com/aofarrel/tree_nine/0.0.16/tree_nine.wdl" as build_treesWF
import "https://raw.githubusercontent.com/aofarrel/vcf_to_diff_wdl/0.0.3/vcf_to_diff.wdl" as diff
Expand All @@ -20,7 +20,7 @@ workflow myco {
Int clean_average_q_score = 29
Boolean clean_before_decontam = true
Boolean covstatsQC_skip_entirely = false
Boolean decontam_use_CDC_varpipe_ref = true
Boolean decontam_use_CDC_varpipe_ref = false
File? mask_bedfile
Int QC_max_pct_low_coverage_sites = 20
Int QC_max_pct_unmapped = 2
Expand Down Expand Up @@ -64,7 +64,7 @@ workflow myco {
scatter(paired_fastqs in paired_fastq_sets) {
call clckwrk_combonation.clean_and_decontam_and_check as decontam_each_sample {
input:
docker_image = if decontam_use_CDC_varpipe_ref then "ashedpotatoes/clockwork-plus:v0.11.3.11-CDC" else "ashedpotatoes/clockwork-plus:v0.11.3.11-CRyPTIC",
docker_image = if decontam_use_CDC_varpipe_ref then "ashedpotatoes/clockwork-plus:v0.11.3.11-CDC" else "ashedpotatoes/clockwork-plus:v0.12.5.1-CRyPTIC",
unsorted_sam = true,
force_rename_out = output_sample_name,
reads_files = paired_fastqs,
Expand Down Expand Up @@ -473,8 +473,6 @@ workflow myco {
Array[String]? debug_vcfdiff_errorcode_if_covstats = vcfdiff_errorcode_if_covstats
Array[String]? debug_vcfdiff_errorcode_if_no_covstats = vcfdiff_errorcode_if_no_covstats
Array[String]? debug_vcfdiff_errorcode_array = vcfdiff_errorcode_array
Int seconds_to_map_reads = decontam_each_sample.timer_5_mapFQ[0]
Int seconds_to_rm_contam = decontam_each_sample.timer_7_dcnFQ[0]
String docker_used = decontam_each_sample.docker_used[0]
}
}
Expand Down
19 changes: 6 additions & 13 deletions myco_sra.wdl
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
version 1.0

import "https://raw.githubusercontent.com/aofarrel/clockwork-wdl/2.13.0/tasks/combined_decontamination.wdl" as clckwrk_combonation
import "https://raw.githubusercontent.com/aofarrel/clockwork-wdl/2.12.2/tasks/variant_call_one_sample.wdl" as clckwrk_var_call
import "https://raw.githubusercontent.com/aofarrel/clockwork-wdl/2.14.0/tasks/combined_decontamination.wdl" as clckwrk_combonation
import "https://raw.githubusercontent.com/aofarrel/clockwork-wdl/2.14.0/tasks/variant_call_one_sample.wdl" as clckwrk_var_call
import "https://raw.githubusercontent.com/aofarrel/SRANWRP/v1.1.24/tasks/pull_fastqs.wdl" as sranwrp_pull
import "https://raw.githubusercontent.com/aofarrel/SRANWRP/v1.1.24/tasks/processing_tasks.wdl" as sranwrp_processing
import "https://raw.githubusercontent.com/aofarrel/tree_nine/0.0.16/tree_nine.wdl" as build_treesWF
Expand Down Expand Up @@ -88,7 +88,7 @@ workflow myco {
scatter(pulled_fastq in pulled_fastqs) {
call clckwrk_combonation.clean_and_decontam_and_check as fastp_decontam_check {
input:
docker_image = if decontam_use_CDC_varpipe_ref then "ashedpotatoes/clockwork-plus:v0.11.3.11-CDC" else "ashedpotatoes/clockwork-plus:v0.11.3.11-CRyPTIC",
docker_image = if decontam_use_CDC_varpipe_ref then "ashedpotatoes/clockwork-plus:v0.11.3.11-CDC" else "ashedpotatoes/clockwork-plus:v0.12.5.1-CRyPTIC",
unsorted_sam = true,
reads_files = pulled_fastq,
fastp_clean_avg_qual = clean_average_q_score,
Expand Down Expand Up @@ -307,20 +307,13 @@ workflow myco {
}
}
}

# TODO: in later releases, the differences between the CDC and CRyPTIC pipelines will
# be handled in the decontamination task itself. This is a bandaid fix to avoid breaking
# the call cache for some previously processed data.

Array[String] CDC_columns = ["BioSample","raw_pct_above_q20","raw_pct_above_q30","raw_total_reads","post_cleaning_pct_above_q20","post_cleaning_pct_above_q30","post_decontam_pct_above_q20","post_decontam_pct_above_q30","post_decontam_total_reads","reads_is_contam","reads_reference","reads_unmapped","docker","status"]

Array[String] CRyPTIC_columns = ["BioSample","raw_pct_above_q20","raw_pct_above_q30","raw_total_reads","post_cleaning_pct_above_q20","post_cleaning_pct_above_q30","post_decontam_pct_above_q20","post_decontam_pct_above_q30","post_decontam_total_reads","reads_bacteria","reads_human","reads_NTM","docker","status"]

Array[String] todays_columns = if decontam_use_CDC_varpipe_ref then CDC_columns else CRyPTIC_columns
Array[String] columns = ["BioSample","raw_pct_above_q20","raw_pct_above_q30","raw_total_reads","post_cleaning_pct_above_q20","post_cleaning_pct_above_q30","post_decontam_pct_above_q20","post_decontam_pct_above_q30","post_decontam_total_reads","reads_is_contam","reads_reference","reads_unmapped","docker","status"]

call sranwrp_processing.several_arrays_to_tsv as fastp_decont_report {
input:
row_keys = fastp_decontam_check.sample,
column_keys = todays_columns,
column_keys = columns,
value1 = fastp_decontam_check.raw_pct_above_q20,
value2 = fastp_decontam_check.raw_pct_above_q30,
value3 = fastp_decontam_check.raw_total_reads,
Expand Down
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