From d9c20a716cb472ca93234c54e30709f85d180022 Mon Sep 17 00:00:00 2001 From: Ash O'Farrell Date: Wed, 20 Nov 2024 18:49:39 -0800 Subject: [PATCH] Update prereqs and dockers --- doc/reference_genomes.md | 1 + myco_raw.wdl | 10 ++++------ myco_simple.wdl | 4 ++-- myco_sra.wdl | 6 +++--- 4 files changed, 10 insertions(+), 11 deletions(-) diff --git a/doc/reference_genomes.md b/doc/reference_genomes.md index c371b4a..28e3f46 100644 --- a/doc/reference_genomes.md +++ b/doc/reference_genomes.md @@ -21,6 +21,7 @@ Ref.download.tar └── remove_contam.tsv ``` ### ClockworkRefPrepTB.bluepeter__tar_indexd_dcontm_ref +--> Note: Starting with v0.12.0, clockwork changed their decontamination reference and now use CHM13 instead of hg38 for human ``` Ref.remove_contam.tar ├── ref.fa diff --git a/myco_raw.wdl b/myco_raw.wdl index 16b7d15..9a95e6d 100644 --- a/myco_raw.wdl +++ b/myco_raw.wdl @@ -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/update-dockers-0.12.5.2/tasks/combined_decontamination.wdl" as clckwrk_combonation +import "https://raw.githubusercontent.com/aofarrel/clockwork-wdl/update-dockers-0.12.5.2/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 @@ -21,7 +21,7 @@ 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 # changed in myco 6.3.0!! File? mask_bedfile Int QC_max_pct_low_coverage_sites = 20 Int QC_max_pct_unmapped = 2 @@ -65,7 +65,7 @@ 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:v0.12.5.2-CDC" else "ashedpotatoes/clockwork-plus:v0.12.5.2-CRyPTIC", unsorted_sam = true, force_rename_out = output_sample_name, reads_files = paired_fastqs, @@ -479,8 +479,6 @@ 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] } } diff --git a/myco_simple.wdl b/myco_simple.wdl index fff598d..4a940e1 100644 --- a/myco_simple.wdl +++ b/myco_simple.wdl @@ -1,7 +1,7 @@ version 1.0 -import "https://raw.githubusercontent.com/aofarrel/clockwork-wdl/2.12.1/tasks/variant_call_one_sample.wdl" as clckwrk_var_call +import "https://raw.githubusercontent.com/aofarrel/clockwork-wdl/update-dockers-0.12.5.2/tasks/variant_call_one_sample.wdl" as clckwrk_var_call import "https://raw.githubusercontent.com/aofarrel/fastp-wdl/0.0.4/fastp_tasks.wdl" as fastp -import "https://raw.githubusercontent.com/aofarrel/parsevcf/1.2.0/vcf_to_diff.wdl" as diff +import "https://raw.githubusercontent.com/aofarrel/vcf_to_diff_wdl/0.0.3/vcf_to_diff.wdl" as diff # This is a stripped-down version of myco which only runs the variant caller, vcf-to-diff, and (optionally) fastp. # There is NO decontamination, TB-Profiler, covstats, or QC beyond "does the variant caller crash/time out or not." diff --git a/myco_sra.wdl b/myco_sra.wdl index 183c15a..89de9f6 100755 --- a/myco_sra.wdl +++ b/myco_sra.wdl @@ -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/update-dockers-0.12.5.2/tasks/combined_decontamination.wdl" as clckwrk_combonation +import "https://raw.githubusercontent.com/aofarrel/clockwork-wdl/update-dockers-0.12.5.2/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 @@ -18,9 +18,9 @@ workflow myco { Int clean_average_q_score = 29 Boolean clean_before_decontam = true Boolean covstatsQC_skip_entirely = true # false in myco_raw - Boolean decontam_use_CDC_varpipe_ref = false # true in myco_raw File? mask_bedfile Boolean TBProf_on_bams_not_fastqs = true # effectively false in myco_raw + Boolean decontam_use_CDC_varpipe_ref = false # QC stuff Float QC_max_pct_low_coverage_sites = 0.20