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update BUSCO to v5.7.1 and small tweaks to WDL task #401

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merged 5 commits into from
Apr 9, 2024
Merged

update BUSCO to v5.7.1 and small tweaks to WDL task #401

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68d2091
update BUSCO to use v5.7.1 docker image by default; added cpu flag; u…
kapsakcj Apr 4, 2024
4cca8f6
update CI for task related changes
kapsakcj Apr 4, 2024
83b8b23
add String busco_docker output to all theiaprok wfs and theiaeuk_illu…
kapsakcj Apr 4, 2024
85a19c4
update CI for theiaprok_illumina_pe and se for wf level change
kapsakcj Apr 4, 2024
984a6a4
add new optional Int input busco_memory with default of 24 to theiaeu…
kapsakcj Apr 9, 2024
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17 changes: 12 additions & 5 deletions tasks/quality_control/advanced_metrics/task_busco.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ task busco {
input {
File assembly
String samplename
String docker = "us-docker.pkg.dev/general-theiagen/ezlabgva/busco:v5.3.2_cv1"
String docker = "us-docker.pkg.dev/general-theiagen/ezlabgva/busco:v5.7.1_cv1"
Int memory = 8
Int cpu = 2
Int disk_size = 100
Expand All @@ -25,6 +25,7 @@ task busco {
# --auto-lineage-prok looks at only prokaryotic organisms; default
busco \
-i ~{assembly} \
-c ~{cpu} \
-m geno \
-o ~{samplename} \
~{true='--auto-lineage-euk' false='--auto-lineage-prok' eukaryote}
Expand All @@ -33,19 +34,25 @@ task busco {
if [ -f ~{samplename}/short_summary.specific.*.~{samplename}.txt ]; then

# grab the database version and format it according to BUSCO recommendations
cat ~{samplename}/short_summary.specific.*.~{samplename}.txt | grep "dataset is:" | cut -d' ' -f 6,9 | sed 's/,//' | sed 's/ / (/' | sed 's/$/)/' | tee DATABASE
# pull line out of final specific summary file
# cut out the database name and date it was created
# sed is to remove extra comma and to add parentheses around the date and remove all tabs
# finally write to a file called DATABASE
cat ~{samplename}/short_summary.specific.*.~{samplename}.txt | grep "dataset is:" | cut -d' ' -f 6,9 | sed 's/,//; s/ / (/; s/$/)/; s|[\t]||g' | tee DATABASE

# extract the results string
cat ~{samplename}/short_summary.specific.*.~{samplename}.txt | grep "C:" | tee BUSCO_RESULTS
# extract the results string; strip off all tab and space characters; write to a file called BUSCO_RESULTS
cat ~{samplename}/short_summary.specific.*.~{samplename}.txt | grep "C:" | sed 's|[\t]||g; s| ||g' | tee BUSCO_RESULTS

cp ~{samplename}/short_summary.specific.*.~{samplename}.txt ~{samplename}_busco-summary.txt
# rename final output file to predictable name
cp -v ~{samplename}/short_summary.specific.*.~{samplename}.txt ~{samplename}_busco-summary.txt
else
echo "BUSCO FAILED" | tee BUSCO_RESULTS
echo "NA" > DATABASE
fi
>>>
output {
String busco_version = read_string("VERSION")
String busco_docker = docker
String busco_database = read_string("DATABASE")
String busco_results = read_string("BUSCO_RESULTS")
File? busco_report = "~{samplename}_busco-summary.txt"
Expand Down
8 changes: 4 additions & 4 deletions tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@
- path: miniwdl_run/call-amrfinderplus_task/work/test_amrfinder_virulence.tsv
md5sum: a5cc7b0baa9e11c9a31540800d0a740c
- path: miniwdl_run/call-busco/command
md5sum: 81ed6d55f143b759289e758bdde4091c
md5sum: 8a4de431119daee0dfc4f2605413b095
- path: miniwdl_run/call-busco/inputs.json
- path: miniwdl_run/call-busco/outputs.json
- path: miniwdl_run/call-busco/stderr.txt
Expand All @@ -67,7 +67,7 @@
- path: miniwdl_run/call-busco/work/BUSCO_RESULTS
- path: miniwdl_run/call-busco/work/DATABASE
- path: miniwdl_run/call-busco/work/VERSION
md5sum: 369fefb1c40f16c2a9c34d4903e9f1e2
md5sum: 3cfdda0096f0689c9829ed27bdef6b1a
- path: miniwdl_run/call-busco/work/_miniwdl_inputs/0/test_contigs.fasta
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: miniwdl_run/call-busco/work/busco_downloads/file_versions.tsv
Expand Down Expand Up @@ -565,7 +565,7 @@
- path: miniwdl_run/wdl/tasks/quality_control/read_filtering/task_bbduk.wdl
md5sum: aec6ef024d6dff31723f44290f6b9cf5
- path: miniwdl_run/wdl/tasks/quality_control/advanced_metrics/task_busco.wdl
md5sum: 0f8b3fbca316cb940a61b2c3cdf6ebab
md5sum: 1e2ccdeac9f2137d8cab70f0de452c4c
- path: miniwdl_run/wdl/tasks/quality_control/basic_statistics/task_cg_pipeline.wdl
md5sum: c8e7ae1ed0fff7b14731228db80c6b30
- path: miniwdl_run/wdl/tasks/quality_control/read_filtering/task_fastp.wdl
Expand Down Expand Up @@ -633,7 +633,7 @@
- path: miniwdl_run/wdl/tasks/utilities/data_export/task_broad_terra_tools.wdl
md5sum: ea141ba65f2948ae2abed7ca791e872b
- path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl
md5sum: d835ff7f54e03f72d4af6375e262b726
md5sum: c28f17110081694ac36a7695fdebea76
- path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl
md5sum: cfb407b32bc9436a0f12e29dc2e3b5a1
- path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_pe.wdl
Expand Down
10 changes: 4 additions & 6 deletions tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@
- path: miniwdl_run/call-amrfinderplus_task/work/test_amrfinder_virulence.tsv
md5sum: a5cc7b0baa9e11c9a31540800d0a740c
- path: miniwdl_run/call-busco/command
md5sum: 81ed6d55f143b759289e758bdde4091c
md5sum: 8a4de431119daee0dfc4f2605413b095
- path: miniwdl_run/call-busco/inputs.json
- path: miniwdl_run/call-busco/outputs.json
- path: miniwdl_run/call-busco/stderr.txt
Expand All @@ -67,7 +67,7 @@
- path: miniwdl_run/call-busco/work/BUSCO_RESULTS
- path: miniwdl_run/call-busco/work/DATABASE
- path: miniwdl_run/call-busco/work/VERSION
md5sum: 369fefb1c40f16c2a9c34d4903e9f1e2
md5sum: 3cfdda0096f0689c9829ed27bdef6b1a
- path: miniwdl_run/call-busco/work/_miniwdl_inputs/0/test_contigs.fasta
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: miniwdl_run/call-busco/work/busco_downloads/file_versions.tsv
Expand Down Expand Up @@ -108,8 +108,6 @@
- path: miniwdl_run/call-busco/work/busco_downloads/placement_files/supermatrix.aln.bacteria_odb10.2019-12-16.faa
- path: miniwdl_run/call-busco/work/busco_downloads/placement_files/tree.bacteria_odb10.2019-12-16.nwk
- path: miniwdl_run/call-busco/work/busco_downloads/placement_files/tree_metadata.bacteria_odb10.2019-12-16.txt
- path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/busco_sequences/single_copy_busco_sequences/84684at2157.faa
- path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/busco_sequences/single_copy_busco_sequences/84684at2157.fna
- path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/full_table.tsv
- path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/hmmer_output/101957at2157.out
- path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/hmmer_output/102178at2157.out
Expand Down Expand Up @@ -532,7 +530,7 @@
- path: miniwdl_run/wdl/tasks/quality_control/read_filtering/task_bbduk.wdl
md5sum: aec6ef024d6dff31723f44290f6b9cf5
- path: miniwdl_run/wdl/tasks/quality_control/advanced_metrics/task_busco.wdl
md5sum: 0f8b3fbca316cb940a61b2c3cdf6ebab
md5sum: 1e2ccdeac9f2137d8cab70f0de452c4c
- path: miniwdl_run/wdl/tasks/quality_control/basic_statistics/task_cg_pipeline.wdl
md5sum: c8e7ae1ed0fff7b14731228db80c6b30
- path: miniwdl_run/wdl/tasks/quality_control/read_filtering/task_fastp.wdl
Expand Down Expand Up @@ -598,7 +596,7 @@
- path: miniwdl_run/wdl/tasks/utilities/data_export/task_broad_terra_tools.wdl
md5sum: ea141ba65f2948ae2abed7ca791e872b
- path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_se.wdl
md5sum: ae0ad6faa3d9f355d0f1561f62fb2e98
md5sum: f920448f13018432be074e3ef06ea4ee
- path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl
md5sum: cfb407b32bc9436a0f12e29dc2e3b5a1
- path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_se.wdl
Expand Down
5 changes: 4 additions & 1 deletion workflows/theiaeuk/wf_theiaeuk_illumina_pe.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,7 @@ workflow theiaeuk_illumina_pe {
Int trim_min_length = 75
Int trim_quality_min_score = 20
Int trim_window_size = 10
Int busco_memory = 24
Boolean skip_screen = false
File? qc_check_table
String? expected_taxon
Expand Down Expand Up @@ -139,7 +140,8 @@ workflow theiaeuk_illumina_pe {
input:
assembly = shovill_pe.assembly_fasta,
samplename = samplename,
eukaryote = true
eukaryote = true,
memory = busco_memory
}
if (defined(qc_check_table)) {
call qc_check.qc_check_phb as qc_check_task {
Expand Down Expand Up @@ -257,6 +259,7 @@ workflow theiaeuk_illumina_pe {
Float? est_coverage_clean = cg_pipeline_clean.est_coverage
# Assembly QC - busco outputs
String? busco_version = busco.busco_version
String? busco_docker = busco.busco_docker
String? busco_database = busco.busco_database
String? busco_results = busco.busco_results
File? busco_report = busco.busco_report
Expand Down
1 change: 1 addition & 0 deletions workflows/theiaprok/wf_theiaprok_fasta.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -422,6 +422,7 @@ workflow theiaprok_fasta {
Float quast_gc_percent = quast.gc_percent
# Assembly QC - BUSCO outputs
String busco_version = busco.busco_version
String busco_docker = busco.busco_docker
String busco_database = busco.busco_database
String busco_results = busco.busco_results
File? busco_report = busco.busco_report
Expand Down
1 change: 1 addition & 0 deletions workflows/theiaprok/wf_theiaprok_illumina_pe.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -640,6 +640,7 @@ workflow theiaprok_illumina_pe {
Float? est_coverage_clean = cg_pipeline_clean.est_coverage
# Assembly QC - busco outputs
String? busco_version = busco.busco_version
String? busco_docker = busco.busco_docker
String? busco_database = busco.busco_database
String? busco_results = busco.busco_results
File? busco_report = busco.busco_report
Expand Down
1 change: 1 addition & 0 deletions workflows/theiaprok/wf_theiaprok_illumina_se.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -588,6 +588,7 @@ workflow theiaprok_illumina_se {
Float? est_coverage_clean = cg_pipeline_clean.est_coverage
# Assembly QC - busco outputs
String? busco_version = busco.busco_version
String? busco_docker = busco.busco_docker
String? busco_database = busco.busco_database
String? busco_results = busco.busco_results
File? busco_report = busco.busco_report
Expand Down
1 change: 1 addition & 0 deletions workflows/theiaprok/wf_theiaprok_ont.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -542,6 +542,7 @@ workflow theiaprok_ont {
Float? est_coverage_clean = nanoplot_clean.est_coverage
# Assembly QC - busco outputs
String? busco_version = busco.busco_version
String? busco_docker = busco.busco_docker
String? busco_database = busco.busco_database
String? busco_results = busco.busco_results
File? busco_report = busco.busco_report
Expand Down