From 8e0a6c359345a2b2bfecdfc986f4bd8a49d43155 Mon Sep 17 00:00:00 2001 From: Sage Wright <40403716+sage-wright@users.noreply.github.com> Date: Tue, 29 Aug 2023 10:56:44 -0400 Subject: [PATCH 1/5] Create issue templates --- .github/ISSUE_TEMPLATE/bug-report.md | 32 +++++++++++++++++++++++ .github/ISSUE_TEMPLATE/feature-request.md | 26 ++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 .github/ISSUE_TEMPLATE/bug-report.md create mode 100644 .github/ISSUE_TEMPLATE/feature-request.md diff --git a/.github/ISSUE_TEMPLATE/bug-report.md b/.github/ISSUE_TEMPLATE/bug-report.md new file mode 100644 index 000000000..b4be0fb98 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug-report.md @@ -0,0 +1,32 @@ +--- +name: Bug Report +about: Tell us about a bug +title: '' +labels: '' +assignees: '' + +--- + +:bug: + +### :pencil: Describe the Issue + + + +### :repeat: How to Reproduce + + + +### :fishing_pole_and_fish: Expected Behavior + + + +### :floppy_disk: Version Information + + + +### :information_source: Additional Information + + diff --git a/.github/ISSUE_TEMPLATE/feature-request.md b/.github/ISSUE_TEMPLATE/feature-request.md new file mode 100644 index 000000000..6db95cf8c --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature-request.md @@ -0,0 +1,26 @@ +--- +name: Feature Request +about: Tell us about what you need +title: '' +labels: '' +assignees: '' + +--- + +:cool: + +### :pushpin: Explain the Request + + + +### :books: Context + + + +### :chart_with_upwards_trend: Desired Behavior + + + +### :information_source: Additional Information + + From 435e6565a14fc7a16272a3f0736bcab410491397 Mon Sep 17 00:00:00 2001 From: kapsakcj Date: Tue, 29 Aug 2023 15:30:35 -0400 Subject: [PATCH 2/5] added some helpful questions to bug report template --- .github/ISSUE_TEMPLATE/bug-report.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.github/ISSUE_TEMPLATE/bug-report.md b/.github/ISSUE_TEMPLATE/bug-report.md index b4be0fb98..6c432dc80 100644 --- a/.github/ISSUE_TEMPLATE/bug-report.md +++ b/.github/ISSUE_TEMPLATE/bug-report.md @@ -15,6 +15,12 @@ assignees: '' ### :repeat: How to Reproduce +- Was this run on the Terra platform? + - Terra on GCP or Azure? +- Or were the workflows run locally using `miniwdl` or `cromwell`? + - **What was the exact command was used to launch the workflow?** +- If possible, we may ask you to share your Terra workspace with us. Usually READER access is sufficient, but we may ask for WRITER access if we need to make changes to the workspace to reproduce the issue. + ### :fishing_pole_and_fish: Expected Behavior From 3a8019c1cc82d75a49f47b6b0548790b2fcf2128 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?In=C3=AAs=20Mendes?= Date: Thu, 14 Sep 2023 18:55:50 +0100 Subject: [PATCH 3/5] Fix kraken2_standalone for SE data (#178) * fix kraken2_standalone for SE data * update md5sum --- tasks/taxon_id/task_kraken2.wdl | 12 ++++++++++-- .../theiaprok/test_wf_theiaprok_illumina_pe.yml | 2 +- .../theiaprok/test_wf_theiaprok_illumina_se.yml | 2 +- 3 files changed, 12 insertions(+), 4 deletions(-) diff --git a/tasks/taxon_id/task_kraken2.wdl b/tasks/taxon_id/task_kraken2.wdl index bcf5f25b9..8a1579b17 100644 --- a/tasks/taxon_id/task_kraken2.wdl +++ b/tasks/taxon_id/task_kraken2.wdl @@ -108,6 +108,14 @@ task kraken2_standalone { gzip *.fastq gzip ~{samplename}.classifiedreads.txt + # rename classified and unclassified read files if SE + if [ -e "~{samplename}.classified#.fastq.gz" ]; then + mv "~{samplename}.classified#.fastq.gz" ~{samplename}.classified_1.fastq.gz + fi + if [ -e "~{samplename}.unclassified#.fastq.gz" ]; then + mv "~{samplename}.unclassified#.fastq.gz" ~{samplename}.unclassified_1.fastq.gz + fi + >>> output { String kraken2_version = read_string("VERSION") @@ -116,9 +124,9 @@ task kraken2_standalone { File kraken2_report = "~{samplename}.report.txt" File kraken2_classified_report = "~{samplename}.classifiedreads.txt.gz" File kraken2_unclassified_read1 = "~{samplename}.unclassified_1.fastq.gz" - File kraken2_unclassified_read2 = "~{samplename}.unclassified_2.fastq.gz" + File? kraken2_unclassified_read2 = "~{samplename}.unclassified_2.fastq.gz" File kraken2_classified_read1 = "~{samplename}.classified_1.fastq.gz" - File kraken2_classified_read2 = "~{samplename}.classified_2.fastq.gz" + File? kraken2_classified_read2 = "~{samplename}.classified_2.fastq.gz" } runtime { docker: "~{docker}" diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml index 5fa38e056..7154a6a28 100644 --- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml +++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml @@ -628,7 +628,7 @@ - path: miniwdl_run/wdl/tasks/taxon_id/task_gambit.wdl md5sum: 08987d952c67c6ff6debf6898af15f9a - path: miniwdl_run/wdl/tasks/taxon_id/task_kraken2.wdl - md5sum: f06823a409a087441c8e70e46f7dfc29 + md5sum: 9d9c266d15130df315ebb60df860cab8 - path: miniwdl_run/wdl/tasks/taxon_id/task_midas.wdl md5sum: 024971d1439dff7d59c0a26a824bd2c6 - path: miniwdl_run/wdl/tasks/utilities/task_broad_terra_tools.wdl diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml index dcb4661b5..6b1a51124 100644 --- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml +++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml @@ -596,7 +596,7 @@ - path: miniwdl_run/wdl/tasks/taxon_id/task_gambit.wdl md5sum: 08987d952c67c6ff6debf6898af15f9a - path: miniwdl_run/wdl/tasks/taxon_id/task_kraken2.wdl - md5sum: f06823a409a087441c8e70e46f7dfc29 + md5sum: 9d9c266d15130df315ebb60df860cab8 - path: miniwdl_run/wdl/tasks/taxon_id/task_midas.wdl md5sum: 024971d1439dff7d59c0a26a824bd2c6 - path: miniwdl_run/wdl/tasks/utilities/task_broad_terra_tools.wdl From 9aa16ba38dbc396856e25d440b6e8cb11bf27e7d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?In=C3=AAs=20Mendes?= Date: Thu, 14 Sep 2023 19:00:46 +0100 Subject: [PATCH 4/5] Patch theiaprok ont - change est_genome_size to Int (#179) * change est_genome_size to Int * change est_genome_size to INT --- tasks/utilities/task_kmc.wdl | 2 +- workflows/theiaprok/wf_theiaprok_ont.wdl | 2 +- workflows/utilities/wf_read_QC_trim_ont.wdl | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/tasks/utilities/task_kmc.wdl b/tasks/utilities/task_kmc.wdl index a8f32be4e..4d62c85a6 100644 --- a/tasks/utilities/task_kmc.wdl +++ b/tasks/utilities/task_kmc.wdl @@ -44,7 +44,7 @@ task kmc { tail -n8 LOG > ~{samplename}_kmer_stats.txt >>> output { - String est_genome_size = read_string("UNIQUE_COUNTED") + Int est_genome_size = read_int("UNIQUE_COUNTED") File kmer_stats = "~{samplename}_kmer_stats.txt" String kmc_version = read_string("VERSION") } diff --git a/workflows/theiaprok/wf_theiaprok_ont.wdl b/workflows/theiaprok/wf_theiaprok_ont.wdl index 06628be0a..6057ddce0 100644 --- a/workflows/theiaprok/wf_theiaprok_ont.wdl +++ b/workflows/theiaprok/wf_theiaprok_ont.wdl @@ -489,7 +489,7 @@ workflow theiaprok_ont { String? nanoplot_version = nanoplot_raw.nanoplot_version String? nanoplot_docker = nanoplot_raw.nanoplot_docker # Read QC - kmc outputs - String? kmc_est_genome_size = read_qc_trim.est_genome_size + Int? kmc_est_genome_size = read_qc_trim.est_genome_size File? kmc_kmer_stats = read_qc_trim.kmc_kmer_stats String? kmc_version = read_qc_trim.kmc_version # Read QC - rasusa outputs diff --git a/workflows/utilities/wf_read_QC_trim_ont.wdl b/workflows/utilities/wf_read_QC_trim_ont.wdl index 779d479c0..c0f361c84 100644 --- a/workflows/utilities/wf_read_QC_trim_ont.wdl +++ b/workflows/utilities/wf_read_QC_trim_ont.wdl @@ -84,7 +84,7 @@ workflow read_QC_trim_ont { } output { # kmc outputs - String est_genome_size = kmc.est_genome_size + Int est_genome_size = kmc.est_genome_size File kmc_kmer_stats = kmc.kmer_stats String kmc_version = kmc.kmc_version From f229903d8d89b7819c469010d5c2ebf427214a92 Mon Sep 17 00:00:00 2001 From: Curtis Kapsak Date: Tue, 19 Sep 2023 14:17:59 -0400 Subject: [PATCH 5/5] plasmidfinder task bugfix and updates (#191) * plasmidfinder task updates: decrease cpus to 2, memory to 8, and disk_size to 50. Also fixed bug with output string of plasmid replicons found. Also made some move commands verbose * update CI --- tasks/gene_typing/task_plasmidfinder.wdl | 14 +++++++------- .../theiaprok/test_wf_theiaprok_illumina_pe.yml | 4 ++-- .../theiaprok/test_wf_theiaprok_illumina_se.yml | 4 ++-- 3 files changed, 11 insertions(+), 11 deletions(-) diff --git a/tasks/gene_typing/task_plasmidfinder.wdl b/tasks/gene_typing/task_plasmidfinder.wdl index b940758ce..d918a3bba 100644 --- a/tasks/gene_typing/task_plasmidfinder.wdl +++ b/tasks/gene_typing/task_plasmidfinder.wdl @@ -4,10 +4,10 @@ task plasmidfinder { input { File assembly String samplename - Int cpu = 8 - Int memory = 16 + Int cpu = 2 + Int memory = 8 String docker = "us-docker.pkg.dev/general-theiagen/staphb/plasmidfinder:2.1.6" - Int disk_size = 100 + Int disk_size = 50 String? database String? database_path String? method_path @@ -41,15 +41,15 @@ task plasmidfinder { if [ ! -f results_tab.tsv ]; then PF="No plasmids detected in database" else - PF="$(tail -n +2 results_tab.tsv | cut -f 2 | sort | uniq -u | paste -s -d, - )" + PF="$(tail -n +2 results_tab.tsv | uniq | cut -f 2 | sort | paste -s -d, - )" if [ "$PF" == "" ]; then PF="No plasmids detected in database" fi fi - echo $PF | tee PLASMIDS + echo "$PF" | tee PLASMIDS - mv results_tab.tsv ~{samplename}_results.tsv - mv Hit_in_genome_seq.fsa ~{samplename}_seqs.fsa + mv -v results_tab.tsv ~{samplename}_results.tsv + mv -v Hit_in_genome_seq.fsa ~{samplename}_seqs.fsa >>> output { diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml index 7154a6a28..5f1ceac9b 100644 --- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml +++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml @@ -264,7 +264,7 @@ - path: miniwdl_run/call-merlin_magic/workflow.log contains: ["wdl", "theiaprok_illumina_pe", "merlin", "done"] - path: miniwdl_run/call-plasmidfinder/command - md5sum: 61f7be9cfd36e3a48585e7f64cbcfe35 + md5sum: 3b70033058bf91c04337e38bfd038b5a - path: miniwdl_run/call-plasmidfinder/inputs.json - path: miniwdl_run/call-plasmidfinder/outputs.json - path: miniwdl_run/call-plasmidfinder/stderr.txt @@ -556,7 +556,7 @@ - path: miniwdl_run/wdl/tasks/gene_typing/task_bakta.wdl md5sum: 0bed8fb60786095843a67b1ad03051dc - path: miniwdl_run/wdl/tasks/gene_typing/task_plasmidfinder.wdl - md5sum: 6ca295b4dcdbe95dd86516ba0a4073f8 + md5sum: 8730e07b1c7ab9d2434a7838ddb1fc72 - path: miniwdl_run/wdl/tasks/gene_typing/task_prokka.wdl md5sum: 8e8423b99d5cd3e92bb89b3c3211d432 - path: miniwdl_run/wdl/tasks/gene_typing/task_resfinder.wdl diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml index 6b1a51124..92d8fbb40 100644 --- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml +++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml @@ -261,7 +261,7 @@ - path: miniwdl_run/call-merlin_magic/workflow.log contains: ["wdl", "theiaprok_illumina_se", "merlin", "done"] - path: miniwdl_run/call-plasmidfinder/command - md5sum: 61f7be9cfd36e3a48585e7f64cbcfe35 + md5sum: 3b70033058bf91c04337e38bfd038b5a - path: miniwdl_run/call-plasmidfinder/inputs.json - path: miniwdl_run/call-plasmidfinder/outputs.json - path: miniwdl_run/call-plasmidfinder/stderr.txt @@ -526,7 +526,7 @@ - path: miniwdl_run/wdl/tasks/gene_typing/task_bakta.wdl md5sum: 0bed8fb60786095843a67b1ad03051dc - path: miniwdl_run/wdl/tasks/gene_typing/task_plasmidfinder.wdl - md5sum: 6ca295b4dcdbe95dd86516ba0a4073f8 + md5sum: 8730e07b1c7ab9d2434a7838ddb1fc72 - path: miniwdl_run/wdl/tasks/gene_typing/task_prokka.wdl md5sum: 8e8423b99d5cd3e92bb89b3c3211d432 - path: miniwdl_run/wdl/tasks/gene_typing/task_resfinder.wdl