diff --git a/.github/ISSUE_TEMPLATE/bug-report.md b/.github/ISSUE_TEMPLATE/bug-report.md new file mode 100644 index 000000000..6c432dc80 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug-report.md @@ -0,0 +1,38 @@ +--- +name: Bug Report +about: Tell us about a bug +title: '' +labels: '' +assignees: '' + +--- + +:bug: + +### :pencil: Describe the Issue + + + +### :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 + + + +### :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 + + 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/tasks/taxon_id/task_kraken2.wdl b/tasks/taxon_id/task_kraken2.wdl index 33822cf6c..cfd3e5d0b 100644 --- a/tasks/taxon_id/task_kraken2.wdl +++ b/tasks/taxon_id/task_kraken2.wdl @@ -111,6 +111,15 @@ task kraken2_standalone { percentage_human=$(grep "Homo sapiens" ~{samplename}.report.txt | cut -f 1) if [ -z "$percentage_human" ] ; then percentage_human="0" ; fi echo $percentage_human | tee PERCENT_HUMAN + + # 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") @@ -119,10 +128,10 @@ 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" Float kraken2_percent_human = read_float("PERCENT_HUMAN") + File? kraken2_classified_read2 = "~{samplename}.classified_2.fastq.gz" } runtime { docker: "~{docker}" 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/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml index f9a83f8c9..2dbf2acf9 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 eedf96090..6ecc1e0cd 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 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