From 9a899e861edfd9aed5dcf620a8c861880d967763 Mon Sep 17 00:00:00 2001 From: Zipho Mashologu Date: Mon, 14 Sep 2020 08:48:32 +0200 Subject: [PATCH] bumped up the version with sed --- tb-sample-report-pipeline-plugin/pom.xml | 4 +- .../workflows/0.2.3/irida_workflow.xml | 184 +++++++ .../0.2.3/irida_workflow_structure.ga | 516 ++++++++++++++++++ .../workflows/0.2.3/messages_en.properties | 60 ++ .../src/raw/galaxy_workflow_tb_.ga | 516 ++++++++++++++++++ 5 files changed, 1278 insertions(+), 2 deletions(-) create mode 100644 tb-sample-report-pipeline-plugin/src/main/resources/workflows/0.2.3/irida_workflow.xml create mode 100644 tb-sample-report-pipeline-plugin/src/main/resources/workflows/0.2.3/irida_workflow_structure.ga create mode 100644 tb-sample-report-pipeline-plugin/src/main/resources/workflows/0.2.3/messages_en.properties create mode 100644 tb-sample-report-pipeline-plugin/src/raw/galaxy_workflow_tb_.ga diff --git a/tb-sample-report-pipeline-plugin/pom.xml b/tb-sample-report-pipeline-plugin/pom.xml index 8897dd8..6f6035c 100644 --- a/tb-sample-report-pipeline-plugin/pom.xml +++ b/tb-sample-report-pipeline-plugin/pom.xml @@ -4,13 +4,13 @@ 4.0.0 ca.corefacility.bioinformatics.irida.plugins tb-sample-report-pipeline-plugin - 0.2.2-SNAPSHOT + 0.2.3-SNAPSHOT tb-sample-report-pipeline-plugin ca.corefacility.bioinformatics.irida.plugins.SnippyPipelinePlugin - 0.2.2 + 0.2.3 COMBAT-TB 1.0.0 diff --git a/tb-sample-report-pipeline-plugin/src/main/resources/workflows/0.2.3/irida_workflow.xml b/tb-sample-report-pipeline-plugin/src/main/resources/workflows/0.2.3/irida_workflow.xml new file mode 100644 index 0000000..6ddf20b --- /dev/null +++ b/tb-sample-report-pipeline-plugin/src/main/resources/workflows/0.2.3/irida_workflow.xml @@ -0,0 +1,184 @@ + + + 174a2e3a-409c-49bb-9737-337646801b00 + TBSampleReport + 0.2.3 + VARIANT_CALLING + + sequence_input + reference + true + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+pipeline.title.TBSampleReport=Pipelines - TBSampleReport +workflow.VARIANT_CALLING.description=M. tuberculosis Variant Analysis\n +pipeline.h1.TBSampleReport=TBSampleReport Pipeline +pipeline.parameters.modal-title.tbsamplereport=TBSampleReport Pipeline Parameters +#Tool Parameters - Tool: text_processing - Workflow Step #: 2 +#Mon Sep 14 08:16:49 SAST 2020 +pipeline.parameters.tbsamplereport.text_processing-2-code=AWK Program +pipeline.parameters.tbsamplereport.text_processing-2-name=text_processing-2-name +pipeline.parameters.tbsamplereport.text_processing-2-adv_opts.adv_opts_selector=text_processing-2-adv_opts.adv_opts_selector +#Tool Parameters - Tool: fastqc - Workflow Step #: 3 +#Mon Sep 14 08:16:49 SAST 2020 +pipeline.parameters.tbsamplereport.fastqc-3-chromInfo=fastqc-3-chromInfo +pipeline.parameters.tbsamplereport.fastqc-3-min_length=fastqc-3-min_length +#Tool Parameters - Tool: trimmomatic - Workflow Step #: 4 +#Mon Sep 14 08:16:49 SAST 2020 +pipeline.parameters.tbsamplereport.trimmomatic-4-illuminaclip.do_illuminaclip=Perform initial ILLUMINACLIP step? +pipeline.parameters.tbsamplereport.trimmomatic-4-readtype.single_or_paired=Single-end or paired-end reads? +#Tool Parameters - Tool: snippy - Workflow Step #: 5 +#Mon Sep 14 08:16:49 SAST 2020 +pipeline.parameters.tbsamplereport.snippy-5-adv.minfrac=snippy-5-adv.minfrac +pipeline.parameters.tbsamplereport.snippy-5-adv.mapqual=snippy-5-adv.mapqual +pipeline.parameters.tbsamplereport.snippy-5-reference_source.reference_source_selector=snippy-5-reference_source.reference_source_selector +pipeline.parameters.tbsamplereport.snippy-5-adv.bwaopt=snippy-5-adv.bwaopt +pipeline.parameters.tbsamplereport.snippy-5-adv.rename_cons=snippy-5-adv.rename_cons +pipeline.parameters.tbsamplereport.snippy-5-adv.rgid=snippy-5-adv.rgid +pipeline.parameters.tbsamplereport.snippy-5-adv.mincov=snippy-5-adv.mincov +pipeline.parameters.tbsamplereport.snippy-5-adv.minqual=snippy-5-adv.minqual +pipeline.parameters.tbsamplereport.snippy-5-fastq_input.fastq_input_selector=snippy-5-fastq_input.fastq_input_selector +#Tool Parameters - Tool: snpeff - Workflow Step #: 6 +#Mon Sep 14 08:16:49 SAST 2020 +pipeline.parameters.tbsamplereport.snpeff-6-spliceRegion.setSpliceRegions=snpeff-6-spliceRegion.setSpliceRegions +pipeline.parameters.tbsamplereport.snpeff-6-filter.specificEffects=snpeff-6-filter.specificEffects +pipeline.parameters.tbsamplereport.snpeff-6-snpDb.reg_section.regulation=snpeff-6-snpDb.reg_section.regulation +pipeline.parameters.tbsamplereport.snpeff-6-outputConditional.outputFormat=snpeff-6-outputConditional.outputFormat +pipeline.parameters.tbsamplereport.snpeff-6-inputFormat=snpeff-6-inputFormat +pipeline.parameters.tbsamplereport.snpeff-6-snpDb.genomeVersion=snpeff-6-snpDb.genomeVersion +pipeline.parameters.tbsamplereport.snpeff-6-snpDb.genomeSrc=snpeff-6-snpDb.genomeSrc +pipeline.parameters.tbsamplereport.snpeff-6-chr=snpeff-6-chr +pipeline.parameters.tbsamplereport.snpeff-6-offset=snpeff-6-offset +#Tool Parameters - Tool: tbprofiler - Workflow Step #: 7 +#Mon Sep 14 08:16:49 SAST 2020 +pipeline.parameters.tbsamplereport.tbprofiler-7-fastq_or_bam.input_select=tbprofiler-7-fastq_or_bam.input_select +pipeline.parameters.tbsamplereport.tbprofiler-7-advanced.min_allele_freq_reporting=tbprofiler-7-advanced.min_allele_freq_reporting +pipeline.parameters.tbsamplereport.tbprofiler-7-advanced.mapper=tbprofiler-7-advanced.mapper +pipeline.parameters.tbsamplereport.tbprofiler-7-advanced.min_allele_freq=tbprofiler-7-advanced.min_allele_freq +pipeline.parameters.tbsamplereport.tbprofiler-7-output_format=tbprofiler-7-output_format +pipeline.parameters.tbsamplereport.tbprofiler-7-platform=tbprofiler-7-platform +pipeline.parameters.tbsamplereport.tbprofiler-7-chromInfo=tbprofiler-7-chromInfo +pipeline.parameters.tbsamplereport.tbprofiler-7-advanced.min_depth=tbprofiler-7-advanced.min_depth 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