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Use Anthropic Claude 3 Haiku to generate topics via AWS Bedrock #503
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<github.url>scm:git:git@github.com:dockstore/dockstore-support.git</github.url> | ||
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding> | ||
<dockstore-core.version>1.16.0-alpha.16</dockstore-core.version> | ||
<dockstore-core.version>1.16.0-SNAPSHOT</dockstore-core.version> | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Probably should be versioned, I think you can use a dated snapshot in a pinch
but I haven't tried it yet There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Yes, I'll update this once I create a new webservice tag 🙂 |
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<maven-surefire.version>3.0.0-M5</maven-surefire.version> | ||
<maven-failsafe.version>2.22.2</maven-failsafe.version> | ||
<skipTests>false</skipTests> | ||
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trsId,version,descriptorUrl,descriptorChecksum,isTruncated,promptTokens,completionTokens,cost,finishReason,aiTopic | ||
"#workflow/github.com/iwc-workflows/sars-cov-2-pe-illumina-artic-variant-calling/COVID-19-PE-ARTIC-ILLUMINA",main,https://raw.githubusercontent.com/iwc-workflows/sars-cov-2-pe-illumina-artic-variant-calling/main//pe-artic-variation.ga,dcc2761eb35156d7d09479112daf089439774fc29938f02cb6ee8cda87906758,false,24595,43,0.0062025,end_turn,"Trim ARTIC primer sequences, realign reads, call and filter variants, annotate variants, and apply a strand-bias soft filter to the final annotated variants." | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. How come some of the verbs have I'd like it if they were all the same, but that's probably just me and probably isn't worth the effort and/or may not even make sense. There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Could be easy to fix by adding a description of the tense to the prompt, ala
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"#workflow/github.com/iwc-workflows/sars-cov-2-variation-reporting/COVID-19-VARIATION-REPORTING",main,https://raw.githubusercontent.com/iwc-workflows/sars-cov-2-variation-reporting/main//variation-reporting.ga,2dce46106d669248d5858b56269c9cbc26057acfdb121f693dd6321d0350105c,false,24503,48,0.00618575,end_turn,"Filters and extracts variants from a VCF dataset, generates tabular lists of variants by Samples and by Variant, and creates an overview plot of variants and their allele-frequencies." | ||
"#workflow/github.com/iwc-workflows/sars-cov-2-ont-artic-variant-calling/COVID-19-ARTIC-ONT",main,https://raw.githubusercontent.com/iwc-workflows/sars-cov-2-ont-artic-variant-calling/main//ont-artic-variation.ga,03c9318d50df9a3c2d725da77f9a175ce7eb78e264cc4a40fa17d48a99dd124b,false,20290,57,0.00514375,end_turn,"Perform read filtering, mapping, primer trimming, variant calling, and annotation on ONT-sequenced ARTIC data using tools like fastp, minimap2, ivar, medaka, and SnpEff." | ||
"#workflow/github.com/iwc-workflows/sars-cov-2-pe-illumina-wgs-variant-calling/COVID-19-PE-WGS-ILLUMINA",main,https://raw.githubusercontent.com/iwc-workflows/sars-cov-2-pe-illumina-wgs-variant-calling/main//pe-wgs-variation.ga,f2357986dd72af73efb2b8110f0f08f6f715017518498edda61d50d23b2e560f,false,11352,48,0.0028980000000000004,end_turn,"Perform paired-end read mapping with bwa-mem, deduplicate and realign the reads, and then call and annotate variants using lofreq and SnpEff." | ||
"#workflow/github.com/iwc-workflows/sars-cov-2-se-illumina-wgs-variant-calling/COVID-19-SE-WGS-ILLUMINA",main,https://raw.githubusercontent.com/iwc-workflows/sars-cov-2-se-illumina-wgs-variant-calling/main//se-wgs-variation.ga,89993f9570eebd53983cdf4f8e4e0f44631f536e855b2e0741f4a5b907858e8d,false,9521,57,0.0024515000000000006,end_turn,"Perform single-end read mapping with Bowtie2, mark duplicates with Picard, realign reads with LoFreq, call variants with LoFreq, and annotate variants with SnpEff." | ||
"#workflow/github.com/iwc-workflows/sars-cov-2-consensus-from-variation/COVID-19-CONSENSUS-CONSTRUCTION",main,https://raw.githubusercontent.com/iwc-workflows/sars-cov-2-consensus-from-variation/main//consensus-from-variation.ga,cb8acce2a1b0d059b117ae3737307be82e81807dad3efcbfe6c8f6a09cbd2798,false,15395,45,0.003905,end_turn,"Build a consensus sequence from FILTER PASS variants with intrasample allele-frequency above a configurable consensus threshold, hard-mask regions with low coverage, and ambiguous sites." | ||
"#workflow/github.com/iwc-workflows/sars-cov-2-pe-illumina-artic-ivar-analysis/SARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE",main,https://raw.githubusercontent.com/iwc-workflows/sars-cov-2-pe-illumina-artic-ivar-analysis/main//pe-wgs-ivar-analysis.ga,11e9e375b01f1a5b33fb64b184798bc6e46181201a255cb23147a7f021007864,false,13894,49,0.00353475,end_turn,"Find and annotate variants in ampliconic SARS-CoV-2 Illumina sequencing data, classify samples with pangolin and nextclade, and generate a quality control report." | ||
"#workflow/github.com/iwc-workflows/parallel-accession-download/main",main,https://raw.githubusercontent.com/iwc-workflows/parallel-accession-download/main//parallel-accession-download.ga,3e9aee6218674651a981b3437b9ca8ec294ff492984b153db0526989e716e674,false,3629,39,9.56E-4,end_turn,"Downloads fastq files for sequencing run accessions provided in a text file using fasterq-dump, creating one job per listed run accession." | ||
"#workflow/github.com/nf-core/rnaseq",1.4.2,https://raw.githubusercontent.com/nf-core/rnaseq/1.4.2//main.nf,0d0db0adf13e907e33e44b1357486cf57747ad78c3a5e31f187919d844530fe9,false,24811,32,0.00624275,end_turn,"Trim the raw reads, align them to the reference genome, perform quality control analysis, and quantify gene expression." | ||
"#workflow/github.com/nf-core/vipr",master,https://raw.githubusercontent.com/nf-core/vipr/master//main.nf,a8b50e8afa5730e6ede16e4588cec2f03c3ae881385daed22edb3e8376af5793,false,4734,78,0.001281,end_turn,"Execute the ViPR workflow, which performs viral amplicon/enrichment analysis and intrahost variant calling, starting with trimming and combining read pairs, followed by decontamination, metagenomics classification, assembly, polishing, mapping, variant calling, coverage computation, and finally plotting and preparing the final reference sequence." | ||
"#workflow/github.com/nf-core/methylseq",1.4,https://raw.githubusercontent.com/nf-core/methylseq/1.4//main.nf,5123fc239af84cd0357ddfe1ca1f582d1f7412f08ecaa9bb2b8f19160bd75cfb,false,16091,46,0.0040802500000000005,end_turn,"Runs the nf-core/methylseq pipeline, which performs alignment, deduplication, methylation extraction, and quality control analysis on bisulfite-sequencing data." | ||
"#workflow/github.com/sevenbridges-openworkflows/Broad-Best-Practice-Data-pre-processing-CWL1.0-workflow-GATK-4.1.0.0/GATK_4_1_0_0_data_pre_processing_workflow",master,https://raw.githubusercontent.com/sevenbridges-openworkflows/Broad-Best-Practice-Data-pre-processing-CWL1.0-workflow-GATK-4.1.0.0/master//broad-best-practice-data-pre-processing-workflow-4-1-0-0_decomposed.cwl,2f87eaf01d47acf0d70b41609d6faba135e11db5ca337f99ae18c614996e387e,false,7682,35,0.0019642500000000003,end_turn,"Perform data pre-processing by aligning to a reference genome, cleaning up the data, and preparing it for variant calling analysis." | ||
"#workflow/github.com/DataBiosphere/topmed-workflows/UM_variant_caller_wdl",1.32.0,https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.32.0/variant-caller/variant-caller-wdl/topmed_freeze3_calling.wdl,03daf00da2f90efd50368bd392f1c32f93b8f48e968dcc573598c9432df5ba21,false,18179,66,0.004627249999999999,end_turn,"Execute the variant caller workflow by creating symlinks for CRAM and CRAI files, configuring the reference files, running the variant detection and merging steps, and optionally performing variant filtering using pedigree information, and finally compressing the output directories into a tar.gz file." | ||
"#workflow/github.com/DataBiosphere/analysis_pipeline_WDL/vcf-to-gds-wdl",v7.1.1,https://raw.githubusercontent.com/DataBiosphere/analysis_pipeline_WDL/v7.1.1/vcf-to-gds/vcf-to-gds.wdl,e92888af471f11793f2c5c4fa7f8da825dfb51603aa6b7f6ecb8d51c9a815fd7,false,3195,41,8.5E-4,end_turn,"Converts VCF files to GDS files, assigns unique variant IDs, and optionally checks the GDS files against the original VCF files." | ||
"#workflow/github.com/DataBiosphere/analysis_pipeline_WDL/ld-pruning-wdl",v7.1.1,https://raw.githubusercontent.com/DataBiosphere/analysis_pipeline_WDL/v7.1.1/ld-pruning/ld-pruning.wdl,eabd52bf3f223c58ad220a418f87f2ec23d2dd91958b61f12066144a8a84a444,false,4460,41,0.0011662500000000002,end_turn,"Calculates linkage disequilibrium, subsets GDS files, merges the subsetted files, and checks the merged file against the inputs." | ||
"#workflow/github.com/AnalysisCommons/genesis_wdl/genesis_GWAS",v1_5,https://raw.githubusercontent.com/AnalysisCommons/genesis_wdl/v1_5//genesis_GWAS.wdl,9c0c50df22bb95869dcc66d77693ecaf702b980878f38feca3ebd75e00eb9fbe,false,4265,43,0.00112,end_turn,"Execute the null model generation, association testing, and summarization tasks to perform a genome-wide association study (GWAS) using the GENESIS biostatistical package." | ||
"#workflow/github.com/aofarrel/covstats-wdl",master,https://raw.githubusercontent.com/aofarrel/covstats-wdl/master/covstats/covstats.wdl,49dec26c695bbb88e0e1198e04c6857f497c80b8b59f8bd86377eaf76ee74a4a,false,2532,42,6.855E-4,end_turn,"Perform read length and coverage analysis on input BAM/CRAM files, generate a report summarizing the results, and handle various file types and runtime configurations." | ||
"#workflow/github.com/broadinstitute/warp/Optimus",aa-PD2413,https://raw.githubusercontent.com/broadinstitute/warp/aa-PD2413/pipelines/skylab/optimus/Optimus.wdl,fb1b9fbd4be73e7210dec444d446c7405afcbcb11f9030391b5e63dd9defe4b6,false,3305,66,9.0875E-4,end_turn,"Imports necessary WDL workflows, defines input parameters, performs input checks, splits FASTQ files, aligns reads, merges BAM files, calculates gene and cell metrics, generates sparse count matrix, runs EmptyDrops, and produces an H5AD output file." | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. "Imports necessary WDL workflows" |
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"#workflow/github.com/theiagen/terra_utilities/Concatenate_Column_Content",v1.4.1,https://raw.githubusercontent.com/theiagen/terra_utilities/v1.4.1/workflows/wf_cat_column.wdl,e080a455cb741c152c056e55af55cb42b2b3b46e24cb7185c2e1a6f1b74389bc,false,225,33,9.750000000000001E-5,end_turn,"Import task files, concatenate column content, capture versioning, and output the concatenated files and versioning details." | ||
"#workflow/github.com/gatk-workflows/seq-format-conversion/BAM-to-Unmapped-BAM",3.0.0,https://raw.githubusercontent.com/gatk-workflows/seq-format-conversion/3.0.0//bam-to-unmapped-bams.wdl,d75de73b26fd49d71a29e4709f77c4decb2b51209d169c1b3fa6fa427f53dd04,false,1266,43,3.7025E-4,end_turn,"Converts a BAM file into unmapped BAMs by reverting the BAM, sorting the unmapped BAMs, and outputting the sorted unmapped BAMs." | ||
"#notebook/github.com/denis-yuen/test-notebooks/ibm-tax-maps",0.2,https://raw.githubusercontent.com/denis-yuen/test-notebooks/0.2/ibm-et/jupyter-samples/tax-maps/Interactive_Data_Maps.ipynb,7ffefdbf8c4ab6333b9ad78c6b811365365e2ae433bca2acf261cc1209c59027,false,107540,42,0.026937500000000003,end_turn,"This notebook analyzes state tax data from the US Census Bureau, creates interactive maps to visualize the data, and provides insights into the tax revenue collected by different states." | ||
quay.io/pancancer/pcawg-sanger-cgp-workflow,2.1.0,https://raw.githubusercontent.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/2.1.0//Dockstore.cwl,5eb9e182fc2e313606a9445604a4b47e0546ed17a641448da12fcc0371ead3d8,false,2573,57,7.145000000000001E-4,end_turn,Execute the Seqware-Sanger-Somatic-Workflow command-line tool to perform somatic variant calling on tumor and normal whole-genome sequencing data using the PCAWG Sanger variant calling workflow. | ||
github.com/dockstore/dockstore-tool-bamstats/bamstats_sort_cwl,1.25-9,https://raw.githubusercontent.com/dockstore/dockstore-tool-bamstats/1.25-9//bamstats_sort.cwl,1fd7d8637cb91e031a6db604898f5728e51f4591bf4acfbb75ecefd0bfda3448,false,426,37,1.5275E-4,end_turn,Utilize the commandlinetool to execute the sort command within a Docker container and generate a sorted file based on the specified key positions. |
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Is this spurious or does it relate to the ai topics somehow?
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Think this was a side-effect of a necessary AWS SDK upgrade
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I should've commented in this PR as well, but here's the reason why this changed: dockstore/dockstore#6003 (comment)