From 8dd14fb8959345bcf3f79130edf3ac355c7a3e88 Mon Sep 17 00:00:00 2001 From: Dave Rogers Date: Thu, 9 Jan 2025 00:26:14 -0800 Subject: [PATCH 1/4] feat: add workflow and assemblies yml files first pass (#206) --- files/source/assemblies.yml | 73 +++++++++++++++++++++++++++++++ files/source/galaxy_workflows.yml | 15 +++++++ 2 files changed, 88 insertions(+) create mode 100644 files/source/assemblies.yml create mode 100644 files/source/galaxy_workflows.yml diff --git a/files/source/assemblies.yml b/files/source/assemblies.yml new file mode 100644 index 0000000..05026f4 --- /dev/null +++ b/files/source/assemblies.yml @@ -0,0 +1,73 @@ +assemblies: + - accession: GCF_000002765.6 + ploidy: haploid + source: plasmodb.org + - accession: GCF_000002415.2 + ploidy: haploid + ncbi_dataset: true + - accession: GCA_900093555.2 + ploidy: haploid + source: plasmodb.org + - accession: GCF_900002385.2 + ploidy: haploid + source: plasmodb.org + - accession: GCF_900681995.1 + ploidy: haploid + source: plasmodb.org + - accession: GCF_016801865.2 + ploidy: diploid + source: vectorbase.org + - accession: GCF_015732765.1 + ploidy: diploid + source: vectorbase.org + - accession: GCF_943734735.2 + ploidy: diploid + ncbi_dataset: true + - accession: GCF_000005575.2 + ploidy: diploid + source: vectorbase.org + - accession: GCF_000006565.2 + ploidy: haploid + source: toxodb.org + - accession: GCF_000195955.2 + ploidy: haploid + - accession: GCF_018416015.2 + ploidy: haploid + ncbi_dataset: true + - accession: GCA_000170175.2 + ploidy: haploid + source: fungidb.org + - accession: GCF_000149335.2 + ploidy: haploid + source: fungidb.org + - accession: GCF_000209065.1 + ploidy: diploid + source: tritrypdb.org + - accession: GCF_000002445.2 + ploidy: diploid + source: tritrypdb.org + - accession: GCF_000002725.2 + ploidy: diploid + source: tritrypdb.org + - accession: GCF_000227135.1 + ploidy: diploid + source: tritrypdb.org + - accession: GCF_000002845.2 + ploidy: diploid + source: tritrypdb.org + - accession: GCF_009858895.2 + ploidy: haploid + - accession: GCF_000857045.1 + ploidy: haploid + - accession: GCF_000002655.1 + ploidy: haploid + source: fungidb.org + - accession: GCF_000182965.3 + ploidy: diploid + source: fungidb.org + - accession: GCF_000091045.1 + ploidy: haploid + ncbi_dataset: true + - accession: GCA_000149245.3 + ploidy: haploid + source: fungidb.org diff --git a/files/source/galaxy_workflows.yml b/files/source/galaxy_workflows.yml new file mode 100644 index 0000000..351f06f --- /dev/null +++ b/files/source/galaxy_workflows.yml @@ -0,0 +1,15 @@ +workflows: + - trs_id: "https://dockstore.org/api/ga4gh/trs/v2/tools/#workflow/github.com/iwc-workflows/rnaseq-pe/main/versions/v0.9" + type: "REGULATION" + description: "Workflows for the analysis of ChIP-seq, ATAC-Seq, and beyond." + ploidy: "any" + + - trs_id: "https://dockstore.org/api/ga4gh/trs/v2/tools/#workflow/github.com/iwc-workflows/chipseq-pe/main/versions/v0.12" + type: "TRANSCRIPTOMICS" + description: "Analyze bulk or single-cell RNA seq data using a variety of approaches." + ploidy: "any" + + - trs_id: "https://dockstore.org/api/ga4gh/trs/v2/tools/#workflow/github.com/iwc-workflows/haploid-variant-calling-wgs-pe/main/versions/v0.1" + type: "VARIANT_CALLING" + description: "Identify nucleotide polymorphisms and short indels from Illumina and Element data." + ploidy: "haploid" From 568f5c52eca7ce365b8def4ef16e4caf1f030622 Mon Sep 17 00:00:00 2001 From: Dave Rogers Date: Thu, 9 Jan 2025 00:44:54 -0800 Subject: [PATCH 2/4] feat: added stub outbreaks.yml (#206) --- files/source/outbreaks.yml | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 files/source/outbreaks.yml diff --git a/files/source/outbreaks.yml b/files/source/outbreaks.yml new file mode 100644 index 0000000..74e1258 --- /dev/null +++ b/files/source/outbreaks.yml @@ -0,0 +1,7 @@ +outbreaks: + - tax_id: 2697049 + name: "SARS-CoV-2" + description: "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus responsible for the COVID-19 pandemic." + - tax_id: 10244 + name: "Mpoxvirus" + description: "Monkeypox virus is a member of the Orthopoxvirus genus in the family Poxviridae." From 672add6f643d5f3306437671f23509eeec8a5a3c Mon Sep 17 00:00:00 2001 From: Danielle Callan Date: Thu, 9 Jan 2025 14:25:34 -0500 Subject: [PATCH 3/4] feat: cleaning up and adding more workflows (#206) --- files/source/assemblies.yml | 22 ++++++++++++++++++ files/source/galaxy_workflows.yml | 37 ++++++++++++++++++++++++++++--- 2 files changed, 56 insertions(+), 3 deletions(-) diff --git a/files/source/assemblies.yml b/files/source/assemblies.yml index 05026f4..7576f57 100644 --- a/files/source/assemblies.yml +++ b/files/source/assemblies.yml @@ -1,70 +1,92 @@ assemblies: + # plasmodium falciparum - accession: GCF_000002765.6 ploidy: haploid source: plasmodb.org + # plasmodium vivax - accession: GCF_000002415.2 ploidy: haploid ncbi_dataset: true - accession: GCA_900093555.2 ploidy: haploid source: plasmodb.org + # plasmodium yoelii - accession: GCF_900002385.2 ploidy: haploid source: plasmodb.org + # plasmodium vinckei - accession: GCF_900681995.1 ploidy: haploid source: plasmodb.org + # culex p. pallens - accession: GCF_016801865.2 ploidy: diploid source: vectorbase.org + # culex p. quinquefasciatus - accession: GCF_015732765.1 ploidy: diploid source: vectorbase.org + # anopheles gambiae - accession: GCF_943734735.2 ploidy: diploid ncbi_dataset: true - accession: GCF_000005575.2 ploidy: diploid source: vectorbase.org + # toxoplasma gondii - accession: GCF_000006565.2 ploidy: haploid source: toxodb.org + # mycobacterium tuberculosis - accession: GCF_000195955.2 ploidy: haploid + # coccidioides posadasii - accession: GCF_018416015.2 ploidy: haploid ncbi_dataset: true - accession: GCA_000170175.2 ploidy: haploid source: fungidb.org + # coccidioides immitis - accession: GCF_000149335.2 ploidy: haploid source: fungidb.org + # trypanosoma cruzi - accession: GCF_000209065.1 ploidy: diploid source: tritrypdb.org + # trypanosoma brucei - accession: GCF_000002445.2 ploidy: diploid source: tritrypdb.org + # leishmania major - accession: GCF_000002725.2 ploidy: diploid source: tritrypdb.org + # leishmania donovani - accession: GCF_000227135.1 ploidy: diploid source: tritrypdb.org + # leishmania braziliensis + # danielle's favorite - accession: GCF_000002845.2 ploidy: diploid source: tritrypdb.org + # covid - accession: GCF_009858895.2 ploidy: haploid + # mpox - accession: GCF_000857045.1 ploidy: haploid + # aspergillus fumigatus - accession: GCF_000002655.1 ploidy: haploid source: fungidb.org + # candida albicans - accession: GCF_000182965.3 ploidy: diploid source: fungidb.org + # crypococcus neoformans - accession: GCF_000091045.1 ploidy: haploid ncbi_dataset: true diff --git a/files/source/galaxy_workflows.yml b/files/source/galaxy_workflows.yml index 351f06f..a39efc8 100644 --- a/files/source/galaxy_workflows.yml +++ b/files/source/galaxy_workflows.yml @@ -1,15 +1,46 @@ workflows: - - trs_id: "https://dockstore.org/api/ga4gh/trs/v2/tools/#workflow/github.com/iwc-workflows/rnaseq-pe/main/versions/v0.9" + # this list of workflows and their annotations are a wip and will be updated as i learn more + # about their status and the tools used, etc. + - trs_id: "#workflow/github.com/iwc-workflows/chipseq-pe/main" type: "REGULATION" description: "Workflows for the analysis of ChIP-seq, ATAC-Seq, and beyond." ploidy: "any" - - trs_id: "https://dockstore.org/api/ga4gh/trs/v2/tools/#workflow/github.com/iwc-workflows/chipseq-pe/main/versions/v0.12" + - trs_id: "#workflow/github.com/iwc-workflows/chipseq-sr/main" + type: "REGULATION" + description: "Workflows for the analysis of ChIP-seq, ATAC-Seq, and beyond." + ploidy: "any" + + - trs_id: "#workflow/github.com/iwc-workflows/rnaseq-pe/main" + type: "TRANSCRIPTOMICS" + description: "Analyze bulk or single-cell RNA seq data using a variety of approaches." + ploidy: "any" + + - trs_id: "#workflow/github.com/iwc-workflows/rnaseq-sr/main" type: "TRANSCRIPTOMICS" description: "Analyze bulk or single-cell RNA seq data using a variety of approaches." ploidy: "any" - - trs_id: "https://dockstore.org/api/ga4gh/trs/v2/tools/#workflow/github.com/iwc-workflows/haploid-variant-calling-wgs-pe/main/versions/v0.1" + - trs_id: "#workflow/github.com/iwc-workflows/haploid-variant-calling-wgs-pe/main" type: "VARIANT_CALLING" description: "Identify nucleotide polymorphisms and short indels from Illumina and Element data." ploidy: "haploid" + + # im starting to wonder looking at this if the default for ploidy shouldnt be any + # maybe it could be multivalued [haploid, diploid].. might not matter depending on ui + - trs_id: "#workflow/github.com/iwc-workflows/generic-variant-calling-wgs-pe/main" + type: "VARIANT_CALLING" + description: "Identify nucleotide polymorphisms and short indels from Illumina and Element data." + ploidy: "any" + + - trs_id: "#workflow/github.com/iwc-workflows/assembly-with-flye/main" + type: "ASSEMBLY" + description: "Best practices for assembly of prokaryotic and eukaryotic genomes sequenced with a variety of technologies." + ploidy: "any" + + # idk yet what makes this specific to bacteria, or if it can be easily generalized + # but we may need a new annotation once i figure it out + - trs_id: "#workflow/github.com/iwc-workflows/bacterial-genome-assembly/main" + type: "ASSEMBLY" + description: "Best practices for assembly of prokaryotic and eukaryotic genomes sequenced with a variety of technologies." + ploidy: "any" From 718e2d9093018e686e6b881019037393462d0def Mon Sep 17 00:00:00 2001 From: Dave Rogers Date: Wed, 15 Jan 2025 14:14:45 -0800 Subject: [PATCH 4/4] feat: update outbreaks.yml example (#206) --- files/source/outbreaks.yml | 33 +++++++++++++++++++++++++++------ 1 file changed, 27 insertions(+), 6 deletions(-) diff --git a/files/source/outbreaks.yml b/files/source/outbreaks.yml index 74e1258..d2dd65f 100644 --- a/files/source/outbreaks.yml +++ b/files/source/outbreaks.yml @@ -1,7 +1,28 @@ outbreaks: - - tax_id: 2697049 - name: "SARS-CoV-2" - description: "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus responsible for the COVID-19 pandemic." - - tax_id: 10244 - name: "Mpoxvirus" - description: "Monkeypox virus is a member of the Orthopoxvirus genus in the family Poxviridae." + - outbreak: + tax_id: 2697049 + resources: + - resource: + title: "Coronavirus: Update Related to the Current Outbreak of COVID-19" + url: "https://pmc.ncbi.nlm.nih.gov/articles/PMC7139198/" + - resource: + title: "COVID-19 Pandemic: A Review of the Global Response" + url: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7162758/" + - resource: + title: "The Impact of COVID-19 on Public Health" + url: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7275854/" + - resource: + title: "COVID-19: Epidemiology, Virology, and Clinical Features" + url: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159299/" + - outbreak: + tax_id: 10244 + resources: + - resource: + title: "Mpox Virus: Understanding the Outbreak" + url: "https://example.com/mpox-outbreak" + - resource: + title: "Mpox Virus: Symptoms and Treatment" + url: "https://example.com/mpox-symptoms-treatment" + - resource: + title: "Global Response to the Mpox Outbreak" + url: "https://example.com/global-response-mpox"