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using 'edge' tags for containers, update schema
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-42
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13 files changed

+44
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lines changed

‎containers/darwin/Dockerfile‎

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@@ -1,4 +1,4 @@
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FROM cbrg/darwin:master AS builder
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FROM cbrg/darwin:2025-01-14 AS builder
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RUN apt-get update \
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&& apt-get install -y --no-install-recommends \
@@ -20,7 +20,7 @@ RUN --mount=type=ssh \
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git clone -b nf-convert ${LABGIT}/pyoma && \
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rm -rf OMA/.git browser/.git pyoma/.git
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FROM cbrg/darwin:master AS runtime
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FROM cbrg/darwin:2025-01-14 AS runtime
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RUN apt-get update \
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&& apt-get install -y --no-install-recommends \

‎modules/local/browser_aux/main.nf‎

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process GEN_BROWSER_AUX_FILES {
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label "process_single"
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container "dessimozlab/omabuild:nf-latest"
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container "dessimozlab/omabuild:edge"
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input:
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path db

‎modules/local/cache_builder/main.nf‎

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process GENERATE_JOBS {
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label "process_single"
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container "dessimozlab/omabuild:nf-latest"
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container "dessimozlab/omabuild:edge"
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input:
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path db
@@ -28,7 +28,7 @@ process GENERATE_JOBS {
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process COMPUTE_CACHE {
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label "process_single"
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label "HIGH_IO_ACCESS"
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container "dessimozlab/omabuild:nf-latest"
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container "dessimozlab/omabuild:edge"
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tag "Cache builder ${job_file}"
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input:
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process COMBINE_JOBS {
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label "process_single"
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container "dessimozlab/omabuild:nf-latest"
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container "dessimozlab/omabuild:edge"
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input:
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path(job_res, stageAs: "res???/*")

‎modules/local/darwin_extract/main.nf‎

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process CONVERT_GS {
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tag "Convert GenomeSummaries to JSON format"
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label "process_single"
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container "dessimozlab/omadarwin:nf-latest"
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container "dessimozlab/omadarwin:edge"
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input:
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path genomes
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process CONVERT_PROTEINS {
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tag "Convert Proteins from ${genome.UniProtSpeciesCode} to JSON format"
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label "process_single"
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container "dessimozlab/omadarwin:nf-latest"
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container "dessimozlab/omadarwin:edge"
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input:
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tuple val(genome), path(dbpath), path(subgenome)
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process CONVERT_OMA_GROUPS {
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tag "Extract OMA Groups"
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label "process_single"
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container "dessimozlab/omabuild:nf-latest"
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container "dessimozlab/omabuild:edge"
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input:
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path matrix_file
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process CONVERT_SPLICE_MAP {
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tag "Convert Splicing information to json"
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label "process_single"
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container "dessimozlab/omadarwin:nf-latest"
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container "dessimozlab/omadarwin:edge"
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input:
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path splice_drw
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process CONVERT_TAXONOMY {
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tag "Convert Taxonomy of genomes using omataxonomy"
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label "process_single"
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container "dessimozlab/omabuild:nf-latest"
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container "dessimozlab/omabuild:edge"
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input:
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path gs_tsv

‎modules/local/domains/main.nf‎

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process ADD_DOMAINS {
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label "process_single"
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label "process_medium_memory"
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container "dessimozlab/omabuild:nf-latest"
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container "dessimozlab/omabuild:edge"
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input:
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path database

‎modules/local/edgehog/main.nf‎

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label "single_process"
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label "process_long"
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label "process_high_memory"
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container "dessimozlab/omabuild:edge"
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input:
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path augmented_orthoxml

‎modules/local/go_import/main.nf‎

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process GO_IMPORT {
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label "process_single"
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label "HIGH_IO_ACCESS"
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container "dessimozlab/omabuild:nf-latest"
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container "dessimozlab/omabuild:edge"
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input:
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path xref_db

‎modules/local/h5_combine/main.nf‎

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process COMBINE_HDF {
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label "process_single"
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container "dessimozlab/omabuild:nf-latest"
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container "dessimozlab/omabuild:edge"
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input:
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path h5files

‎modules/local/hdf5import/main.nf‎

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process ADD_GENOMES {
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label "process_single"
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label "process_long"
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container "dessimozlab/omabuild:nf-latest"
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container "dessimozlab/omabuild:edge"
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input:
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path gs_tsv
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process BUILD_SEQINDEX {
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label "process_single"
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label "process_medium_memory"
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container "dessimozlab/omabuild:nf-latest"
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container "dessimozlab/omabuild:edge"
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input:
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process BUILD_HOG_H5 {
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label "process_low"
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label "process_medium_memory"
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container "dessimozlab/omabuild:nf-latest"
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container "dessimozlab/omabuild:edge"
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input:
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process ADD_PAIRWISE_ORTHOLOGS {
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label "process_medium"
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container "dessimozlab/omabuild:nf-latest"
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container "dessimozlab/omabuild:edge"
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input:
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path database
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process COMBINE_H5_FILES {
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label "process_single"
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container "dessimozlab/omabuild:nf-latest"
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container "dessimozlab/omabuild:edge"
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input:
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path input_db, stageAs: 'OmaServer_input.h5'

‎modules/local/hogprop/main.nf‎

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process HOGPROP_COLLECT {
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label "process_single"
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label "process_high_memory"
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container "${workflow.projectDir}/container/omabuild.sif"
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container "dessimozlab/omabuild:edge"
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input:
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path "results/*"

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