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Merge branch 'rel-1.3.1' into release
# Conflicts: # modules/local/browser_aux/main.nf # modules/local/cache_builder/main.nf # modules/local/cath_tools/assign_cath_superfamilies/main.nf # modules/local/darwin_extract/main.nf # modules/local/domains/main.nf # modules/local/edgehog/main.nf # modules/local/fastoma_extract/main.nf # modules/local/fingerprints/main.nf # modules/local/go_import/main.nf # modules/local/h5_combine/main.nf # modules/local/hdf5import/main.nf # modules/local/hogprofile/main.nf # modules/local/hogprop/main.nf # modules/local/keywords/main.nf # modules/local/xref_fetch/main.nf # nextflow.config
2 parents 847bcda + 0114773 commit 7ffb5d6

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‎config/base.config‎

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@@ -58,4 +58,19 @@ process {
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errorStrategy = 'retry'
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maxRetries = 2
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}
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// requirements for SeqIndex based on technical considerations
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withName: '.*:BUILD_SEQINDEX' {
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cpus = { 1 }
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memory = { 800.MB + (meta.nr_of_amino_acids * 24.B) * ((task.attempt + 1) / 2) }
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// time ~ 30sec * TotAA[MB]*log(TotAA[MB])
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time = { 1.min * (0.5 * meta.nr_of_amino_acids / Math.pow(2,20) * Math.log(meta.nr_of_amino_acids / Math.pow(2, 20)) + 10) * task.attempt }
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}
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withName: '.*:BUILD_HOG_H5'{
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cpus = { 1 }
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memory = { 500.MB + 6.B * orthoxml.size() * task.attempt }
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time = { 1.min * (Math.ceil( meta.nr_of_genomes / 3 ) + 10) * task.attempt }
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}
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}

‎config/sib_hpc.config‎

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@@ -2,7 +2,7 @@
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process {
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module = ["singularityce"] // set to correct singularity module to be loaded in sib hpc
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// Node options
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resourceLimits = [ cpus: 96, memory: 350.GB, time: 72.h ]
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resourceLimits = [ cpus: 96, memory: 650.GB, time: 72.h ]
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withLabel: HIGH_IO_ACCESS {
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stageInMode = "copy"

‎containers/oma/Pipfile.lock‎

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‎modules.json‎

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@@ -12,8 +12,9 @@
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},
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"hmmer/hmmsearch": {
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"branch": "master",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["modules"]
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/hmmer/hmmsearch/hmmer-hmmsearch.diff"
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},
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"untar": {
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"branch": "master",

‎modules/local/browser_aux/main.nf‎

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@@ -1,6 +1,6 @@
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process GEN_BROWSER_AUX_FILES {
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label "process_single"
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container "docker.io/dessimozlab/omabuild:1.3.0"
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container "docker.io/dessimozlab/omabuild:1.3.1"
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input:
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path db
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touch genomes.json
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touch speciestree.nwk speciestree.phyloxml
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"""
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}
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}

‎modules/local/cache_builder/main.nf‎

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@@ -2,7 +2,7 @@
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process GENERATE_JOBS {
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label "process_single"
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container "docker.io/dessimozlab/omabuild:1.3.0"
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container "docker.io/dessimozlab/omabuild:1.3.1"
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input:
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path db
@@ -28,12 +28,11 @@ 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 "docker.io/dessimozlab/omabuild:1.3.0"
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container "docker.io/dessimozlab/omabuild:1.3.1"
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tag "Cache builder ${job_file}"
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input:
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path(job_file)
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path(db)
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tuple path(job_file), path(db)
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output:
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path("cache-res.h5"), emit: cache_chunk
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process COMBINE_JOBS {
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label "process_single"
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container "docker.io/dessimozlab/omabuild:1.3.0"
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container "docker.io/dessimozlab/omabuild:1.3.1"
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input:
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path(job_res, stageAs: "res???/*")

‎modules/local/cath_tools/assign_cath_superfamilies/main.nf‎

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@@ -1,7 +1,7 @@
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process ASSIGN_CATH_SUPERFAMILIES {
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label "process_single"
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container "docker.io/dessimozlab/omabuild:1.3.0"
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container "docker.io/dessimozlab/omabuild:1.3.1"
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input:
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tuple val(meta), path(resolve_csh)

‎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 "docker.io/dessimozlab/omadarwin:1.3.0"
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container "docker.io/dessimozlab/omadarwin:1.3.1"
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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 "docker.io/dessimozlab/omadarwin:1.3.0"
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container "docker.io/dessimozlab/omadarwin:1.3.1"
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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 "docker.io/dessimozlab/omabuild:1.3.0"
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container "docker.io/dessimozlab/omabuild:1.3.1"
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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 "docker.io/dessimozlab/omadarwin:1.3.0"
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container "docker.io/dessimozlab/omadarwin:1.3.1"
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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 "docker.io/dessimozlab/omabuild:1.3.0"
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container "docker.io/dessimozlab/omabuild:1.3.1"
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input:
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path gs_tsv

‎modules/local/domains/main.nf‎

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process IDENTIFY_PROTEINS_WITHOUT_DOMAIN_ANNOTATION {
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label "process_single"
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container "docker.io/dessimozlab/omabuild:1.3.0"
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container "docker.io/dessimozlab/omabuild:1.3.1"
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input:
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path database
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process COLLECT_RESOLVED_DOMAIN_ANNOTATIONS {
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label "process_single"
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container "docker.io/dessimozlab/omabuild:1.3.0"
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container "docker.io/dessimozlab/omabuild:1.3.1"
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input:
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path domain_files
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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 "docker.io/dessimozlab/omabuild:1.3.0"
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container "docker.io/dessimozlab/omabuild:1.3.1"
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input:
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path database

‎modules/local/edgehog/main.nf‎

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@@ -3,7 +3,7 @@ process EDGEHOG {
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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 "docker.io/dessimozlab/omabuild:1.3.0"
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container "docker.io/dessimozlab/omabuild:1.3.1"
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input:
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path augmented_orthoxml
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script:
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def unzip = (augmented_orthoxml.endsWith(".gz")) ? "gunzip -c $augmented_orthoxml > \$TMPDIR/oma-hogs.orthoxml" : "ln -s ${augmented_orthoxml} edgehog-hogs.orthoxml"
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def hog_path = (augmented_orthoxml.endsWith(".gz")) ? "\$TMPDIR/oma-hogs.orthoxml" : "edgehog-hogs.orthoxml"
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def trimed_tree = "simplified_${speciestree}"
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"""
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$unzip
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trim_uninformative_levels.py \\
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--tree $speciestree \\
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--out $trimed_tree
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edgehog --hogs $hog_path \\
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--species_tree $speciestree \\
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--species_tree $trimed_tree \\
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--hdf5 $oma_db \\
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--date_edges \\
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--out-format HDF5
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"""
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touch edgehog_output/Synteny.h5
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"""
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}
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}

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