bump version -> 1.4.0

alpae · alpae · commit 5ad195af36d9 · 2025-04-25T16:40:32.000+02:00
diff --git a/modules/local/browser_aux/main.nf b/modules/local/browser_aux/main.nf
@@ -1,6 +1,6 @@
 process GEN_BROWSER_AUX_FILES {
     label "process_single"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         path db
diff --git a/modules/local/cache_builder/main.nf b/modules/local/cache_builder/main.nf
@@ -2,7 +2,7 @@
 
 process GENERATE_JOBS {
     label "process_single"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
     
     input:
         path db
@@ -28,7 +28,7 @@ process GENERATE_JOBS {
 process COMPUTE_CACHE {
     label "process_single"
     label "HIGH_IO_ACCESS"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
     tag "Cache builder ${job_file}"
 
     input:
@@ -53,7 +53,7 @@ process COMPUTE_CACHE {
 
 process COMBINE_JOBS {
     label "process_single"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
     
     input:
         path(job_res, stageAs: "res???/*")
diff --git a/modules/local/cath_tools/assign_cath_superfamilies/main.nf b/modules/local/cath_tools/assign_cath_superfamilies/main.nf
@@ -1,7 +1,7 @@
 process ASSIGN_CATH_SUPERFAMILIES {
     label "process_single"
     
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         tuple val(meta), path(resolve_csh)
diff --git a/modules/local/darwin_extract/main.nf b/modules/local/darwin_extract/main.nf
@@ -1,7 +1,7 @@
 process CONVERT_GS {
     tag "Convert GenomeSummaries to JSON format"
     label "process_single"
-    container "docker.io/dessimozlab/omadarwin:edge"
+    container "docker.io/dessimozlab/omadarwin:1.4.0"
 
     input:
         path genomes
@@ -29,7 +29,7 @@ process CONVERT_GS {
 process CONVERT_PROTEINS {
     tag "Convert Proteins from ${genome.UniProtSpeciesCode} to JSON format"
     label "process_single"
-    container "docker.io/dessimozlab/omadarwin:edge"
+    container "docker.io/dessimozlab/omadarwin:1.4.0"
 
     input:
         tuple val(genome), path(dbpath), path(subgenome)
@@ -56,7 +56,7 @@ process CONVERT_PROTEINS {
 process CONVERT_OMA_GROUPS {
     tag "Extract OMA Groups"
     label "process_single"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         path matrix_file
@@ -73,7 +73,7 @@ process CONVERT_OMA_GROUPS {
 process CONVERT_SPLICE_MAP {
     tag "Convert Splicing information to json"
     label "process_single"
-    container "docker.io/dessimozlab/omadarwin:edge"
+    container "docker.io/dessimozlab/omadarwin:1.4.0"
 
     input:
         path splice_drw
@@ -99,7 +99,7 @@ process CONVERT_SPLICE_MAP {
 process CONVERT_TAXONOMY {
     tag "Convert Taxonomy of genomes using omataxonomy"
     label "process_single"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         path gs_tsv
diff --git a/modules/local/domains/main.nf b/modules/local/domains/main.nf
@@ -1,6 +1,6 @@
 process IDENTIFY_PROTEINS_WITHOUT_DOMAIN_ANNOTATION {
     label "process_single"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         path database
@@ -21,7 +21,7 @@ process IDENTIFY_PROTEINS_WITHOUT_DOMAIN_ANNOTATION {
 
 process COLLECT_RESOLVED_DOMAIN_ANNOTATIONS {
     label "process_single"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         path domain_files
@@ -41,7 +41,7 @@ process COLLECT_RESOLVED_DOMAIN_ANNOTATIONS {
 process ADD_DOMAINS {
     label "process_single"
     label "process_medium_memory"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         path database
diff --git a/modules/local/edgehog/main.nf b/modules/local/edgehog/main.nf
@@ -3,7 +3,7 @@ process EDGEHOG {
     label "single_process"
     label "process_long"
     label "process_high_memory"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         path augmented_orthoxml
diff --git a/modules/local/fastoma_extract/main.nf b/modules/local/fastoma_extract/main.nf
@@ -1,6 +1,6 @@
 process CONVERT_SPECIES_TREE {
     label "process_single"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         path speciestree
@@ -23,7 +23,7 @@ process CONVERT_SPECIES_TREE {
 
 process CONVERT_PROTEOME {
     label "process_single"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         tuple val(meta), path(genome), path(matrix)
@@ -51,7 +51,7 @@ process CONVERT_PROTEOME {
 
 process CONVERT_SPLICINGS {
     label "process_single"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         path splicefolder
@@ -68,7 +68,7 @@ process CONVERT_SPLICINGS {
 
 process FINALIZE_GS {
     label "process_single"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         path gs_tsv
@@ -88,7 +88,7 @@ process FINALIZE_GS {
 
 process  MERGE_JSON {
     label "process_single"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         path json_files
diff --git a/modules/local/fingerprints/main.nf b/modules/local/fingerprints/main.nf
@@ -1,6 +1,6 @@
 process INFER_FINGERPRINTS {
     label "process_single"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         tuple val(meta), path(db_h5), path(seqidx_h5)
diff --git a/modules/local/go_import/main.nf b/modules/local/go_import/main.nf
@@ -3,7 +3,7 @@
 process GO_IMPORT {
     label "process_single"
     label "HIGH_IO_ACCESS"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
     
     input:
         path xref_db
diff --git a/modules/local/h5_combine/main.nf b/modules/local/h5_combine/main.nf
@@ -1,6 +1,6 @@
 process COMBINE_HDF_AND_UPDATE_SUMMARY_DATA {
     label "process_single"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         path h5files
@@ -28,7 +28,7 @@ process COMBINE_HDF_AND_UPDATE_SUMMARY_DATA {
 
 process COMBINE_HDFS {
     label "process_single"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         path h5files
diff --git a/modules/local/hdf5import/main.nf b/modules/local/hdf5import/main.nf
@@ -2,7 +2,7 @@
 process ADD_GENOMES {
     label "process_single"
     label "process_long"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         path gs_tsv
@@ -40,7 +40,7 @@ process ADD_GENOMES {
 process BUILD_SEQINDEX {
     label "process_single"
     label "process_medium_memory"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
     tag "Building Sequence Index with ${meta.nr_of_amino_acids} AAs"
 
     input:
@@ -64,7 +64,7 @@ process BUILD_SEQINDEX {
 process BUILD_HOG_H5 {
     label "process_low"
     label "process_medium_memory"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
     tag "Building HOG HDF5 with ${meta.nr_of_sequences} proteins"
 
     input:
@@ -99,7 +99,7 @@ process BUILD_HOG_H5 {
 
 process ADD_PAIRWISE_ORTHOLOGS {
     label "process_medium"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         tuple val(meta), path(database)
@@ -130,7 +130,7 @@ process ADD_PAIRWISE_ORTHOLOGS {
 
 process COMBINE_H5_FILES {
     label "process_single"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         path input_db, stageAs: 'OmaServer_input.h5'
diff --git a/modules/local/hogprofile/main.nf b/modules/local/hogprofile/main.nf
@@ -1,6 +1,6 @@
 process INFER_HOG_PROFILES {
     label "process_medium"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         path db_h5
diff --git a/modules/local/hogprop/main.nf b/modules/local/hogprop/main.nf
@@ -1,7 +1,7 @@
 // Processes
 process COUNT_GENES_WITH_ANNOTATION {
     label "process_single"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         path omadb
@@ -18,7 +18,7 @@ process COUNT_GENES_WITH_ANNOTATION {
 
 process HOGPROP {
     label "process_single"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         tuple val(chunk), val(nr_chunks), path(orthoxml),  path(omadb)
@@ -46,7 +46,7 @@ process HOGPROP {
 process HOGPROP_COLLECT {
     label "process_single"
     label "process_high_memory"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         path "results/*"
@@ -69,7 +69,7 @@ process HOGPROP_COLLECT {
 
 process HOGPROP_CONVERT_TO_BROWSERDB_FORMAT {
     label "process_single"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         path omadb
diff --git a/modules/local/keywords/main.nf b/modules/local/keywords/main.nf
@@ -1,6 +1,6 @@
 process INFER_KEYWORDS {
     label "process_single"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         val meta
diff --git a/modules/local/rdf_export/from_db/main.nf b/modules/local/rdf_export/from_db/main.nf
@@ -1,6 +1,6 @@
  process RDF_FROM_HDF5{
     label "process_medium"
-    container "docker.io/dessimozlab/omabuild-rdf-py:edge"
+    container "docker.io/dessimozlab/omabuild-rdf-py:1.4.0"
 
     input:
         path database
diff --git a/modules/local/rdf_export/from_orthoxml/main.nf b/modules/local/rdf_export/from_orthoxml/main.nf
@@ -1,6 +1,6 @@
 process RDF_FROM_ORTHOXML {
     label "process_medium"
-    container "docker.io/dessimozlab/omabuild-rdf-java:edge"
+    container "docker.io/dessimozlab/omabuild-rdf-java:1.4.0"
 
     input:
         val meta
diff --git a/modules/local/xref_fetch/main.nf b/modules/local/xref_fetch/main.nf
@@ -1,7 +1,7 @@
 
 process FETCH_REFSEQ {
     label "process_low"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     output:
         path "*.gpff.gz", emit: refseq_proteins
@@ -17,7 +17,7 @@ process FETCH_REFSEQ {
 process FILTER_AND_SPLIT {
     tag "$source"
     label "process_single"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         tuple path(xref), val(format), val(source)
@@ -37,7 +37,7 @@ process FILTER_AND_SPLIT {
 
 process RELEVANT_TAXID_MAP {
     label "process_single"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         path gs_tsv
@@ -68,7 +68,7 @@ process MAP_XREFS {
     label "process_single"
     label "process_long"
     label "HIGH_IO_ACCESS"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
 
     input:
         tuple path(xref_in), val(format), val(source), 
@@ -96,7 +96,7 @@ process MAP_XREFS {
 
 process COLLECT_XREFS {
     label "process_single"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
     tag "Collecting xrefs for $source"
 
     input:
@@ -119,7 +119,7 @@ process COLLECT_XREFS {
 
 process COMBINE_ALL_XREFS {
     label "process_single"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
     tag "Combining all xrefs into single hdf5 db"
 
     input:
@@ -138,7 +138,7 @@ process COMBINE_ALL_XREFS {
 
 process BUILD_REDUCED_XREFS {
     label "process_low"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
     tag "Building a reduced set of xrefs for lookup and search"
 
     input:
@@ -161,7 +161,7 @@ process BUILD_REDUCED_XREFS {
 
 process BUILD_NCBITAX_DB {
     label "process_single"
-    container "docker.io/dessimozlab/omabuild:edge"
+    container "docker.io/dessimozlab/omabuild:1.4.0"
     tag "Verify / Build NCBITax database"
 
     input:
diff --git a/nextflow.config b/nextflow.config
