various small fixes

DessimozLab · Oct 30, 2024 · c9e8470 · c9e8470
1 parent 4f33ea6
commit c9e8470
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Showing 4 changed files with 10 additions and 9 deletions.
diff --git a/modules/local/xref_fetch/main.nf b/modules/local/xref_fetch/main.nf
@@ -32,7 +32,7 @@ process FILTER_AND_SPLIT {
         """
         oma-build -vv filter-xref \\
             --xref $xref \\
-            --out-prefix ./xref-${source}- \\
+            --out-prefix ./xref-${source} \\
             --format $format \\
             --gs-tsv $gs_tsv \\
             --tax-sqlite $tax_sqlite
@@ -65,7 +65,7 @@ process MAP_XREFS {
             --source $source \\
             --gs-tsv $gs_tsv \\
             --tax-sqlite $tax_sqlite \\
-            --out xref.pkl \\
+            --out xref-${source}.pkl \\
             --db $db \\
             --seq-idx-db $seq_idx_db \\
             --xref-source-db $src_xref_db
@@ -98,18 +98,18 @@ process COLLECT_XREFS {
 process COMBINE_ALL_XREFS {
     label "process_single"
     container "dessimozlab/omabuild:nf-latest"
-    tag "Collecting xrefs for $source"
+    tag "Combining all xrefs into single hdf5 db"
 
     input:
         path xref_dbs
 
     output:
-        tuple "XRef-db.h5", emit: xref_db_h5
+        path("XRef-db.h5"), emit: xref_db_h5
 
     script:
         """
         oma-build -vv combine-xrefs \\
-            --out "XRef-db.h5"
+            --out XRef-db.h5 \\
             --xrefs $xref_dbs \\
         """
-}
+}
diff --git a/nextflow.config b/nextflow.config
@@ -15,7 +15,7 @@ params {
     // domains directory
     known_domains = null
     cath_names_path = "http://download.cathdb.info/cath/releases/latest-release/cath-classification-data/cath-names.txt"
-    pfam_names_path = "ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.clans.tsv.gz"
+    pfam_names_path = "https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.clans.tsv.gz"
 
     // xref paths
     xref_uniprot_swissprot = "https://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot.dat.gz"

diff --git a/subworkflows/local/hdf5import/main.nf b/subworkflows/local/hdf5import/main.nf
@@ -28,9 +28,10 @@ workflow IMPORT_HDF5 {
             pw_h5 = null
         }
         if (params.known_domains != null) {
-            domains = Channel.fromPath(params.known_domains).collect()
+            domains = Channel.fromPath("${params.known_domains}/*")
             cath_names = Channel.fromPath(params.cath_names_path)
             pfam_names = Channel.fromPath(params.pfam_names_path)
+
             ADD_DOMAINS(ADD_GENOMES.out.db_h5, domains, cath_names, pfam_names)
             domains_h5 = ADD_DOMAINS.out.domains_h5
         } else {

diff --git a/subworkflows/local/xrefs/main.nf b/subworkflows/local/xrefs/main.nf
@@ -63,7 +63,7 @@ workflow MAP_XREFS_WF {
         MAP_XREFS(map_xref_params, taxonomy_sqlite, tax_traverse_pkl)
         grouped_by_source = MAP_XREFS.out.matched_xrefs
             .groupTuple()
-            .map { source, map_resList, format, xrefList -> [source, map_resList, format, xrefList.flatten()]
+            .map { source, map_resList, format, xrefList -> [source, map_resList, format[0], xrefList.flatten()] }
         COLLECT_XREFS(grouped_by_source)
         xref_dbs_list = COLLECT_XREFS.out.xref_by_source_h5
             .map{ source, db -> db}