fixing syntax

DessimozLab · Oct 14, 2024 · 02f9c51 · 02f9c51
1 parent 1874da4
commit 02f9c51
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Showing 3 changed files with 23 additions and 12 deletions.
diff --git a/modules/local/xref_fetch/main.nf b/modules/local/xref_fetch/main.nf
@@ -41,7 +41,7 @@ process FILTER_AND_SPLIT {
 
 
 process MAP_XREFS {
-    label process_single
+    label "process_single"
     container "dessimozlab/omabuild:nf-latest"
 
     input:
@@ -68,4 +68,4 @@ process MAP_XREFS {
             --seq-idx-db $seq_idx_db \\
             --xref-source-db $src_xref_db
         """
-}
+}
diff --git a/subworkflows/local/hdf5import/main.nf b/subworkflows/local/hdf5import/main.nf
@@ -2,7 +2,7 @@
 
 // Modules
 include { ADD_GENOMES; BUILD_SEQINDEX; BUILD_HOG_H5; ADD_PAIRWISE_ORTHOLOGS; ADD_DOMAINS; COMBINE_H5_FILES } from "./../../../modules/local/hdf5import"
-include { PREPARE_XREFS, MAP_XREFS_WF } from "./../xrefs"
+include { PREPARE_XREFS; MAP_XREFS_WF } from "./../xrefs"
 
 
 workflow IMPORT_HDF5 {
@@ -43,7 +43,7 @@ workflow IMPORT_HDF5 {
         PREPARE_XREFS(gs_tsv, genomes_folder, uniprot_swissprot, uniprot_trembl)
         MAP_XREFS_WF(PREPARE_XREFS.out.xref,
                   gs_tsv,
-                  genomes_folder
+                  genomes_folder,
                   COMBINE_H5_FILES.out.db_h5,
                   BUILD_SEQINDEX.out.seqidx_h5,
                   ADD_GENOMES.out.source_xref_h5)

diff --git a/subworkflows/local/xrefs/main.nf b/subworkflows/local/xrefs/main.nf
@@ -13,18 +13,19 @@ workflow PREPARE_XREFS {
         // Transform swissprot and trembl channels into tuples
         def swissprot_channel = uniprot_swissprot.map { path -> tuple(path, 'swiss', 'swissprot') }
         def trembl_channel = uniprot_trembl.map { path -> tuple(path, 'swiss', 'trembl') }
-        def refseq_channel = FETCH_REFSEQ().out.refseq_proteins.map{ path -> tuple(path, 'genbank', 'refseq') }
+        FETCH_REFSEQ()
+        def refseq_channel = FETCH_REFSEQ.out.refseq_proteins.map{ path -> tuple(path, 'genbank', 'refseq') }
 
         // Concatenate the three channels
         def xref_channel = swissprot_channel.concat(trembl_channel, refseq_channel)
         xref_channel.view()
 
-	    def taxonomy_sqlite = genome_folder / "taxonomy.sqlite"
+        def taxonomy_sqlite = genome_folder / "taxonomy.sqlite"
         def tax_traverse_pkl = genome_folder / "taxonomy.sqlite.traverse.pkl"
-        FILTER_AND_SPLIT(up_channel, gs_tsv, taxonomy_sqlite, tax_traverse_pkl)
+        FILTER_AND_SPLIT(xref_channel, gs_tsv, taxonomy_sqlite, tax_traverse_pkl)
 
         // debug output
-	    FILTER_AND_SPLIT.out.split_xref.view()
+        FILTER_AND_SPLIT.out.split_xref.view()
 
     emit:
         xref = FILTER_AND_SPLIT.out.split_xref
@@ -35,11 +36,11 @@ workflow PREPARE_XREFS {
 
 workflow MAP_XREFS_WF {
     take:
-        xref,
-        gs_tsv,
+        xref
+        gs_tsv
         genome_folder
-        db,
-        seq_idx_db,
+        db
+        seq_idx_db
         source_xref_db
 
     main:
@@ -50,3 +51,13 @@ workflow MAP_XREFS_WF {
     emit:
         xref_db = MAP_XREFS.out.xref_h5
 }
+
+workflow {
+   def gs_tsv = Channel.fromPath("/cluster/scratch/adriaal/nf-oma-work/c9/4450a31daf64694adf62909bace554/gs.tsv")
+   def genomes_folder = file("/cluster/scratch/adriaal/OMA/genomes1/")
+   def uniprot_swissprot = Channel.fromPath(params.xref_uniprot_swissprot)
+   def uniprot_trembl = Channel.fromPath(params.xref_uniprot_trembl)
+
+   PREPARE_XREFS(gs_tsv, genomes_folder, uniprot_swissprot, uniprot_trembl)
+   //MAP_XREFS_WF(PREPARE_XREFS.out.xref, gs_tsv, genome_folder)
+}