Merge branch 'dp24_btk_datasets' into dp24_btk_datasets_ea10_edits2

sanger-tol · Aug 7, 2024 · 7e7370b · 7e7370b
2 parents e3b8db9 + 6d6b6fa
commit 7e7370b
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Showing 5 changed files with 9 additions and 3 deletions.
diff --git a/assets/test.yaml b/assets/test.yaml
@@ -19,6 +19,7 @@ ncbi_accessionids_folder: /nfs/treeoflife-01/teams/tola/users/dp24/ascc/20240709
 ncbi_taxonomy_path: /lustre/scratch123/tol/resources/taxonomy/latest/new_taxdump
 ncbi_rankedlineage_path: /lustre/scratch123/tol/teams/tola/users/ea10/databases/taxdump/rankedlineage.dmp
 busco_lineages_folder: /lustre/scratch123/tol/resources/busco/data/v5/2021-08-27/lineages
+busco_lineages: "diptera_odb10,insecta_odb10"
 fcs_gx_database_path: /lustre/scratch124/tol/projects/asg/sub_projects/ncbi_decon/0.4.0/gxdb/
 vecscreen_database_path: /nfs/treeoflife-01/teams/tola/users/dp24/ascc/vecscreen/
 diamond_uniprot_database_path: /lustre/scratch123/tol/teams/tola/users/ea10/pipeline_testing/20240704_diamond_tiny_testdb/ascc_tinytest_diamond_db.dmnd

diff --git a/conf/modules.config b/conf/modules.config
@@ -23,6 +23,7 @@ process {
         ext.executor        = "bsub -Is -tty -e test.e -o test.log -n 2 -q oversubscribed -M1400 -R'select[mem>1400] rusage[mem=1400] span[hosts=1]'"
         ext.profiles        = "singularity,sanger"
         ext.get_versions    = "lsid | head -n1 | cut -d ',' -f 1"
+        ext.version         = "draft_assemblies"
     }
 
     withName: SEQKIT_SLIDING {

diff --git a/modules/local/sanger_tol_btk.nf b/modules/local/sanger_tol_btk.nf
@@ -42,14 +42,18 @@ process SANGER_TOL_BTK {
 
     // outdir should be an arg
 
+    // blastx and blastp use the same database hence the StageAs
+
+
     """
     $executor 'nextflow run sanger-tol/blobtoolkit \\
         -r $pipeline_version \\
         -profile  $profiles \\
         --input "\$(realpath $samplesheet_csv)" \\
         --outdir ${prefix}_btk_out \\
         --fasta "\$(realpath REFERENCE.fa)" \\
-        --busco_lineages eukaryota_odb10 \\
+        --yaml "\$(realpath BTK.yaml)" \\
+        --busco_lineages $busco_lineages \\
         --taxon $taxon \\
         --taxdump "\$(realpath $tax_dump)" \\
         --blastp "\$(realpath blastp.dmnd)" \\

diff --git a/subworkflows/local/yaml_input.nf b/subworkflows/local/yaml_input.nf
@@ -148,7 +148,7 @@ workflow YAML_INPUT {
     ncbi_taxonomy_path               = group.ncbi_taxonomy_path
     ncbi_rankedlineage_path          = group.ncbi_rankedlineage_path
     busco_lineages_folder            = group.busco_lineages_folder
-    busco_lineages                   = group.busco_lineages
+    busco_lineages                    = group.busco_lineages
     fcs_gx_database_path             = group.fcs_gx_database_path
     diamond_uniprot_database_path    = group.diamond_uniprot_database_path
     diamond_nr_database_path         = group.diamond_nr_database_path

diff --git a/workflows/ascc.nf b/workflows/ascc.nf
@@ -464,7 +464,7 @@ workflow ASCC {
         GENERATE_SAMPLESHEET (
             new_bam
         )
-        //ch_versions              = ch_versions.mix(GENERATE_SAMPLESHEET.out.versions)
+        ch_versions              = ch_versions.mix(GENERATE_SAMPLESHEET.out.versions)
 
         SANGER_TOL_BTK (
             YAML_INPUT.out.reference_tuple,