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sanger-tol · Dec 5, 2024 · e35a762 · e35a762
1 parent b05a4a6
commit e35a762
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Showing 4 changed files with 17 additions and 5 deletions.
diff --git a/conf/base.config b/conf/base.config
@@ -20,6 +20,10 @@ process {
     maxErrors     = '-1'
 
 
+    withName: 'SANGER_TOL_BTK|SANGER_TOL_BTK_CASCADE' {
+        time = { check_max (48.h* task.attempt, 'time') }
+    }
+
     withName: 'MINIMAP2_ALIGN_SE' {
         cpus   = { check_max( 6        * task.attempt, 'cpus'    ) }
         memory = { check_max( 2.GB     * ( reference.size() < 2e9 ? 70 : Math.ceil( ( reference.size() / 1e+9 ) * 50 ) * Math.ceil( task.attempt * 1 ) ) , 'memory') }
@@ -53,6 +57,12 @@ process {
         memory  = { check_max( 50.GB     * task.attempt, 'memory') }
     }
 
+    withName: DIAMOND_BLASTX {
+        cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
+        memory = { check_max( 80.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 20.h  * task.attempt, 'time'    ) }
+    }
+
     // PYTHON BASED MODULES WHICH SHOULDN'T NEED MORE THAN 1 CORE AND A MIDDLING AMOUNT OF MEMORY
     // WILL BE REVIEWED
     withName: 'VALIDATE_TAXID|TRAILINGNS|GC_CONTENT|GET_KMERS_PROFILE|PARSE_FCSGX_RESULT|ASCC_MERGE_TABLES|GET_LARGEST_SCAFF|KMER_COUNT_DIM_REDUCTION|KMER_COUNT_DIM_REDUCTION_COMBINE_CSV|REFORMAT_DIAMOND_OUTFMT6|CONVERT_TO_HITS_FILE|DIAMOND_BLAST_CHUNK_TO_FULL|GENERATE_SAMPLESHEET' {

diff --git a/modules/local/sanger_tol_btk.nf b/modules/local/sanger_tol_btk.nf
@@ -29,7 +29,6 @@ process SANGER_TOL_BTK {
     def profiles            =   task.ext.profiles       ?:  ""
     def get_version         =   task.ext.version_data   ?:  "UNKNOWN - SETTING NOT SET"
     def pipeline_version    =   task.ext.version        ?: "0.6.0"
-    def busco_path          =   busco_lineages_folder ? "--busco ${busco_lineages_folder}" : ""
     // Seems to be an issue where a nested pipeline can't see the files in the same directory
     // Running realpath gets around this but the files copied into the folder are
     // now just wasted space. Should be fixed with using Mahesh's method of nesting but
@@ -47,13 +46,14 @@ process SANGER_TOL_BTK {
         --input "\$(realpath $samplesheet_csv)" \\
         --outdir ${prefix}_btk_out \\
         --fasta "\$(realpath $reference)" \\
-        busco \\
+        --busco $busco_lineages_folder \\
         --busco_lineages $busco_lineages \\
         --taxon $taxon \\
         --taxdump "\$(realpath $tax_dump)" \\
         --blastp "\$(realpath blastp.dmnd)" \\
         --blastn "\$(realpath $blastn)" \\
         --blastx "\$(realpath $blastx)" \\
+        --use_work_dir_as_temp true \\
         $args
 
     mv ${prefix}_btk_out/pipeline_info blobtoolkit_pipeline_info

diff --git a/workflows/ascc_genomic.nf b/workflows/ascc_genomic.nf
@@ -468,7 +468,7 @@ workflow ASCC_GENOMIC {
             params.diamond_uniprot_database_path,
             params.ncbi_taxonomy_path,
             params.btk_yaml,
-            [], //params.busco_lineages_folder,
+            params.busco_lineages_folder,
             params.busco_lineages,
             params.taxid,
         )
@@ -515,7 +515,9 @@ workflow ASCC_GENOMIC {
                     busco: busco_folder,
                     busco_lineages: busco_lineage_vals,
                     taxon: taxid,
-                    blastx_outext: "txt"
+                    blastx_outext: "txt",
+                    use_work_dir_as_temp: true
+
                 ]
             }
             .set{ pipeline_input }

diff --git a/workflows/ascc_organellar.nf b/workflows/ascc_organellar.nf
@@ -410,7 +410,7 @@ workflow ASCC_ORGANELLAR {
             params.diamond_uniprot_database_path,
             params.ncbi_taxonomy_path,
             params.btk_yaml,
-            [], //params.busco_lineages_folder,
+            params.busco_lineages_folder,
             params.busco_lineages,
             params.taxid,
         )