switch freyja update to happen in the work dir

workflows/process/freyja.nf

@@ -12,10 +12,18 @@ process freyja {
         tuple val(name), path("*_freyja_plot.svg"), path("*_freyja_plot.png"), emit: plots, optional: true
 
     script:
-        if      ( params.freyja_update )  { freyja_update_cmd = "freyja update" }
-        else                                { freyja_update_cmd = " " }
+        if ( params.freyja_update )  
+            {   freyja_update_cmd = "mkdir data; freyja update --outdir data" 
+                // here we will download the latest Freyja data again instead of using the files obtained when installing the conda env
+                freyja_ref_data = "data"
+            }
+        else
+            {   freyja_update_cmd = " "
+                // this is the original path where inside of the container the Freyja data is stored
+                freyja_ref_data = "/opt/conda/envs/freyja-env/lib/python3.10/site-packages/freyja/data/"
+            }
         """
-        sed -i "s/^>.*\$/>MN908947.3/" ${reference} #rename reference-sequence as Alignment is done with this sequence-name even so using the same reference freyja will detect deviating names and thro an error
+        sed -i "s/^>.*\$/>MN908947.3/" ${reference} #rename reference-sequence as Alignment is done with this sequence-name even so using the same reference freyja will detect deviating names and throw an error
         mkdir -p freyja_result/
 
         ${freyja_update_cmd}
@@ -28,19 +36,23 @@ process freyja {
         freyja demix ${name}_freyja_variants.tsv \
             ${name}_freyja_depths.tsv \
             --output freyja_result/${name}_freyja_demix.tsv \
+            --barcodes ${freyja_ref_data}/usher_barcodes.csv \
+            --lineageyml ${freyja_ref_data}/lineages.yml
 
         freyja aggregate freyja_result/ \
             --output ${name}_freyja_aggregate.tsv \
 
         freyja plot ${name}_freyja_aggregate.tsv \
             --output ${name}_freyja_plot.svg \
             --lineages \
-            --mincov 10.0 #default minCoverage: 60
+            --mincov 10.0 #default minCoverage: 60 \
+            --lineageyml ${freyja_ref_data}/lineages.yml
 
         freyja plot ${name}_freyja_aggregate.tsv \
             --output ${name}_freyja_plot.png \
             --lineages \
-            --mincov 10.0 #default minCoverage: 60
+            --mincov 10.0 #default minCoverage: 60 \
+            --lineageyml ${freyja_ref_data}/lineages.yml
 
         mv freyja_result/${name}_freyja_demix.tsv \$PWD #freyha_demix.tsv is put into a folder before to give it to freyja aggregate
         """