refer to nt/nr as input names

chanzuckerberg · Nov 20, 2023 · 3467ac9 · 3467ac9
1 parent 7d3a62c
commit 3467ac9
Showing 1 changed file with 2 additions and 4 deletions.
diff --git a/workflows/index-generation/index-generation.wdl b/workflows/index-generation/index-generation.wdl
@@ -687,15 +687,14 @@ task CompressNT {
         Boolean logging_enabled
         String docker_image_id
         Int cpu
-        Int threads = if cpu * 0.5 < 1 then 1 else floor(cpu * 0.5)
     }
 
     command <<< 
         set -euxo pipefail
 
         if [ "~{logging_enabled}" ]; then
             ncbi-compress \
-                --input-fasta nt_sorted \
+                --input-fasta ~{nt_sorted} \
                 --accession-mapping-files ~{accession2taxid}nucl_wgs.accession2taxid \
                 --accession-mapping-files ~{accession2taxid}nucl_gb.accession2taxid \
                 --accession-mapping-files ~{accession2taxid}pdb.accession2taxid \
@@ -742,15 +741,14 @@ task CompressNR {
         Boolean logging_enabled
         String docker_image_id
         Int cpu
-        Int threads = if cpu * 0.5 < 1 then 1 else floor(cpu * 0.5)
     }
 
     command <<<
         set -euxo pipefail
 
         if [ "~{logging_enabled}" ]; then
             ncbi-compress \
-                --input-fasta nr_sorted \
+                --input-fasta ~{nr_sorted} \
                 --accession-mapping-files ~{accession2taxid}prot.accession2taxid.FULL \
                 --accession-mapping-files ~{accession2taxid}pdb.accession2taxid \
                 --output-fasta nr_compressed.fa \