reduce unnecessary logging in MIDAS task (#210)

* made untar/decompression of midas database quiet since it produces 41k lines of output. also made the 2 mv commands verbose (but it's only 2 lines!) * update CI
theiagen · Oct 26, 2023 · 1023eb0 · 1023eb0
1 parent 1da4a58
commit 1023eb0
Show file tree

Hide file tree

Showing 3 changed files with 6 additions and 5 deletions.
diff --git a/tasks/taxon_id/task_midas.wdl b/tasks/taxon_id/task_midas.wdl
@@ -16,14 +16,15 @@ task midas {
 
     # Decompress the Midas database
     mkdir db
-    tar -C ./db/ -xzvf ~{midas_db}  
+    echo "Decompressing Midas database. Please be patient, this may take a few minutes."
+    tar -C ./db/ -xzf ~{midas_db}  
 
     # Run Midas
     run_midas.py species ~{samplename} -1 ~{read1} ~{'-2 ' + read2} -d db/midas_db_v1.2/ -t ~{cpu} 
 
     # rename output files
-    mv ~{samplename}/species/species_profile.txt ~{samplename}/species/~{samplename}_species_profile.tsv
-    mv ~{samplename}/species/log.txt ~{samplename}/species/~{samplename}_log.txt
+    mv -v ~{samplename}/species/species_profile.txt ~{samplename}/species/~{samplename}_species_profile.tsv
+    mv -v ~{samplename}/species/log.txt ~{samplename}/species/~{samplename}_log.txt
 
     # Run a python block to parse output file for terra data tables
     # pandas is available in default docker image for python2 but not python3

diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
@@ -630,7 +630,7 @@
     - path: miniwdl_run/wdl/tasks/taxon_id/task_kraken2.wdl
       md5sum: a1f287e6e6feaf2d7d3c74a70e3b5a28
     - path: miniwdl_run/wdl/tasks/taxon_id/task_midas.wdl
-      md5sum: 024971d1439dff7d59c0a26a824bd2c6
+      md5sum: faacd87946ee3fbdf70f3a15b79ce547
     - path: miniwdl_run/wdl/tasks/utilities/task_broad_terra_tools.wdl
       md5sum: 43ef050bde1fb8755f38e697a1794918
     - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl

diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
@@ -598,7 +598,7 @@
     - path: miniwdl_run/wdl/tasks/taxon_id/task_kraken2.wdl
       md5sum: a1f287e6e6feaf2d7d3c74a70e3b5a28
     - path: miniwdl_run/wdl/tasks/taxon_id/task_midas.wdl
-      md5sum: 024971d1439dff7d59c0a26a824bd2c6
+      md5sum: faacd87946ee3fbdf70f3a15b79ce547
     - path: miniwdl_run/wdl/tasks/utilities/task_broad_terra_tools.wdl
       md5sum: 43ef050bde1fb8755f38e697a1794918
     - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_se.wdl