From 1023eb07a906e1e91122c3b2ac67eb578ac057ad Mon Sep 17 00:00:00 2001 From: Curtis Kapsak Date: Thu, 26 Oct 2023 18:36:02 -0400 Subject: [PATCH] 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 --- tasks/taxon_id/task_midas.wdl | 7 ++++--- .../workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml | 2 +- .../workflows/theiaprok/test_wf_theiaprok_illumina_se.yml | 2 +- 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/tasks/taxon_id/task_midas.wdl b/tasks/taxon_id/task_midas.wdl index a5761a5cb..6d3827370 100644 --- 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 index a60d9641e..56731c094 100644 --- 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 index 034238008..f4671cf72 100644 --- 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