From e492dec53b14942f87db4bab3718f81ba0070baf Mon Sep 17 00:00:00 2001 From: Sage Wright <40403716+sage-wright@users.noreply.github.com> Date: Fri, 30 Dec 2022 13:53:01 -0500 Subject: [PATCH] Smw excluded mercury dev (#205) * quality exclusion write out * terrafied * quick fix Co-authored-by: kevinlibuit --- tasks/task_mercury_file_wrangling.wdl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tasks/task_mercury_file_wrangling.wdl b/tasks/task_mercury_file_wrangling.wdl index c6094aea..ba7708ec 100644 --- a/tasks/task_mercury_file_wrangling.wdl +++ b/tasks/task_mercury_file_wrangling.wdl @@ -98,7 +98,7 @@ task sm_metadata_wrangling { # the sm stands for supermassive quality_exclusion = pd.DataFrame() for index, row in table.iterrows(): - if ("VADR skipped due to poor assembly") in row["vadr_num_alerts"]: + if ("VADR skipped due to poor assembly") in str(row["vadr_num_alerts"]): notification = "VADR skipped due to poor assembly" quality_exclusion = quality_exclusion.append({"sample_name": row["~{table_name}_id".lower()], "message": notification}, ignore_index=True) elif int(row["vadr_num_alerts"]) > ~{vadr_alert_limit}: @@ -441,7 +441,7 @@ task sm_metadata_wrangling { # the sm stands for supermassive CODE echo "DEBUG: performing file transfers and manipulations" - + # this version of gsutil only works on python2.7 export CLOUDSDK_PYTHON=python2.7