fix bad sra len and report num jobs completed

ktmeaton · Sep 30, 2020 · 95520ad · 95520ad
1 parent 88369b3
commit 95520ad
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/workflow/rules/functions.smk b/workflow/rules/functions.smk
@@ -77,7 +77,8 @@ def identify_sra_sample():
     sra_fetch = cur.execute(config["sqlite_select_command_sra"]).fetchall()
     max_datasets = config["max_datasets_sra"]
     if max_datasets >= (len(sra_fetch) - 1):
-        max_datasets = len(sra_fetch) - 1
+        # This is purposefully different from asm max
+        max_datasets = len(sra_fetch)
     for record in sra_fetch[0:max_datasets]:
         if record:
             file_acc = record[1].split(";")

diff --git a/workflow/scripts/slack_log.py b/workflow/scripts/slack_log.py
@@ -47,7 +47,7 @@ def log_handler(msg):
                             "type": "mrkdwn",
                             "text": ":cyclone: Snakemake workflow on *"
                             + node_name
-                            + "* started running the following rules at "
+                            + "* started running the following jobs at "
                             + "*"
                             + current_time
                             + "*.",
@@ -94,7 +94,9 @@ def log_handler(msg):
                             "type": "mrkdwn",
                             "text": ":heavy_check_mark: Snakemake workflow on *"
                             + node_name
-                            + "* completed sucessfully at "
+                            + "* completed "
+                            + str(msg["total"])
+                            + " jobs sucessfully at "
                             + "*"
                             + current_time
                             + "*.",