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Commit c78ae311 authored by Kedi Cao's avatar Kedi Cao
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add option to turn on and off email notifications

parent 77aeb7c4
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snake_config.yaml
+ 2
− 1
View file @ c78ae311
......@@ -53,7 +53,8 @@ k_merge: 63 # for rule popins2_merge_contigs
readlen: 150 # for rules popins2_place_refalign and popins2_place_splitalign
min-qual: 30 # for rule popins2_crop_unmapped, Minimum average quality value in windows for read quality trimming.
min-read-len: 60 # for rule popins2_crop_unmapped, Minimum read length to keep the read after quality trimming.
email: "user@email.com" #replace with your email address to receive email notifications before each notebook execution.
receive_email_notifications: "no" # choose between "yes" or "no" to receive email notifications or not
email: "user@example.com" # specify your email address here to receive email notifications before each notebook execution.
# Sub-directories for OUTPUT_PATH
......
snakemodules/analysis.smk
+ 51
− 20
View file @ c78ae311
......@@ -9,12 +9,16 @@ if config["SICKLE"]=="no":
params:
email=config["email"], # Replace with your email or retrieve from config
subject="Snakemake Notification",
message="Rule unmapped_analysis is ready to execute."
message="Rule unmapped_analysis is ready to execute.",
receive_email=config["receive_email_notifications"] # "yes" or "no"
shell:
"""
echo "{params.message}" | mail -s "{params.subject}" {params.email}
if [ "{params.receive_email}" = "yes" ]; then
echo "{params.message}" | mail -s "{params.subject}" {params.email}
fi
touch {output.notify_file}
"""
rule unmapped_analysis:
input:
notify="notify/unmapped_analysis.txt"
......@@ -40,10 +44,13 @@ if config["SICKLE"]=="no":
params:
email=config["email"], # Replace with your email or retrieve from config
subject="Snakemake Notification",
message="Rule unmapped_analysis_no_filtler_after_clean is ready to execute."
message="Rule unmapped_analysis_no_filtler_after_clean is ready to execute.",
receive_email=config["receive_email_notifications"] # "yes" or "no"
shell:
"""
echo "{params.message}" | mail -s "{params.subject}" {params.email}
if [ "{params.receive_email}" = "yes" ]; then
echo "{params.message}" | mail -s "{params.subject}" {params.email}
fi
touch {output.notify_file}
"""
rule unmapped_analysis_no_filtler_after_clean:
......@@ -72,10 +79,13 @@ elif config["SICKLE"]=="yes":
params:
email=config["email"], # Replace with your email or retrieve from config
subject="Snakemake Notification",
message="Rule unmapped_analysis_before_filter is ready to execute."
message="Rule unmapped_analysis_before_filter is ready to execute.",
receive_email=config["receive_email_notifications"] # "yes" or "no"
shell:
"""
echo "{params.message}" | mail -s "{params.subject}" {params.email}
if [ "{params.receive_email}" = "yes" ]; then
echo "{params.message}" | mail -s "{params.subject}" {params.email}
fi
touch {output.notify_file}
"""
rule unmapped_analysis_before_filter:
......@@ -102,10 +112,13 @@ elif config["SICKLE"]=="yes":
params:
email=config["email"], # Replace with your email or retrieve from config
subject="Snakemake Notification",
message="Rule unmapped_analysis_after_filter is ready to execute."
message="Rule unmapped_analysis_after_filter is ready to execute.",
receive_email=config["receive_email_notifications"] # "yes" or "no"
shell:
"""
echo "{params.message}" | mail -s "{params.subject}" {params.email}
if [ "{params.receive_email}" = "yes" ]; then
echo "{params.message}" | mail -s "{params.subject}" {params.email}
fi
touch {output.notify_file}
"""
rule unmapped_analysis_after_filter:
......@@ -133,10 +146,13 @@ elif config["SICKLE"]=="yes":
params:
email=config["email"], # Replace with your email or retrieve from config
subject="Snakemake Notification",
message="Rule unmapped_analysis_before_clean_filter is ready to execute."
message="Rule unmapped_analysis_before_clean_filter is ready to execute.",
receive_email=config["receive_email_notifications"] # "yes" or "no"
shell:
"""
echo "{params.message}" | mail -s "{params.subject}" {params.email}
if [ "{params.receive_email}" = "yes" ]; then
echo "{params.message}" | mail -s "{params.subject}" {params.email}
fi
touch {output.notify_file}
"""
rule unmapped_analysis_before_clean_filter:
......@@ -162,10 +178,13 @@ elif config["SICKLE"]=="yes":
params:
email=config["email"], # Replace with your email or retrieve from config
subject="Snakemake Notification",
message="Rule unmapped_analysis_after_clean is ready to execute."
message="Rule unmapped_analysis_after_clean is ready to execute.",
receive_email=config["receive_email_notifications"] # "yes" or "no"
shell:
"""
echo "{params.message}" | mail -s "{params.subject}" {params.email}
if [ "{params.receive_email}" = "yes" ]; then
echo "{params.message}" | mail -s "{params.subject}" {params.email}
fi
touch {output.notify_file}
"""
rule unmapped_analysis_after_clean:
......@@ -191,10 +210,13 @@ elif config["SICKLE"]=="yes":
params:
email=config["email"], # Replace with your email or retrieve from config
subject="Snakemake Notification",
message="Rule unmapped_analysis_after_clean_filter is ready to execute."
message="Rule unmapped_analysis_after_clean_filter is ready to execute.",
receive_email=config["receive_email_notifications"] # "yes" or "no"
shell:
"""
echo "{params.message}" | mail -s "{params.subject}" {params.email}
if [ "{params.receive_email}" = "yes" ]; then
echo "{params.message}" | mail -s "{params.subject}" {params.email}
fi
touch {output.notify_file}
"""
rule unmapped_analysis_after_clean_filter:
......@@ -221,10 +243,13 @@ rule email_assembly_analysis_table:
params:
email=config["email"], # Replace with your email or retrieve from config
subject="Snakemake Notification",
message="Rule assembly_analysis_table is ready to execute."
message="Rule assembly_analysis_table is ready to execute.",
receive_email=config["receive_email_notifications"] # "yes" or "no"
shell:
"""
echo "{params.message}" | mail -s "{params.subject}" {params.email}
if [ "{params.receive_email}" = "yes" ]; then
echo "{params.message}" | mail -s "{params.subject}" {params.email}
fi
touch {output.notify_file}
"""
rule assembly_analysis_table:
......@@ -249,10 +274,13 @@ rule email_assembly_analysis:
params:
email=config["email"], # Replace with your email or retrieve from config
subject="Snakemake Notification",
message="Rule assembly_analysis is ready to execute."
message="Rule assembly_analysis is ready to execute.",
receive_email=config["receive_email_notifications"] # "yes" or "no"
shell:
"""
echo "{params.message}" | mail -s "{params.subject}" {params.email}
if [ "{params.receive_email}" = "yes" ]; then
echo "{params.message}" | mail -s "{params.subject}" {params.email}
fi
touch {output.notify_file}
"""
rule assembly_analysis:
......@@ -296,10 +324,13 @@ rule email_coverage_analysis:
params:
email=config["email"], # Replace with your email or retrieve from config
subject="Snakemake Notification",
message="Rule coverage_analysis is ready to execute."
message="Rule coverage_analysis is ready to execute.",
receive_email=config["receive_email_notifications"] # "yes" or "no"
shell:
"""
echo "{params.message}" | mail -s "{params.subject}" {params.email}
if [ "{params.receive_email}" = "yes" ]; then
echo "{params.message}" | mail -s "{params.subject}" {params.email}
fi
touch {output.notify_file}
"""
rule coverage_analysis:
......
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