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datetime logging
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@k-florek
k-florek committed May 12, 2020
1 parent 2c4a466 commit 5e8dfd3
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Showing 2 changed files with 17 additions and 14 deletions.
2 changes: 1 addition & 1 deletion packaging/setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@

setuptools.setup(
name="staphb_toolkit",
version="1.0.1",
version="1.0.3",
author="Kelsey Florek, Kevin Libuit",
author_email="[email protected], [email protected]",
description="A ToolKit of commonly used Public Health Bioinformatics Tools",
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29 changes: 16 additions & 13 deletions staphb_toolkit/toolkit_workflows.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
import sys,os,re
import argparse
from shutil import which, copyfile
from datetime import date
from datetime import date, datetime
import pexpect
import staphb_toolkit.core.update_app as autoupdate

Expand Down Expand Up @@ -146,6 +146,9 @@ def error(self, message):
sys.exit(1)
program = args.subparser_name

#current time for log files
exec_time = datetime.now().strftime("%y_%m_%d_%H_%M_%S_")

#################################
#Program specific execution code#
#################################
Expand Down Expand Up @@ -183,12 +186,12 @@ def error(self, message):

#set work dir into local logs dir if profile not aws
work = ""
if profile:
if profile and not args.config:
work = f"-w {args.output}/logs/work"

#build command
command = nextflow_path
command = command + f" {config} run {tredegar_path}/tredegar.nf {profile} {args.resume} --reads {args.reads_path} --outdir {args.output} -with-trace {args.output}/logs/Tredegar_trace.txt -with-report {args.output}/logs/Tredegar_execution_report.html {work}"
command = command + f" {config} run {tredegar_path}/tredegar.nf {profile} {args.resume} --reads {args.reads_path} --outdir {args.output} -with-trace {args.output}/logs/{exec_time}Tredegar_trace.txt -with-report {args.output}/logs/{exec_time}Tredegar_execution_report.html {work}"
print(command)

#run command using nextflow in a subprocess
Expand Down Expand Up @@ -236,12 +239,12 @@ def error(self, message):

#set work dir into local logs dir if profile not aws
work = ""
if profile:
if profile and not args.config:
work = f"-w {args.output}/logs/work"

if args.monroe_command == 'pe_assembly':
#build command
command = nextflow_path + f" {config} run {monroe_path}/monroe_pe_assembly.nf {profile} {args.resume} --pipe pe --reads {args.reads_path} --primers {args.primers} --outdir {args.output} -with-trace {args.output}/logs/Monroe_trace.txt -with-report {args.output}/logs/Monroe_execution_report.html {work}"
command = nextflow_path + f" {config} run {monroe_path}/monroe_pe_assembly.nf {profile} {args.resume} --pipe pe --reads {args.reads_path} --primers {args.primers} --outdir {args.output} -with-trace {args.output}/logs/{exec_time}Monroe_trace.txt -with-report {args.output}/logs/{exec_time}Monroe_execution_report.html {work}"
#run command using nextflow in a subprocess
print("Starting the Monroe paired-end assembly:")
child = pexpect.spawn(command)
Expand All @@ -262,7 +265,7 @@ def error(self, message):
sys.exit(1)

#build command
command = nextflow_path + f" {config} run {monroe_path}/monroe_cluster_analysis.nf {profile} {args.resume} --pipe cluster --assemblies {args.assemblies_path} --report {args.report} --outdir {args.output} -with-trace {args.output}/logs/Monroe_trace.txt -with-report {args.output}/logs/Monroe_execution_report.html {work}"
command = nextflow_path + f" {config} run {monroe_path}/monroe_cluster_analysis.nf {profile} {args.resume} --pipe cluster --assemblies {args.assemblies_path} --report {args.report} --outdir {args.output} -with-trace {args.output}/logs/{exec_time}Monroe_trace.txt -with-report {args.output}/logs/{exec_time}Monroe_execution_report.html {work}"
#run command using nextflow in a subprocess
print("Starting the Monroe cluster analysis:")
child = pexpect.spawn(command)
Expand All @@ -287,7 +290,7 @@ def error(self, message):
else:
seq_summary = ""

command = nextflow_path + f" {config} run {monroe_path}/monroe_ont_assembly.nf {profile} {args.resume} {read_paths} --pipe ont {seq_summary} --polishing {args.polish_method} --primers {args.primers} --outdir {args.output} --run_prefix {args.run_prefix} -with-trace {args.output}/logs/Monroe_trace.txt -with-report {args.output}/logs/Monroe_execution_report.html {work}"
command = nextflow_path + f" {config} run {monroe_path}/monroe_ont_assembly.nf {profile} {args.resume} {read_paths} --pipe ont {seq_summary} --polishing {args.polish_method} --primers {args.primers} --outdir {args.output} --run_prefix {args.run_prefix} -with-trace {args.output}/logs/{exec_time}Monroe_trace.txt -with-report {args.output}/logs/{exec_time}Monroe_execution_report.html {work}"
#run command using nextflow in a subprocess
print("Starting the Monroe ONT assembly:")
child = pexpect.spawn(command)
Expand Down Expand Up @@ -326,12 +329,12 @@ def error(self, message):

#set work dir into local logs dir if profile not aws
work = ""
if profile:
if profile and not args.config:
work = f"-w {args.output}/logs/work"

#build command
command = nextflow_path
command = command + f" {config} run {foushee_path}/foushee.nf {profile} {args.resume} --reads {args.reads_path} --report {args.report} --outdir {args.output} -with-trace {args.output}/logs/Foushee_trace.txt -with-report {args.output}/logs/Foushee_execution_report.html {work}"
command = command + f" {config} run {foushee_path}/foushee.nf {profile} {args.resume} --reads {args.reads_path} --report {args.report} --outdir {args.output} -with-trace {args.output}/logs/{exec_time}Foushee_trace.txt -with-report {args.output}/logs/{exec_time}Foushee_execution_report.html {work}"
print(command)

#run command using nextflow in a subprocess
Expand Down Expand Up @@ -381,7 +384,7 @@ def error(self, message):
work = ""
output_path = os.path.join(os.getcwd(),'rebuild_results')
output_work = os.path.join(output_path,'report_work')
if profile:
if profile and not args.config:
work = f"-w {output_work}"

rmd = os.path.abspath(args.rmd)
Expand All @@ -395,7 +398,7 @@ def error(self, message):

#build command
command = nextflow_path
command = command + f" {config} run {dryad_path}/rebuild_report.nf {profile} --logo {logo_path} --outdir {output_path} --rmd {rmd} {snp_mat} {cg_tree} {ar_tsv} {work}"
command = command + f" {config} run {dryad_path}/rebuild_report.nf {profile} --logo {logo_path} --outdir {output_path} --rmd {rmd} {snp_mat} {cg_tree} {ar_tsv} -with-trace {args.output}/logs/{exec_time}dryad_trace.txt -with-report {args.output}/logs/{exec_time}dryad_execution_report.html {work}"

#run command using nextflow in a subprocess
print("Rebuilding Dryad Report:")
Expand Down Expand Up @@ -432,7 +435,7 @@ def error(self, message):

#set work dir into local logs dir if profile not aws
work = ""
if profile:
if profile and not args.config:
work = f"-w {args.output}/logs/work"

#build nextflow command
Expand All @@ -457,7 +460,7 @@ def error(self, message):

#build command
command = nextflow_path
command = command + f" {config} run {dryad_path}/dryad.nf {profile} {args.resume} --reads {args.reads_path} {selections} {other_args} {mqc_config_path} {mqc_logo_path} -with-trace {args.output}/logs/dryad_trace.txt -with-report {args.output}/logs/dryad_execution_report.html {work}"
command = command + f" {config} run {dryad_path}/dryad.nf {profile} {args.resume} --reads {args.reads_path} {selections} {other_args} {mqc_config_path} {mqc_logo_path} -with-trace {args.output}/logs/{exec_time}dryad_trace.txt -with-report {args.output}/logs/{exec_time}dryad_execution_report.html {work}"

#run command using nextflow in a subprocess
print("Starting the Dryad pipeline:")
Expand Down

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