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update for release 2.1.1
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@julieaorjuela
julieaorjuela committed Jul 20, 2022
1 parent 7748fa3 commit b6d8925
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Showing 10 changed files with 174 additions and 182 deletions.
10 changes: 4 additions & 6 deletions culebrONT/module.py
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Original file line number Diff line number Diff line change
Expand Up @@ -146,25 +146,23 @@ def __build_quality_step_list(self, only_last=False):
last_steps_list = []
suffix = ""
if bool(self.config["FIXSTART"]):
suffix = "_STARTFIXED"
suffix = "sFIX"
if self.correction_tools_activated:
step = "CORRECTION"
for corrector in self.correction_tools_activated:
last_steps_list.append(f"STEP_{step}_{corrector}{suffix if step in self.pipeline_stop else ''}")
last_steps_list.append(f"{corrector}{suffix if step in self.pipeline_stop else ''}")
if only_last:
return last_steps_list

if self.polishing_tools_activated:
step = "POLISHING"
for polisher in self.polishing_tools_activated:
last_steps_list.append(f"STEP_{step}_{polisher}{suffix if step in self.pipeline_stop else ''}")
last_steps_list.append(f"{polisher}{suffix if step in self.pipeline_stop else ''}")
if only_last:
return last_steps_list
if self.assembly_tools_activated:
step = "ASSEMBLY"
last_steps_list.append(f"STEP_{step}{suffix if step in self.pipeline_stop else ''}")
# for assembler in self.assembly_tools_activated:
# last_steps_list.append(f"STEP_{step}_{assembler}{suffix}" )
last_steps_list.append(f"ASSEMBLY{suffix if step in self.pipeline_stop else ''}")
if only_last:
return last_steps_list
return last_steps_list
Expand Down
48 changes: 22 additions & 26 deletions culebrONT/snakeWrapper/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,24 @@ def rewrite_if_bind(snakemake_other):
return snakemake_other


def build_pdf(cmd_snakemake_base):
dag_cmd_snakemake = f"{cmd_snakemake_base} --dag | dot -Tpdf > schema_pipeline_dag.pdf"
click.secho(f" {dag_cmd_snakemake}\n", fg='bright_blue')
process = subprocess.run(dag_cmd_snakemake, shell=True, check=False, stdout=sys.stdout, stderr=sys.stderr)
if int(process.returncode) >= 1:
sys.exit(1)
rulegraph_cmd_snakemake = f"{cmd_snakemake_base} --rulegraph | dot -Tpdf > schema_pipeline_global.pdf"
click.secho(f" {rulegraph_cmd_snakemake}\n", fg='bright_blue')
process = subprocess.run(rulegraph_cmd_snakemake, shell=True, check=False, stdout=sys.stdout, stderr=sys.stderr)
if int(process.returncode) >= 1:
sys.exit(1)
filegraph_cmd_snakemake = f"{cmd_snakemake_base} --filegraph | dot -Tpdf > schema_pipeline_files.pdf"
click.secho(f" {filegraph_cmd_snakemake}\n", fg='bright_blue')
process = subprocess.run(filegraph_cmd_snakemake, shell=True, check=False, stdout=sys.stdout, stderr=sys.stderr)
if int(process.returncode) >= 1:
sys.exit(1)


@click.command("run_cluster", short_help='Run workflow on HPC', context_settings=dict(ignore_unknown_options=True, max_content_width=800), no_args_is_help=True)
@click.option('--config', '-c', type=click.Path(exists=True, file_okay=True, readable=True, resolve_path=True), required=True, show_default=True, help=f'Configuration file for run {package_name()}')
@click.option('--pdf', '-pdf', is_flag=True, required=False, default=False, show_default=True, help='Run snakemake with --dag, --rulegraph and --filegraph')
Expand Down Expand Up @@ -61,23 +79,12 @@ def run_cluster(config, pdf, snakemake_other):

cmd_snakemake_base = f"snakemake --show-failed-logs -p -s {SNAKEFILE} --configfile {config} --profile {profile} {cmd_clusterconfig} {' '.join(rewrite_if_bind(snakemake_other))}"
click.secho(f"\n {cmd_snakemake_base}\n", fg='bright_blue')
process = subprocess.run(cmd_snakemake_base, shell=True, check=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
process = subprocess.run(cmd_snakemake_base, shell=True, check=False, stdout=sys.stdout, stderr=sys.stderr)
if int(process.returncode) >= 1:
sys.stderr.buffer.write(process.stderr) #snakemake writes error in stdout
sys.stdout.buffer.write(process.stdout)
sys.exit(1)
sys.stdout.buffer.write(process.stdout)

if pdf:
dag_cmd_snakemake = f"{cmd_snakemake_base} --dag | dot -Tpdf > schema_pipeline_dag.pdf"
click.secho(f" {dag_cmd_snakemake}\n", fg='bright_blue')
os.system(dag_cmd_snakemake)
rulegraph_cmd_snakemake = f"{cmd_snakemake_base} --rulegraph | dot -Tpdf > schema_pipeline_global.pdf"
click.secho(f" {rulegraph_cmd_snakemake}\n", fg='bright_blue')
os.system(rulegraph_cmd_snakemake)
filegraph_cmd_snakemake = f"{cmd_snakemake_base} --filegraph | dot -Tpdf > schema_pipeline_files.pdf"
click.secho(f" {filegraph_cmd_snakemake}\n", fg='bright_blue')
os.system(filegraph_cmd_snakemake)
build_pdf(cmd_snakemake_base)


@click.command("run_local", short_help='Run a workflow on local computer (use singularity mandatory)', context_settings=dict(ignore_unknown_options=True, max_content_width=800),
Expand Down Expand Up @@ -111,20 +118,9 @@ def run_local(config, threads, pdf, snakemake_other):

cmd_snakemake_base = f"snakemake --latency-wait 1296000 --cores {threads} --use-singularity --show-failed-logs --printshellcmds -s {SNAKEFILE} --configfile {config} {' '.join(rewrite_if_bind(snakemake_other))}"
click.secho(f"\n {cmd_snakemake_base}\n", fg='bright_blue')
process = subprocess.run(cmd_snakemake_base, shell=True, check=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
process = subprocess.run(cmd_snakemake_base, shell=True, check=False, stdout=sys.stdout, stderr=sys.stderr)
if int(process.returncode) >= 1:
sys.stderr.buffer.write(process.stderr) #snakemake writes error in stdout
sys.stdout.buffer.write(process.stdout)
sys.exit(1)
sys.stdout.buffer.write(process.stdout)

if pdf:
dag_cmd_snakemake = f"{cmd_snakemake_base} --dag | dot -Tpdf > schema_pipeline_dag.pdf"
click.secho(f" {dag_cmd_snakemake}\n", fg='bright_blue')
os.system(dag_cmd_snakemake)
rulegraph_cmd_snakemake = f"{cmd_snakemake_base} --rulegraph | dot -Tpdf > schema_pipeline_global.pdf"
click.secho(f" {rulegraph_cmd_snakemake}\n", fg='bright_blue')
os.system(rulegraph_cmd_snakemake)
filegraph_cmd_snakemake = f"{cmd_snakemake_base} --filegraph | dot -Tpdf > schema_pipeline_files.pdf"
click.secho(f" {filegraph_cmd_snakemake}\n", fg='bright_blue')
os.system(filegraph_cmd_snakemake)
build_pdf(cmd_snakemake_base)
52 changes: 23 additions & 29 deletions culebrONT/snakefiles/Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -186,10 +186,10 @@ rule rule_graph:
tmp = f"{output_dir}FINAL_REPORT/dag.tmp",
cmd = culebront.string_to_dag
output:
dag = f"{output_dir}FINAL_REPORT/dag.png"
dag = f"{output_dir}FINAL_REPORT/dag.png",
log:
output = f"{output_dir}LOGS/Graph.o",
error = f"{output_dir}LOGS/Graph.e"
output = f"{output_dir}FINAL_REPORT/LOGS/GRAPH.o",
error = f"{output_dir}FINAL_REPORT/LOGS/GRAPH.e"
message:
"""
making dag ...
Expand All @@ -212,8 +212,8 @@ rule run_report_snakemake:
output:
report_snakemake = f"{output_dir}FINAL_REPORT/snake_report.html"
log:
output = f"{output_dir}LOGS/run_report_snakemake.o",
error = f"{output_dir}LOGS/run_report_snakemake.e"
output = f"{output_dir}FINAL_REPORT/LOGS/REPORT-SNAKE.o",
error = f"{output_dir}FINAL_REPORT/LOGS/REPORT-SNAKE.e"
message:
"""
making report ...
Expand All @@ -239,8 +239,8 @@ rule run_flagstats_stats:
assembly_list = culebront.assembly_tools_activated,
out_dir = directory(f"{output_dir}{{fastq}}/")
log:
output = f"{output_dir}LOGS/run_flagstats_stats/{{fastq}}.o",
error = f"{output_dir}LOGS/run_flagstats_stats/{{fastq}}.e"
output = f"{output_dir}{{fastq}}/REPORT/LOGS/run_flagstats_stats/{{fastq}}.o",
error = f"{output_dir}{{fastq}}/REPORT/LOGS/run_flagstats_stats/{{fastq}}.e"
message:
"""
make stats from flagstats
Expand All @@ -262,8 +262,8 @@ rule run_busco_stats:
assembly_list = culebront.assembly_tools_activated,
out_dir = directory(f"{output_dir}{{fastq}}/")
log:
output = f"{output_dir}LOGS/run_busco_stats/{{fastq}}.o",
error = f"{output_dir}LOGS/run_busco_stats/{{fastq}}.e"
output = f"{output_dir}{{fastq}}/REPORT/LOGS/{{fastq}}_BUSCO-STATS.o",
error = f"{output_dir}{{fastq}}/REPORT/LOGS/{{fastq}}_BUSCO-STATS.e"
message:
"""
make stats
Expand All @@ -281,8 +281,8 @@ rule run_racon_version:
output:
version = f"{output_dir}{{fastq}}/REPORT/RACON-version.txt"
log:
output = f"{output_dir}LOGS/run_racon_version/{{fastq}}-RACON.o",
error = f"{output_dir}LOGS/run_racon_version/{{fastq}}-RACON.e"
output = f"{output_dir}{{fastq}}/REPORT/LOGS/{{fastq}}-RACON-VERSION.o",
error = f"{output_dir}{{fastq}}/REPORT/LOGS/{{fastq}}-RACON-VERSION.e"
singularity:
tools_config['SINGULARITY']['TOOLS']
envmodules:
Expand All @@ -305,8 +305,8 @@ rule run_busco_version:
busco_version = f"{output_dir}{{fastq}}/REPORT/BUSCO-version.txt",
augustus_version = f"{output_dir}{{fastq}}/REPORT/BUSCO_AUGUSTUS-version.txt"
log:
output = f"{output_dir}LOGS/run_busco_version/{{fastq}}.o",
error = f"{output_dir}LOGS/run_busco_version/{{fastq}}.e"
output = f"{output_dir}{{fastq}}/REPORT/LOGS/{{fastq}}_BUSCO-VERSION.o",
error = f"{output_dir}{{fastq}}/REPORT/LOGS/{{fastq}}_BUSCO-VERSION.e"
message:
"""
busco version
Expand Down Expand Up @@ -347,12 +347,6 @@ def get_inputs_benchmark(wildcards):
assemblers=culebront.assembly_tools_activated,
correction=['PILON'],
nb = range(1, int(nb_pilon_rounds)+1))
# if culebront.quality_tools_activated:
# dico_benchmark_inputs["quality_list"] = expand(f"{output_dir}{{{{fastq}}}}/BENCHMARK/POLISHING/{{assemblers}}_{{polishers}}{{nb}}.txt",
# assemblers=culebront.assembly_tools_activated,
# polishers=culebront.polishing_tools_activated,
# nb = range(1, int(nb_racon_rounds)+1))
#pprint.pprint(dico_benchmark_inputs)
return dico_benchmark_inputs

rule run_benchmark_time:
Expand All @@ -369,8 +363,8 @@ rule run_benchmark_time:
sample = f"{{fastq}}",
dico = get_inputs_benchmark
log:
output = f"{output_dir}LOGS/run_benchmark_time/{{fastq}}.o",
error = f"{output_dir}LOGS/run_benchmark_time/{{fastq}}.e"
output = f"{output_dir}{{fastq}}/REPORT/LOGS/{{fastq}}_BENCHMARK-TIME.o",
error = f"{output_dir}{{fastq}}/REPORT/LOGS/{{fastq}}_BENCHMARK-TIME.e"
message:
"""
unpacking final dico and benchmark
Expand Down Expand Up @@ -399,8 +393,8 @@ rule run_get_versions:
picking software versions used by CulebrONT
"""
log:
output=f"{output_dir}LOGS/GETVERSIONS/get_versions.o",
error = f"{output_dir}LOGS/GETVERSIONS/get_versions.e"
output = f'{output_dir}versions/LOGS/GET-VERSIONS.o',
error = f'{output_dir}versions/LOGS/GET-VERSIONS.e'
script:
f"{SNAKEMAKE_SCRIPTS}/get_versions.py"

Expand All @@ -414,8 +408,8 @@ rule stats_assembly:
params:
sample = '{fastq}'
log:
output = f"{output_dir}LOGS/stats_assembly/{{fastq}}.o",
error = f"{output_dir}LOGS/stats_assembly/{{fastq}}.e"
output = f"{output_dir}FINAL_REPORT/LOGS/{{fastq}}_STATS-ASSEMBLIES.o",
error = f"{output_dir}FINAL_REPORT/LOGS/{{fastq}}_STATS-ASSEMBLIES.e"
message:
"""
Launching {rule}
Expand All @@ -442,8 +436,8 @@ rule copy_final_assemblies:
params:
sample = '{fastq}'
log:
output = f"{output_dir}LOGS/copy_final_assemblies/{{fastq}}_{{assemblers}}_{{quality_step}}.o",
error = f"{output_dir}LOGS/copy_final_assemblies/{{fastq}}_{{assemblers}}_{{quality_step}}.e"
output = f"{output_dir}ASSEMBLIES/LOGS/{{fastq}}_{{assemblers}}_{{quality_step}}_CP-FINAL-ASSEMBLIES.o",
error = f"{output_dir}ASSEMBLIES/LOGS/{{fastq}}_{{assemblers}}_{{quality_step}}_CP-FINAL-ASSEMBLIES.e"
message:
"""
Launching {rule}
Expand Down Expand Up @@ -524,8 +518,8 @@ rule run_report:
output:
report = f"{output_dir}FINAL_REPORT/CulebrONT_report.html"
log:
output = f"{output_dir}LOGS/run_report.o",
error = f"{output_dir}LOGS/run_report.e"
output = f"{output_dir}FINAL_REPORT/LOGS/REPORT.o",
error = f"{output_dir}FINAL_REPORT/LOGS/REPORT.e"
message:
"""
print final CulebrONT_report ...
Expand Down
35 changes: 17 additions & 18 deletions culebrONT/snakefiles/assemblers.snake
View file
Original file line number Diff line number Diff line change
Expand Up @@ -18,8 +18,8 @@ rule run_flye:
options= f"{config['params']['FLYE']['OPTIONS']}",
mode= f"{config['params']['FLYE']['MODE']}",
log:
output = f"{output_dir}{{fastq}}/LOGS/ASSEMBLER/FLYE/{{fastq}}_FLYE.o",
error = f"{output_dir}{{fastq}}/LOGS/ASSEMBLER/FLYE/{{fastq}}_FLYE.e",
output = f"{output_dir}{{fastq}}/ASSEMBLERS/FLYE/ASSEMBLER/LOGS/{{fastq}}_FLYE.o",
error = f"{output_dir}{{fastq}}/ASSEMBLERS/FLYE/ASSEMBLER/LOGS/{{fastq}}_FLYE.e",
benchmark:
f"{output_dir}{{fastq}}/BENCHMARK/ASSEMBLER/FLYE.txt"
message:
Expand Down Expand Up @@ -73,8 +73,8 @@ rule run_canu:
options = f"{config['params']['CANU']['OPTIONS']}",
mode= f"{config['params']['CANU']['MODE']}",
log:
output = f"{output_dir}{{fastq}}/LOGS/ASSEMBLER/CANU/{{fastq}}_CANU.o",
error = f"{output_dir}{{fastq}}/LOGS/ASSEMBLER/CANU/{{fastq}}_CANU.e",
output = f"{output_dir}{{fastq}}/ASSEMBLERS/CANU/ASSEMBLER/LOGS/{{fastq}}_CANU.o",
error = f"{output_dir}{{fastq}}/ASSEMBLERS/CANU/ASSEMBLER/LOGS/{{fastq}}_CANU.e",
benchmark:
f"{output_dir}{{fastq}}/BENCHMARK/ASSEMBLER/CANU.txt"
message:
Expand Down Expand Up @@ -119,7 +119,7 @@ rule run_minimap_for_miniasm:
paf = f"{output_dir}{{fastq}}/ASSEMBLERS/MINIASM/ASSEMBLER/output_minimap2.paf",
version = f"{output_dir}{{fastq}}/ASSEMBLERS/MINIASM/ASSEMBLER/MINIMAP2-version.txt"
log:
error = f"{output_dir}{{fastq}}/LOGS/ASSEMBLER/MINIASM/{{fastq}}_MINIASM.e",
error = f"{output_dir}{{fastq}}/ASSEMBLERS/MINIASM/ASSEMBLER/LOGS/{{fastq}}_MINIMAP4MINIASM.e",
benchmark:
f"{output_dir}{{fastq}}/BENCHMARK/ASSEMBLER/MINIASM.txt"
message:
Expand Down Expand Up @@ -157,7 +157,7 @@ rule run_miniasm:
gfa_miniasm = f"{output_dir}{{fastq}}/ASSEMBLERS/MINIASM/ASSEMBLER/output_miniasm.gfa", # voir si à utiliser par gfapy
version = f"{output_dir}{{fastq}}/ASSEMBLERS/MINIASM/ASSEMBLER/MINIASM-version.txt"
log:
error = f"{output_dir}{{fastq}}/LOGS/ASSEMBLER/MINIASM/{{fastq}}_MINIASM.e",
error = f"{output_dir}{{fastq}}/ASSEMBLERS/MINIASM/ASSEMBLER/LOGS/{{fastq}}_MINIASM.e",
benchmark:
f"{output_dir}{{fastq}}/BENCHMARK/ASSEMBLER/MINIMAP4MINIASM.txt"
message:
Expand Down Expand Up @@ -197,14 +197,13 @@ rule run_minipolish:
gfa_miniasm = rules.run_miniasm.output.gfa_miniasm
output:
gfa_minipolish = f"{output_dir}{{fastq}}/ASSEMBLERS/MINIASM/ASSEMBLER/output_minipolish.gfa",
#fasta = f"{output_dir}{{fastq}}/ASSEMBLERS/MINIASM/POLISHING/RACON/racon_{nb_racon_rounds}/assembly.racon{nb_racon_rounds}{TMP}.fasta" if config['POLISHING']['RACON'] else f"{output_dir}{{fastq}}/ASSEMBLERS/MINIASM/ASSEMBLER/assembly{add_circular_name}.fasta",
fasta = f"{output_dir}{{fastq}}/ASSEMBLERS/MINIASM/POLISHING/RACON/racon_{nb_racon_rounds}/assembly.racon{nb_racon_rounds}{TMP}.fasta",
info = f"{output_dir}{{fastq}}/ASSEMBLERS/MINIASM/ASSEMBLER/assembly_info{TMP}.txt",
version = f"{output_dir}{{fastq}}/ASSEMBLERS/MINIASM/ASSEMBLER/MINIPOLISH-version.txt"
params:
racon_rounds = config['params']['RACON']['RACON_ROUNDS'] if config['POLISHING']['RACON'] else 2,
log:
error = f"{output_dir}{{fastq}}/LOGS/ASSEMBLER/MINIASM/{{fastq}}_MINIASM_MINIPOLISH.e"
error = f"{output_dir}{{fastq}}/ASSEMBLERS/MINIASM/ASSEMBLER/LOGS/{{fastq}}_MINIASM_MINIPOLISH.e"
benchmark:
f"{output_dir}{{fastq}}/BENCHMARK/ASSEMBLER/MINIASM_MINIPOLISH.txt"
message:
Expand Down Expand Up @@ -250,8 +249,8 @@ rule run_raven:
gfa = f"{output_dir}{{fastq}}/ASSEMBLERS/RAVEN/ASSEMBLER/assembly_info.txt",
version = f"{output_dir}{{fastq}}/ASSEMBLERS/RAVEN/ASSEMBLER/RAVEN-version.txt"
log:
output = f"{output_dir}{{fastq}}/LOGS/ASSEMBLER/RAVEN/{{fastq}}_RAVEN.o",
error = f"{output_dir}{{fastq}}/LOGS/ASSEMBLER/RAVEN/{{fastq}}_RAVEN.e",
error = f"{output_dir}{{fastq}}/ASSEMBLERS/RAVEN/ASSEMBLER/LOGS/{{fastq}}_RAVEN.e",
output = f"{output_dir}{{fastq}}/ASSEMBLERS/RAVEN/ASSEMBLER/LOGS/{{fastq}}_RAVEN.o"
benchmark:
f"{output_dir}{{fastq}}/BENCHMARK/ASSEMBLER/RAVEN.txt"
message:
Expand Down Expand Up @@ -292,8 +291,8 @@ rule convert_fastq_to_fasta:
output:
reads_on_fasta = f"{output_dir}{{fastq}}/MISC/FASTQ2FASTA/{{fastq}}.fasta",
log:
output = f"{output_dir}{{fastq}}/LOGS/MISC/FASTQ2FASTA/{{fastq}}_FASTQ2FASTA.o",
error = f"{output_dir}{{fastq}}/LOGS/MISC/FASTQ2FASTA/{{fastq}}_FASTQ2FASTA.e",
output = f"{output_dir}{{fastq}}/MISC/FASTQ2FASTA/LOGS/{{fastq}}_FASTQ2FASTA.o",
error = f"{output_dir}{{fastq}}/MISC/FASTQ2FASTA/LOGS/{{fastq}}_FASTQ2FASTA.e",
benchmark:
f"{output_dir}{{fastq}}/BENCHMARK/ASSEMBLER/FASTQ2FASTA.txt"
shell:
Expand Down Expand Up @@ -322,8 +321,8 @@ rule run_smartdenovo:
fasta = f"{output_dir}{{fastq}}/ASSEMBLERS/SMARTDENOVO/ASSEMBLER/assembly2Circ.fasta" if config['CIRCULAR'] else f"{output_dir}{{fastq}}/ASSEMBLERS/SMARTDENOVO/ASSEMBLER/assembly.fasta",
version = f"{output_dir}{{fastq}}/ASSEMBLERS/SMARTDENOVO/ASSEMBLER/SMARTDENOVO-version.txt",
log:
output = f"{output_dir}{{fastq}}/LOGS/ASSEMBLER/SMARTDENOVO/{{fastq}}_SMARTDENOVO.o",
error = f"{output_dir}{{fastq}}/LOGS/ASSEMBLER/SMARTDENOVO/{{fastq}}_SMARTDENOVO.e",
error = f"{output_dir}{{fastq}}/ASSEMBLERS/SMARTDENOVO/ASSEMBLER/LOGS/{{fastq}}_SMARTDENOVO.e",
output = f"{output_dir}{{fastq}}/ASSEMBLERS/SMARTDENOVO/ASSEMBLER/LOGS/{{fastq}}_SMARTDENOVO.o"
benchmark:
f"{output_dir}{{fastq}}/BENCHMARK/ASSEMBLER/SMARTDENOVO.txt"
message:
Expand Down Expand Up @@ -376,8 +375,9 @@ rule run_shasta:
gfa = f"{output_dir}{{fastq}}/ASSEMBLERS/SHASTA/ASSEMBLER/assembly_info.txt",
version = f"{output_dir}{{fastq}}/ASSEMBLERS/SHASTA/ASSEMBLER/SHASTA-version.txt",
log:
output = f"{output_dir}{{fastq}}/LOGS/ASSEMBLER/SHASTA/{{fastq}}_SHASTA.o",
error = f"{output_dir}{{fastq}}/LOGS/ASSEMBLER/SHASTA/{{fastq}}_SHASTA.e",
error = f"{output_dir}{{fastq}}/ASSEMBLERS/SHASTA/ASSEMBLER/LOGS/{{fastq}}_SHASTA.e",
output = f"{output_dir}{{fastq}}/ASSEMBLERS/SHASTA/ASSEMBLER/LOGS/{{fastq}}_SHASTA.o"

benchmark:
f"{output_dir}{{fastq}}/BENCHMARK/ASSEMBLER/SHASTA.txt"
message:
Expand Down Expand Up @@ -408,5 +408,4 @@ rule run_shasta:
shasta --command assemble --input {input.reads_on_fasta} {params.memory_mode} {params.memory_backing} --threads {threads} {params.options};
{params.cmd_mv_fasta};
{params.cmd_mv_gfa} ) 1>{log.output} 2>{log.error}
"""

"""
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