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This is an archived project. Repository and other project resources are read-only.
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center-for-computational-genomics-and-data-science
public
QuaC
Commits
c4ef7d51
Commit
c4ef7d51
authored
4 years ago
by
Manavalan Gajapathy
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improves usage doc in readme
parent
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!2
QC under one umbrella (well mostly) under QuaC
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README.md
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-36
46 additions, 36 deletions
README.md
src/run_quac.py
+1
-1
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and
37 deletions
README.md
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46
−
36
View file @
c4ef7d51
...
...
@@ -12,8 +12,8 @@
-
[
Testing
](
#testing
)
-
[
How to run QuaC
](
#how-to-run-quac
)
-
[
Example usage
](
#example-usage
)
-
[
Output
](
#output
)
-
[
Dummy pedigree file creator
](
#dummy-pedigree-file-creator
)
-
[
Output
](
#output
)
-
[
Contributing
](
#contributing
)
-
[
Changelog
](
#changelog
)
...
...
@@ -167,13 +167,14 @@ python src/run_quac.py \
## How to run QuaC
In the activate conda environment, QuaC is run using script
`src/quac.py`
. Here are all the options available:
After activating the conda environment, QuaC pipeline is run using the wrapper script
`src/run_quac.py`
. Here are all
the options available:
```
sh
$
./src/run_quac.py
-h
usage: run_quac.py
[
-h
]
[
--project_name
]
[
--projects_path
]
[
--pedigree
]
[
--outdir
]
[
-m
]
[
--exome
]
[
--cluster_config
]
[
--log_dir
]
[
-e
]
[
-n
]
[
-l
]
[
--rerun_failed
]
[
--outdir
]
[
--exome
]
[
--cluster_config
]
[
--log_dir
]
[
-e
]
[
-n
]
[
-l
]
[
--rerun_failed
]
[
--slurm_partition
]
Wrapper tool
for
QuaC pipeline.
...
...
@@ -182,13 +183,13 @@ optional arguments:
QuaC workflow options:
--project_name
Project name
(
default: None
)
--projects_path
Path where all projects are hosted. Do
n
t include
--projects_path
Path where all projects are hosted. Do
no
t include
project name here.
(
default:
/data/project/worthey_lab/projects/
)
--pedigree
Pedigree filepath. Must correspond to the project
supplied via
--project_name
(
default: None
)
--outdir
Out directory path
(
default:
$USER_SCRATCH
/tmp/quac/results
)
$USER_SCRATCH
/tmp/quac/results
/test_project/analysis
)
--exome
Flag to run
in
exome mode
(
default: False
)
QuaC wrapper options:
...
...
@@ -198,7 +199,7 @@ QuaC wrapper options:
onfig.json
)
--log_dir
Directory path where logs
(
both workflow
's and
wrapper'
s
)
will be stored
(
default:
$USER_SCRATCH
/tmp/quac/
results/../
logs
)
$USER_SCRATCH
/tmp/quac/logs
)
-e
,
--extra_args
Pass additional custom args to snakemake. Equal symbol
is needed
for
assignment as
in
this example:
-e
=
'--
forceall'
(
default: None
)
...
...
@@ -210,55 +211,64 @@ QuaC wrapper options:
--rerun_failed
Number of
times
snakemake restarts failed jobs. This may
be
set
to
>
0 to avoid pipeline failing due to job fails
due to random SLURM issues
(
default: 0
)
--slurm_partition
Request a specific partition
for
the slurm resource
allocation
for
QuaC workflow. Available partitions
in
Cheaha are: express
(
max 2 hrs
)
, short
(
max 12 hrs
)
,
medium
(
max 50 hrs
)
, long
(
max 150 hrs
)
(
default: short
)
```
Note that options
`--project_name`
and
`--pedigree`
are both necessary. All samples, belonging to a project, that ne ed
to be analyzed should be supplied in a pedigree file format and provided to QuaC's wrapper script via
`--pedigree`
. This
repo also
[
includes a script that can create a dummy pedigree file
](
#dummy-pedigree-file-creator
)
with all samples
belonging to a project.
### Example usage
`project_name`
and
`pedigree`
are required
options
to run the tool.
Options
`project_name`
and
`pedigree`
are required to run the tool.
```
sh
# for a WGS projetcquac
python src/run_quac.py
--project_name
CF_CFF_PFarrell
--pedigree
data/raw/ped/CF_CFF_PFarrell.ped
# for an exome project
python src/run_quac.py
--project_name
HCC
--pedigree
data/raw/ped/HCC.ped
--exome
# run for an exome project which is not in the default CGDS projects_path
python src/run_quac.py
\
--project_name
UnusualCancers_CMGalluzi
\
--projects_path
/data/project/sloss/cgds_path_cmgalluzzi/
\
--pedigree
data/raw/ped/UnusualCancers_CMGalluzi.ped
\
--exome
# for a WGS project, and write results to a dir of choice
# to quack on a WGS project
python src/run_quac.py
\
--slurm_partition
medium
\
--project_name
CF_CFF_PFarrell
\
--pedigree
data/raw/ped/CF_CFF_PFarrell.ped
\
--outdir
/some/lake/with/plenty/ducks/
--pedigree
"data/raw/ped/CF_CFF_PFarrell.ped"
PROJECT
=
"MuscDyst_SU_MAlexander"
# to quack on a WGS project and write results to a dir of choice
PROJECT
=
"CF_CFF_PFarrell"
python src/run_quac.py
\
--slurm_partition
medium
\
--project_name
${
PROJECT
}
\
--outdir
/data/scratch/manag/tmp/quac/results/test_
${
PROJECT
}
/analysis
\
--pedigree
data/raw/ped/
${
PROJECT
}
.ped
-n
--pedigree
"data/raw/ped/
${
PROJECT
}
.ped"
\
--outdir
"/data/scratch/manag/tmp/quac/results/test_
${
PROJECT
}
/analysis"
# to quack on an exome project
python src/run_quac.py
\
--project_name
HCC
\
--pedigree
"data/raw/ped/HCC.ped"
\
--exome
# to quack on an exome project which is not in the default CGDS projects_path
python src/run_quac.py
\
--project_name
UnusualCancers_CMGalluzi
\
--projects_path
"/data/project/sloss/cgds_path_cmgalluzzi/"
\
--pedigree
"data/raw/ped/UnusualCancers_CMGalluzi.ped"
\
--exome
```
### Dummy pedigree file creator
Script
`src/create_dummy_ped.py`
creates a "dummy" pedigree file given a project's path as input. It's purpose is just
to create a basic pedigree file, which will lack sex (unless project tracking sheet is provided), relatedness and
affectedness info. See header of the script for usage instructions.
Note that we plan to use
[
phenotips
](
https://phenotips.com/
)
in future to produce fully capable pedigree file. One may
manually create them as well, but this could be error-prone.
## Output
QuaC results are stored at path specified via option
`--outdir`
(default:
`$USER_SCRATCH/tmp/quac/results`
). This
includes aggregated QC results produced by
[
multiqc
](
https://multiqc.info/
)
.
### Dummy pedigree file creator
Script
`src/create_dummy_ped.py`
creates a "dummy" pedigree file given a project path as input. It's purpose is just to
create a basic pedigree file, which will lack sex (unless project tracking sheet is provided), relatedness and affected
info. See header of the script for usage instructions.
Note that we plan to use phenotips in future to produce fully capable pedigree file. One may manually create them as
well, but this could be error-prone.
## Contributing
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src/run_quac.py
+
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−
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c4ef7d51
...
...
@@ -230,7 +230,7 @@ if __name__ == "__main__":
PROJECT_PATH_DEFAULT
=
"
/data/project/worthey_lab/projects/
"
WORKFLOW
.
add_argument
(
"
--projects_path
"
,
help
=
"
Path where all projects are hosted. Do
n
'
t include project name here.
"
,
help
=
"
Path where all projects are hosted. Do
no
t include project name here.
"
,
default
=
PROJECT_PATH_DEFAULT
,
type
=
lambda
x
:
is_valid_dir
(
PARSER
,
x
),
metavar
=
""
,
...
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