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Commit 527d38c6 authored by Laura Denies's avatar Laura Denies
Browse files

update envs

parent 660212ac
...@@ -19,5 +19,5 @@ pathofact: ...@@ -19,5 +19,5 @@ pathofact:
long: "02:00:00" long: "02:00:00"
mem: mem:
normal_mem_per_core_gb: "4G" normal_mem_per_core_gb: "4G"
big_mem_cores: 4 big_mem_cores: 8
big_mem_per_core_gb: "30G" big_mem_per_core_gb: "30G"
name: DeepARG_env_new
channels: channels:
- bioconda - bioconda
- conda-forge - conda-forge
- defaults - defaults
dependencies: dependencies:
- _libgcc_mutex=0.1=conda_forge - _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=0_gnu - _openmp_mutex=4.5=1_gnu
- biopython=1.76=py27h516909a_0
- boost=1.68.0=py27h8619c78_1001 - boost=1.68.0=py27h8619c78_1001
- boost-cpp=1.68.0=h11c811c_1000 - boost-cpp=1.68.0=h11c811c_1000
- bzip2=1.0.8=h516909a_2 - bzip2=1.0.8=h516909a_2
- ca-certificates=2020.4.5.2=hecda079_0 - ca-certificates=2020.6.20=hecda079_0
- certifi=2019.11.28=py27h8c360ce_1 - certifi=2019.11.28=py27h8c360ce_1
- diamond=0.9.24=ha888412_1 - diamond=0.9.24=ha888412_1
- icu=58.2=hf484d3e_1000 - icu=58.2=hf484d3e_1000
- ld_impl_linux-64=2.34=h53a641e_5 - libblas=3.8.0=17_openblas
- libblas=3.8.0=14_openblas - libcblas=3.8.0=17_openblas
- libcblas=3.8.0=14_openblas - libffi=3.3=he6710b0_2
- libedit=3.1.20191231=h46ee950_0 - libgcc-ng=9.3.0=h24d8f2e_14
- libffi=3.2.1=he1b5a44_1007 - libgfortran-ng=7.5.0=hdf63c60_14
- libgcc-ng=9.2.0=h24d8f2e_2 - libgomp=9.3.0=h24d8f2e_14
- libgfortran-ng=7.5.0=hdf63c60_6 - liblapack=3.8.0=17_openblas
- libgomp=9.2.0=h24d8f2e_2 - libopenblas=0.3.10=pthreads_hb3c22a3_4
- liblapack=3.8.0=14_openblas - libstdcxx-ng=9.3.0=hdf63c60_14
- libopenblas=0.3.7=h5ec1e0e_6 - ncurses=6.2=he1b5a44_1
- libstdcxx-ng=9.2.0=hdf63c60_2
- ncurses=6.1=hf484d3e_1002
- numpy=1.16.5=py27h95a1406_0 - numpy=1.16.5=py27h95a1406_0
- openssl=1.1.1g=h516909a_0
- pip=20.1.1=pyh9f0ad1d_0 - pip=20.1.1=pyh9f0ad1d_0
- python=2.7.16=h9bab390_7 - python=2.7.18=h15b4118_1
- python_abi=2.7=1_cp27mu - python_abi=2.7=1_cp27mu
- readline=7.0=hf8c457e_1001 - readline=8.0=he28a2e2_2
- setuptools=44.0.0=py27_0 - setuptools=44.0.0=py27_0
- sqlite=3.31.1=h7b6447c_0 - sqlite=3.32.3=hcee41ef_1
- tk=8.6.10=hed695b0_0 - tk=8.6.10=hed695b0_0
- wheel=0.34.2=py_1 - wheel=0.34.2=py_1
- xz=5.2.5=h516909a_0 - xz=5.2.5=h516909a_1
- zlib=1.2.11=h516909a_1006 - zlib=1.2.11=h516909a_1006
- pip:
- biopython==1.73
- deeparg==1.0.1
- idna==2.6
- joblib==0.13.0
- requests==2.18.4
- scikit-learn==0.19.1
- six==1.15.0
- tabulate==0.8.7
- theano==0.8.2
- tqdm==4.48.2
- urllib3==1.22
prefix: /home/users/ldenies/apps/miniconda3/envs/DeepARG_env_new
name: virfinder
channels: channels:
- bioconda
- conda-forge - conda-forge
- bioconda
- defaults - defaults
dependencies: dependencies:
- _libgcc_mutex=0.1=main - _libgcc_mutex=0.1=main
...@@ -11,8 +12,8 @@ dependencies: ...@@ -11,8 +12,8 @@ dependencies:
- binutils_linux-64=2.31.1=h6176602_8 - binutils_linux-64=2.31.1=h6176602_8
- biopython=1.74=py36h516909a_0 - biopython=1.74=py36h516909a_0
- c-ares=1.15.0=h516909a_1001 - c-ares=1.15.0=h516909a_1001
- ca-certificates=2020.4.5.1=hecc5488_0 - ca-certificates=2019.9.11=hecc5488_0
- certifi=2020.4.5.1=py36h9f0ad1d_0 - certifi=2019.9.11=py36_0
- gast=0.3.2=py_0 - gast=0.3.2=py_0
- gcc_impl_linux-64=7.3.0=habb00fd_1 - gcc_impl_linux-64=7.3.0=habb00fd_1
- gcc_linux-64=7.3.0=h553295d_8 - gcc_linux-64=7.3.0=h553295d_8
...@@ -22,7 +23,6 @@ dependencies: ...@@ -22,7 +23,6 @@ dependencies:
- gxx_linux-64=7.3.0=h553295d_8 - gxx_linux-64=7.3.0=h553295d_8
- h5py=2.10.0=nompi_py36h513d04c_100 - h5py=2.10.0=nompi_py36h513d04c_100
- hdf5=1.10.5=nompi_h3c11f04_1103 - hdf5=1.10.5=nompi_h3c11f04_1103
- intel-openmp=2020.1=217
- joblib=0.13.2=py_0 - joblib=0.13.2=py_0
- keras=2.3.0=py36_0 - keras=2.3.0=py36_0
- keras-applications=1.0.8=py_1 - keras-applications=1.0.8=py_1
...@@ -40,16 +40,13 @@ dependencies: ...@@ -40,16 +40,13 @@ dependencies:
- mako=1.1.0=py_0 - mako=1.1.0=py_0
- markdown=3.1.1=py_0 - markdown=3.1.1=py_0
- markupsafe=1.1.1=py36h14c3975_0 - markupsafe=1.1.1=py36h14c3975_0
- mkl=2020.1=217
- mkl-service=2.3.0=py36he904b0f_0
- ncurses=6.1=hf484d3e_1002 - ncurses=6.1=hf484d3e_1002
- numpy=1.17.2=py36h95a1406_0 - numpy=1.17.2=py36h95a1406_0
- openssl=1.1.1g=h516909a_0 - openssl=1.1.1c=h516909a_0
- pip=19.2.3=py36_0 - pip=19.2.3=py36_0
- protobuf=3.9.2=py36he1b5a44_0 - protobuf=3.9.2=py36he1b5a44_0
- pygpu=0.7.6=py36h3010b51_1000 - pygpu=0.7.6=py36h3010b51_1000
- python=3.6.7=h357f687_1005 - python=3.6.7=h357f687_1005
- python_abi=3.6=1_cp36m
- pyyaml=5.1.2=py36h516909a_0 - pyyaml=5.1.2=py36h516909a_0
- readline=8.0=hf8c457e_0 - readline=8.0=hf8c457e_0
- scikit-learn=0.21.3=py36hcdab131_0 - scikit-learn=0.21.3=py36hcdab131_0
...@@ -70,4 +67,5 @@ dependencies: ...@@ -70,4 +67,5 @@ dependencies:
- xz=5.2.4=h14c3975_1001 - xz=5.2.4=h14c3975_1001
- yaml=0.1.7=h14c3975_1001 - yaml=0.1.7=h14c3975_1001
- zlib=1.2.11=h516909a_1006 - zlib=1.2.11=h516909a_1006
prefix: /home/users/ldenies/apps/miniconda3/envs/virfinder
name: MOB_suit_new
channels: channels:
- bioconda/label/cf201901
- bioconda - bioconda
- conda-forge - conda-forge
- defaults - defaults
dependencies: dependencies:
- _libgcc_mutex=0.1=conda_forge - _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=1_llvm - _openmp_mutex=4.5=1_gnu
- biopython=1.76=py38h516909a_0 - bcftools=1.8=h4da6232_3
- bio_assembly_refinement=0.5.1=py36_1
- biopython=1.77=py36h8c4c3a4_0
- blast=2.5.0=hc0b0e79_3 - blast=2.5.0=hc0b0e79_3
- blosc=1.19.0=he1b5a44_0 - blosc=1.20.0=he1b5a44_0
- boost=1.73.0=py38hd103949_0 - boost=1.73.0=py36h6957fcd_1
- boost-cpp=1.73.0=h6c875cf_0 - boost-cpp=1.73.0=h9359b55_3
- bwa=0.7.17=ha92aebf_3
- bzip2=1.0.8=h516909a_2 - bzip2=1.0.8=h516909a_2
- ca-certificates=2020.4.5.2=hecda079_0 - c-ares=1.11.0=h470a237_1
- capnproto=0.6.1=hfc679d8_1 - ca-certificates=2020.6.20=hecda079_0
- certifi=2020.4.5.2=py38h32f6830_0 - certifi=2020.6.20=py36h9f0ad1d_0
- dbus=1.13.6=he372182_0 - circlator=1.5.5=py36_1
- ete3=3.1.1=pyh9f0ad1d_2 - curl=7.71.1=he644dc0_4
- expat=2.2.9=he1b5a44_2 - et_xmlfile=1.0.1=py_1001
- fontconfig=2.13.1=h86ecdb6_1001 - hdf5=1.10.6=nompi_h3c11f04_101
- freetype=2.10.2=he06d7ca_0 - htslib=1.7=0
- gettext=0.19.8.1=hc5be6a0_1002 - icu=67.1=he1b5a44_0
- glib=2.64.3=h6f030ca_0 - jdcal=1.4.1=py_0
- gsl=2.5=h294904e_1 - krb5=1.17.1=hfafb76e_2
- gst-plugins-base=1.14.5=h0935bb2_2 - ld_impl_linux-64=2.34=hc38a660_9
- gstreamer=1.14.5=h36ae1b5_2 - libblas=3.8.0=17_openblas
- hdf5=1.10.6=nompi_h3c11f04_100 - libcblas=3.8.0=17_openblas
- icu=64.2=he1b5a44_1 - libcurl=7.71.1=hcdd3856_4
- jpeg=9d=h516909a_0 - libdeflate=1.0=h470a237_0
- krb5=1.17.1=h2fd8d38_0 - libedit=3.1.20191231=h46ee950_1
- ld_impl_linux-64=2.34=h53a641e_5 - libev=4.33=h516909a_0
- libblas=3.8.0=16_openblas
- libcblas=3.8.0=16_openblas
- libclang=9.0.1=default_hde54327_0
- libcurl=7.69.1=hf7181ac_0
- libedit=3.1.20191231=h46ee950_0
- libffi=3.2.1=he1b5a44_1007 - libffi=3.2.1=he1b5a44_1007
- libgcc-ng=9.2.0=h24d8f2e_2 - libgcc=7.2.0=h69d50b8_2
- libgfortran-ng=7.5.0=hdf63c60_6 - libgcc-ng=9.3.0=h24d8f2e_14
- libiconv=1.15=h516909a_1006 - libgfortran-ng=7.5.0=hdf63c60_14
- liblapack=3.8.0=16_openblas - libgomp=9.3.0=h24d8f2e_14
- libllvm9=9.0.1=he513fc3_1 - liblapack=3.8.0=17_openblas
- libopenblas=0.3.9=h5ec1e0e_0 - libnghttp2=1.41.0=hab1572f_1
- libpng=1.6.37=hed695b0_1 - libopenblas=0.3.10=pthreads_hb3c22a3_4
- libssh2=1.9.0=hab1572f_2 - libssh2=1.9.0=hab1572f_5
- libstdcxx-ng=9.2.0=hdf63c60_2 - libstdcxx-ng=9.3.0=hdf63c60_14
- libuuid=2.32.1=h14c3975_1000
- libxcb=1.13=h14c3975_1002
- libxkbcommon=0.10.0=he1b5a44_0
- libxml2=2.9.10=hee79883_0
- libxslt=1.1.33=h31b3aaa_0
- llvm-openmp=10.0.0=hc9558a2_0
- lxml=4.5.1=py38hbb43d70_0
- lz4-c=1.9.2=he1b5a44_1 - lz4-c=1.9.2=he1b5a44_1
- lzo=2.10=h14c3975_1000 - lzo=2.10=h14c3975_1000
- mash=2.2.2=h3d38be6_1 - mash=1.1=0
- mob_suite=3.0.0=py_1 - mob_suite=1.4.9=py_1
- mock=4.0.2=py38h32f6830_0 - mock=4.0.2=py36h9f0ad1d_0
- ncurses=6.1=hf484d3e_1002 - mummer=3.23=pl526_8
- nspr=4.25=he1b5a44_0 - ncurses=6.2=he1b5a44_1
- nss=3.47=he751ad9_0 - numexpr=2.7.1=py36h830a2c2_1
- numexpr=2.7.1=py38hcb8c335_1 - numpy=1.19.1=py36h7314795_0
- numpy=1.18.5=py38h8854b6b_0 - openpyxl=2.4.0=py36_0
- openssl=1.1.1g=h516909a_0 - openssl=1.1.1g=h516909a_1
- pandas=1.0.4=py38hcb8c335_0 - pandas=1.1.0=py36h831f99a_0
- pcre=8.44=he1b5a44_0 - perl=5.26.2=h516909a_1006
- pip=20.1.1=py_1 - pip=20.2.1=py_0
- pthread-stubs=0.4=h14c3975_1001 - prodigal=2.6.3=1
- pycurl=7.43.0.5=py38h16ce93b_0 - pycurl=7.43.0.5=py36h2e6c563_2
- pyqt=5.12.3=py38ha8c2ead_3 - pyfastaq=3.17.0=py36_1
- pytables=3.6.1=py38h1b207d3_2 - pymummer=0.10.3=py36_1
- python=3.8.3=cpython_he5300dc_0 - pysam=0.14.1=py36hae42fb6_1
- pytables=3.6.1=py36h7b0bd57_2
- python=3.6.11=h425cb1d_1_cpython
- python-dateutil=2.8.1=py_0 - python-dateutil=2.8.1=py_0
- python_abi=3.8=1_cp38 - python_abi=3.6=1_cp36m
- pytz=2020.1=pyh9f0ad1d_0 - pytz=2020.1=pyh9f0ad1d_0
- qt=5.12.5=hd8c4c69_1 - readline=8.0=he28a2e2_2
- readline=8.0=hf8c457e_0 - samtools=1.7=1
- scipy=1.4.1=py38h18bccfc_3 - scipy=1.5.2=py36h3a855aa_0
- setuptools=47.1.1=py38h32f6830_0 - setuptools=49.2.1=py36h9f0ad1d_0
- six=1.15.0=pyh9f0ad1d_0 - six=1.15.0=pyh9f0ad1d_0
- sqlite=3.30.1=hcee41ef_0 - spades=3.13.0=0
- sqlite=3.32.3=hcee41ef_1
- tk=8.6.10=hed695b0_0 - tk=8.6.10=hed695b0_0
- wheel=0.34.2=py_1 - wheel=0.34.2=py_1
- xorg-kbproto=1.0.7=h14c3975_1002 - xz=5.2.5=h516909a_1
- xorg-libice=1.0.10=h516909a_0
- xorg-libsm=1.2.3=h84519dc_1000
- xorg-libx11=1.6.9=h516909a_0
- xorg-libxau=1.0.9=h14c3975_0
- xorg-libxdmcp=1.1.3=h516909a_0
- xorg-libxext=1.3.4=h516909a_0
- xorg-libxrender=0.9.10=h516909a_1002
- xorg-renderproto=0.11.1=h14c3975_1002
- xorg-xextproto=7.3.0=h14c3975_1002
- xorg-xproto=7.0.31=h14c3975_1007
- xz=5.2.5=h516909a_0
- zlib=1.2.11=h516909a_1006 - zlib=1.2.11=h516909a_1006
- zstd=1.4.4=h6597ccf_3 - zstd=1.4.5=h6597ccf_2
- pip: prefix: /home/users/ldenies/apps/miniconda3/envs/MOB_suit_new
- pyqt5-sip==4.19.18
- pyqtchart==5.12
- pyqtwebengine==5.12.1
...@@ -63,7 +63,7 @@ rule run_VirFinder: ...@@ -63,7 +63,7 @@ rule run_VirFinder:
threads: config["pathofact"]["mem"]["big_mem_cores"] threads: config["pathofact"]["mem"]["big_mem_cores"]
message: "Executing Deep-VirFinder with {threads} threads on the following sample(s): {wildcards.project} - {wildcards.sample}" message: "Executing Deep-VirFinder with {threads} threads on the following sample(s): {wildcards.project} - {wildcards.sample}"
shell: shell:
"python {config[pathofact][deepvirfinder]} -i {input} -o {config[pathofact][datadir]}/{wildcards.project}/MGE/PathoFact_intermediate/phage/{wildcards.sample}/virfinder -c {threads} &> {log}" "python {config[pathofact][deepvirfinder]} -i {input} -o {config[pathofact][datadir]}/{wildcards.project}/PathoFact_intermediate/MGE/phage/{wildcards.sample}/virfinder -c {threads} &> {log}"
def aggregate_VirFinder(wildcards): def aggregate_VirFinder(wildcards):
checkpoint_output= checkpoints.splitcontig.get(**wildcards).output.split checkpoint_output= checkpoints.splitcontig.get(**wildcards).output.split
......
...@@ -65,7 +65,7 @@ rule generate_translation: ...@@ -65,7 +65,7 @@ rule generate_translation:
renamed=os.path.join(DATA_DIR,"{project}/PathoFact_intermediate/renamed/{sample}_ID.faa"), renamed=os.path.join(DATA_DIR,"{project}/PathoFact_intermediate/renamed/{sample}_ID.faa"),
original=os.path.join(DATA_DIR,"{project}/PathoFact_intermediate/Prodigal/{sample}.faa") original=os.path.join(DATA_DIR,"{project}/PathoFact_intermediate/Prodigal/{sample}.faa")
output: output:
os.path.join(DATA_DIR,"{project}/renamed/{sample}_translation.tsv") os.path.join(DATA_DIR,"{project}/PathoFact_intermediate/renamed/{sample}_translation.tsv")
message: message:
"Generate {output} containing original fasta header with corresponding ID number: {wildcards.project} - {wildcards.sample}" "Generate {output} containing original fasta header with corresponding ID number: {wildcards.project} - {wildcards.sample}"
params: params:
......
...@@ -73,7 +73,7 @@ rule HMM_R_VIR: ...@@ -73,7 +73,7 @@ rule HMM_R_VIR:
positive=config["pathofact"]["vir_domains"] + "/positive_domains.tsv", positive=config["pathofact"]["vir_domains"] + "/positive_domains.tsv",
negative=config["pathofact"]["vir_domains"] + "/negative_domains.tsv", negative=config["pathofact"]["vir_domains"] + "/negative_domains.tsv",
shared=config["pathofact"]["vir_domains"] + "/shared_domains.tsv", shared=config["pathofact"]["vir_domains"] + "/shared_domains.tsv",
ID=os.path.join(DATA_DIR,"{project}/renamed/{sample}_translation.tsv") ID=os.path.join(DATA_DIR,"{project}/PathoFact_intermediate/renamed/{sample}_translation.tsv")
output: output:
temp(os.path.join(DATA_DIR,"{project}/PathoFact_intermediate/VIRULENCE/HMM_virulence/{sample}.hmm_results.csv")) temp(os.path.join(DATA_DIR,"{project}/PathoFact_intermediate/VIRULENCE/HMM_virulence/{sample}.hmm_results.csv"))
log: log:
......
This source diff could not be displayed because it is too large. You can view the blob instead.
This source diff could not be displayed because it is too large. You can view the blob instead.
This source diff could not be displayed because it is too large. You can view the blob instead.
# Test workflow: complete PathoFact pipeline + result checks
##################################################
# Configuration
# Config file
CONFIG = "test/test_config.yaml"
configfile: CONFIG
DATA_DIR=config["pathofact"]["datadir"]
# Libs
import os
import sys
import pandas
##################################################
# Sub-workflows
# PathoFact
subworkflow pathofact:
workdir:
"../"
snakefile:
"../Snakefile"
configfile:
CONFIG
##################################################
# Targets
os.path.join(DATA_DIR,
# PathoFact
PF = pathofact(
expand(
[
os.path.join(DATA_DIR,"{project}/PathoFact_report/AMR_MGE_prediction_{sample}_report.tsv"),
os.path.join(DATA_DIR,"{project}/PathoFact_report/Toxin_gene_library_{sample}_report.tsv"),
os.path.join(DATA_DIR,"{project}/PathoFact_report/Toxin_prediction_{sample}_report.tsv"),
os.path.join(DATA_DIR,"{project}/PathoFact_report/Virulence_prediction_{sample}_report.tsv"),
os.path.join(DATA_DIR,"{project}/PathoFact_report/PathoFact_{sample}_predictions.tsv")
],
project=config["pathofact"]["project"],
sample=config["pathofact"]["sample"]
)
)
# Checks
CHECKS = expand(
[
os.path.join(DATA_DIR,"{project}/PathoFact_report/AMR_MGE_prediction_{sample}_report.tsv.checked"),
os.path.join(DATA_DIR,"{project}/PathoFact_report/Toxin_gene_library_{sample}_report.tsv.checked"),
os.path.join(DATA_DIR,"{project}/PathoFact_report/Toxin_prediction_{sample}_report.tsv.checked"),
os.path.join(DATA_DIR,"{project}/PathoFact_report/Virulence_prediction_{sample}_report.tsv.checked"),
os.path.join(DATA_DIR,"{project}/PathoFact_report/PathoFact_{sample}_predictions.tsv.checked")
],
project=config["pathofact"]["project"],
sample=config["pathofact"]["sample"]
)
##################################################
# Rules
# All
rule all:
input:
# PathoFact
PF,
# Result checks
CHECKS
# Compare files
rule check:
input:
exp=os.path.join(DATA_DIR,"{project}/PathoFact_report/{{bname}}".format(
project=config["test"]["project"]
),
res=pathofact(os.path.join(DATA_DIR,"{project}/PathoFact_report/{{bname}}").format(
project=config["pathofact"]["project"]
)
output:
os.path.join(DATA_DIR,"{project}/PathoFact_report/{{bname}}.checked").format(
project=config["pathofact"]["project"]
)
log:
os.path.join(DATA_DIR,"{project}/PathoFact_report/{{bname}}.diff").format(
project=config["pathofact"]["project"]
)
params:
runtime=config["pathofact"]["runtime"]["short"],
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
shell:
"""
diff {input.exp} {input.res} > {log} && [ -s {log} ] || touch {output}
"""
# Test workflow: complete PathoFact pipeline + result checks
##################################################
# Configuration
# Config file
CONFIG = "test/test_config.yaml"
configfile: CONFIG
DATA_DIR=config["pathofact"]["datadir"]
# Libs
import os
import sys
import pandas
##################################################
# Sub-workflows
# PathoFact
subworkflow pathofact:
workdir:
"../"
snakefile:
"../Snakefile"
configfile:
CONFIG
##################################################
# Rules
rule all:
input: expand(os.path.join(DATA_DIR,"{project}/AMR_MGE_{sample}.checked"), project=config["pathofact"]["project"], sample=config["pathofact"]["sample"])
rule check_AMR_MGE:
input:
res=pathofact(os.path.join(DATA_DIR,"{project}/PathoFact_report/AMR_MGE_prediction_{sample}_report.tsv")),
exp=os.path.join(DATA_DIR,"output_expected/PathoFact_report/AMR_MGE_prediction_{sample}_report.tsv")
output: os.path.join(DATA_DIR,"{project}/AMR_MGE_{sample}.checked")
log: os.path.join(DATA_DIR,"{project}/AMR_MGE_{sample}.diff")
shell: "diff {input.exp} {input.res} > {log} && [ -s {log} ] || touch {output}"
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...@@ -23,4 +23,4 @@ pathofact: ...@@ -23,4 +23,4 @@ pathofact:
big_mem_per_core_gb: "30G" big_mem_per_core_gb: "30G"
test: test:
datadir: "test" datadir: "test"
project: "output_expected" project: "output_test"
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