chore: use composite snakemake action [test] #1946
johanneskoesterAnnotations
1 error and 25 warnings
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Quick_Tests
Process completed with exit code 1.
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Linting
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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Formatting
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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Dryrun_Tests
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:198: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3.
To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels:
conda config --add channels defaults
For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html
deprecated.topic(
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Dryrun_Tests
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
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Dryrun_Tests
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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Dryrun_Tests
warning libmamba [ca-certificates-2024.8.30-hbcca054_0] The following files were already present in the environment:
- ssl/cacert.pem
- ssl/cert.pem
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Dryrun_Tests
warning libmamba [ld_impl_linux-64-2.43-h712a8e2_2] The following files were already present in the environment:
- bin/x86_64-conda-linux-gnu-ld
- bin/x86_64-conda_cos6-linux-gnu-ld
- x86_64-conda-linux-gnu/bin/ld
- x86_64-conda_cos6-linux-gnu/bin/ld
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Dryrun_Tests
warning libmamba [tzdata-2024b-hc8b5060_0] The following files were already present in the environment:
- share/zoneinfo/Africa/Abidjan
- share/zoneinfo/Africa/Accra
- share/zoneinfo/Africa/Addis_Ababa
- share/zoneinfo/Africa/Algiers
- share/zoneinfo/Africa/Asmara
- share/zoneinfo/Africa/Asmera
- share/zoneinfo/Africa/Bamako
- share/zoneinfo/Africa/Bangui
- share/zoneinfo/Africa/Banjul
- share/zoneinfo/Africa/Bissau
- share/zoneinfo/Africa/Blantyre
- share/zoneinfo/Africa/Brazzaville
- share/zoneinfo/Africa/Bujumbura
- share/zoneinfo/Africa/Cairo
- share/zoneinfo/Africa/Casablanca
- share/zoneinfo/Africa/Ceuta
- share/zoneinfo/Africa/Conakry
- share/zoneinfo/Africa/Dakar
- share/zoneinfo/Africa/Dar_es_Salaam
- share/zoneinfo/Africa/Djibouti
- share/zoneinfo/Africa/Douala
- share/zoneinfo/Africa/El_Aaiun
- share/zoneinfo/Africa/Freetown
- share/zoneinfo/Africa/Gaborone
- share/zoneinfo/Africa/Harare
- share/zoneinfo/Africa/Johannesburg
- share/zoneinfo/Africa/Juba
- share/zoneinfo/Africa/Kampala
- share/zoneinfo/Africa/Khartoum
- share/zoneinfo/Africa/Kigali
- share/zoneinfo/Africa/Kinshasa
- share/zoneinfo/Africa/Lagos
- share/zoneinfo/Africa/Libreville
- share/zoneinfo/Africa/Lome
- share/zoneinfo/Africa/Luanda
- share/zoneinfo/Africa/Lubumbashi
- share/zoneinfo/Africa/Lusaka
- share/zoneinfo/Africa/Malabo
- share/zoneinfo/Africa/Maputo
- share/zoneinfo/Africa/Maseru
- share/zoneinfo/Africa/Mbabane
- share/zoneinfo/Africa/Mogadishu
- share/zoneinfo/Africa/Monrovia
- share/zoneinfo/Africa/Nairobi
- share/zoneinfo/Africa/Ndjamena
- share/zoneinfo/Africa/Niamey
- share/zoneinfo/Africa/Nouakchott
- share/zoneinfo/Africa/Ouagadougou
- share/zoneinfo/Africa/Porto-Novo
- share/zoneinfo/Africa/Sao_Tome
- share/zoneinfo/Africa/Timbuktu
- share/zoneinfo/Africa/Tripoli
- share/zoneinfo/Africa/Tunis
- share/zoneinfo/Africa/Windhoek
- share/zoneinfo/America/Adak
- share/zoneinfo/America/Anchorage
- share/zoneinfo/America/Anguilla
- share/zoneinfo/America/Antigua
- share/zoneinfo/America/Araguaina
- share/zoneinfo/America/Argentina/Buenos_Aires
- share/zoneinfo/America/Argentina/Catamarca
- share/zoneinfo/America/Argentina/ComodRivadavia
- share/zoneinfo/America/Argentina/Cordoba
- share/zoneinfo/America/Argentina/Jujuy
- share/zoneinfo/America/Argentina/La_Rioja
- share/zoneinfo/America/Argentina/Mendoza
- share/zoneinfo/America/Argentina/Rio_Gallegos
- share/zoneinfo/America/Argentina/Salta
- share/zoneinfo/America/Argentina/San_Juan
- share/zoneinfo/America/Argentina/San_Luis
- share/zoneinfo/America/Argentina/Tucuman
- share/zoneinfo/America/Argentina/Ushuaia
- share/zoneinfo/America/Aruba
- share/zoneinfo/America/Asuncion
- share/zoneinfo/America/Atikokan
- share/zoneinfo/America/Atka
- share/zoneinfo/America/Bahia
- share/zoneinfo/America/Bahia_Banderas
- share/zoneinfo/America/Barbados
- share/zoneinfo/America/Belem
- share/zoneinfo/America/Belize
- share/zoneinfo/America/Blanc-Sablon
- share/zoneinfo/America/Boa_Vista
- share/zoneinfo/America/Bogota
- share/zoneinfo/America/Boise
- share/zoneinfo/America/Buenos_Aires
- share/zoneinfo/America/Cambridge_Bay
- share/zoneinfo/America/Campo_Grande
- share/zoneinfo/America/Cancun
- share/zoneinfo/America/Caracas
- share/zoneinfo/America/Catamarca
- share/zoneinfo/America/Cayenne
- share/zoneinfo/America/Cayman
- share/zoneinfo/America/Chicago
- share/zoneinfo/America/Chihuahua
- share/zoneinfo/America/Ciudad_Juarez
- share/zoneinfo/America/Coral_Harbour
- share/zoneinfo/America/Cordoba
- share/zoneinfo/America/Costa_Rica
- share/zoneinfo/America/Creston
- share/zoneinfo/America/Cuiaba
- share/zoneinfo/America/Curacao
- share/zoneinfo/America/Danmarkshavn
- share/zoneinfo/A
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Dryrun_Tests
warning libmamba [libgomp-14.2.0-h77fa898_1] The following files were already present in the environment:
- lib/libgomp.so
- lib/libgomp.so.1.0.0
- share/licenses/gcc-libs/RUNTIME.LIBRARY.EXCEPTION.gomp_copy
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Dryrun_Tests
warning libmamba [_openmp_mutex-4.5-2_gnu] The following files were already present in the environment:
- lib/libgomp.so.1
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Dryrun_Tests
warning libmamba [libgcc-14.2.0-h77fa898_1] The following files were already present in the environment:
- lib/libatomic.so
- lib/libatomic.so.1
- lib/libatomic.so.1.2.0
- lib/libgcc_s.so
- lib/libgcc_s.so.1
- lib/libitm.so
- lib/libitm.so.1
- lib/libitm.so.1.0.0
- lib/libquadmath.so
- lib/libquadmath.so.0
- lib/libquadmath.so.0.0.0
- share/info/libgomp.info
- share/info/libquadmath.info
- share/licenses/gcc-libs/RUNTIME.LIBRARY.EXCEPTION
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Dryrun_Tests
warning libmamba [libexpat-2.6.4-h5888daf_0] The following files were already present in the environment:
- lib/libexpat.so.1
- lib/libexpat.so.1.10.0
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Long_Tests
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:198: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3.
To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels:
conda config --add channels defaults
For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html
deprecated.topic(
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Long_Tests
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
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Long_Tests
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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Quick_Tests
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:198: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3.
To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels:
conda config --add channels defaults
For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html
deprecated.topic(
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Quick_Tests
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
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Quick_Tests
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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Quick_Tests
warning libmamba [ca-certificates-2024.8.30-hbcca054_0] The following files were already present in the environment:
- ssl/cacert.pem
- ssl/cert.pem
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Quick_Tests
warning libmamba [ld_impl_linux-64-2.43-h712a8e2_2] The following files were already present in the environment:
- bin/x86_64-conda-linux-gnu-ld
- bin/x86_64-conda_cos6-linux-gnu-ld
- x86_64-conda-linux-gnu/bin/ld
- x86_64-conda_cos6-linux-gnu/bin/ld
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Quick_Tests
warning libmamba [tzdata-2024b-hc8b5060_0] The following files were already present in the environment:
- share/zoneinfo/Africa/Abidjan
- share/zoneinfo/Africa/Accra
- share/zoneinfo/Africa/Addis_Ababa
- share/zoneinfo/Africa/Algiers
- share/zoneinfo/Africa/Asmara
- share/zoneinfo/Africa/Asmera
- share/zoneinfo/Africa/Bamako
- share/zoneinfo/Africa/Bangui
- share/zoneinfo/Africa/Banjul
- share/zoneinfo/Africa/Bissau
- share/zoneinfo/Africa/Blantyre
- share/zoneinfo/Africa/Brazzaville
- share/zoneinfo/Africa/Bujumbura
- share/zoneinfo/Africa/Cairo
- share/zoneinfo/Africa/Casablanca
- share/zoneinfo/Africa/Ceuta
- share/zoneinfo/Africa/Conakry
- share/zoneinfo/Africa/Dakar
- share/zoneinfo/Africa/Dar_es_Salaam
- share/zoneinfo/Africa/Djibouti
- share/zoneinfo/Africa/Douala
- share/zoneinfo/Africa/El_Aaiun
- share/zoneinfo/Africa/Freetown
- share/zoneinfo/Africa/Gaborone
- share/zoneinfo/Africa/Harare
- share/zoneinfo/Africa/Johannesburg
- share/zoneinfo/Africa/Juba
- share/zoneinfo/Africa/Kampala
- share/zoneinfo/Africa/Khartoum
- share/zoneinfo/Africa/Kigali
- share/zoneinfo/Africa/Kinshasa
- share/zoneinfo/Africa/Lagos
- share/zoneinfo/Africa/Libreville
- share/zoneinfo/Africa/Lome
- share/zoneinfo/Africa/Luanda
- share/zoneinfo/Africa/Lubumbashi
- share/zoneinfo/Africa/Lusaka
- share/zoneinfo/Africa/Malabo
- share/zoneinfo/Africa/Maputo
- share/zoneinfo/Africa/Maseru
- share/zoneinfo/Africa/Mbabane
- share/zoneinfo/Africa/Mogadishu
- share/zoneinfo/Africa/Monrovia
- share/zoneinfo/Africa/Nairobi
- share/zoneinfo/Africa/Ndjamena
- share/zoneinfo/Africa/Niamey
- share/zoneinfo/Africa/Nouakchott
- share/zoneinfo/Africa/Ouagadougou
- share/zoneinfo/Africa/Porto-Novo
- share/zoneinfo/Africa/Sao_Tome
- share/zoneinfo/Africa/Timbuktu
- share/zoneinfo/Africa/Tripoli
- share/zoneinfo/Africa/Tunis
- share/zoneinfo/Africa/Windhoek
- share/zoneinfo/America/Adak
- share/zoneinfo/America/Anchorage
- share/zoneinfo/America/Anguilla
- share/zoneinfo/America/Antigua
- share/zoneinfo/America/Araguaina
- share/zoneinfo/America/Argentina/Buenos_Aires
- share/zoneinfo/America/Argentina/Catamarca
- share/zoneinfo/America/Argentina/ComodRivadavia
- share/zoneinfo/America/Argentina/Cordoba
- share/zoneinfo/America/Argentina/Jujuy
- share/zoneinfo/America/Argentina/La_Rioja
- share/zoneinfo/America/Argentina/Mendoza
- share/zoneinfo/America/Argentina/Rio_Gallegos
- share/zoneinfo/America/Argentina/Salta
- share/zoneinfo/America/Argentina/San_Juan
- share/zoneinfo/America/Argentina/San_Luis
- share/zoneinfo/America/Argentina/Tucuman
- share/zoneinfo/America/Argentina/Ushuaia
- share/zoneinfo/America/Aruba
- share/zoneinfo/America/Asuncion
- share/zoneinfo/America/Atikokan
- share/zoneinfo/America/Atka
- share/zoneinfo/America/Bahia
- share/zoneinfo/America/Bahia_Banderas
- share/zoneinfo/America/Barbados
- share/zoneinfo/America/Belem
- share/zoneinfo/America/Belize
- share/zoneinfo/America/Blanc-Sablon
- share/zoneinfo/America/Boa_Vista
- share/zoneinfo/America/Bogota
- share/zoneinfo/America/Boise
- share/zoneinfo/America/Buenos_Aires
- share/zoneinfo/America/Cambridge_Bay
- share/zoneinfo/America/Campo_Grande
- share/zoneinfo/America/Cancun
- share/zoneinfo/America/Caracas
- share/zoneinfo/America/Catamarca
- share/zoneinfo/America/Cayenne
- share/zoneinfo/America/Cayman
- share/zoneinfo/America/Chicago
- share/zoneinfo/America/Chihuahua
- share/zoneinfo/America/Ciudad_Juarez
- share/zoneinfo/America/Coral_Harbour
- share/zoneinfo/America/Cordoba
- share/zoneinfo/America/Costa_Rica
- share/zoneinfo/America/Creston
- share/zoneinfo/America/Cuiaba
- share/zoneinfo/America/Curacao
- share/zoneinfo/America/Danmarkshavn
- share/zoneinfo/A
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Quick_Tests
warning libmamba [libgomp-14.2.0-h77fa898_1] The following files were already present in the environment:
- lib/libgomp.so
- lib/libgomp.so.1.0.0
- share/licenses/gcc-libs/RUNTIME.LIBRARY.EXCEPTION.gomp_copy
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Quick_Tests
warning libmamba [_openmp_mutex-4.5-2_gnu] The following files were already present in the environment:
- lib/libgomp.so.1
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Quick_Tests
warning libmamba [libgcc-14.2.0-h77fa898_1] The following files were already present in the environment:
- lib/libatomic.so
- lib/libatomic.so.1
- lib/libatomic.so.1.2.0
- lib/libgcc_s.so
- lib/libgcc_s.so.1
- lib/libitm.so
- lib/libitm.so.1
- lib/libitm.so.1.0.0
- lib/libquadmath.so
- lib/libquadmath.so.0
- lib/libquadmath.so.0.0.0
- share/info/libgomp.info
- share/info/libquadmath.info
- share/licenses/gcc-libs/RUNTIME.LIBRARY.EXCEPTION
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Quick_Tests
warning libmamba [libexpat-2.6.4-h5888daf_0] The following files were already present in the environment:
- lib/libexpat.so.1
- lib/libexpat.so.1.10.0
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