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Merge pull request #19 from snakemake-workflows/fix/use-recommended-y… #2

Merge pull request #19 from snakemake-workflows/fix/use-recommended-y…

Merge pull request #19 from snakemake-workflows/fix/use-recommended-y… #2

Triggered via push July 28, 2025 09:21
Status Success
Total duration 4m 33s
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main.yaml

on: push
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14 warnings
Linting
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'.
Linting
/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 25.9. 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(
Testing
warning libmamba [libiconv-1.18-h4ce23a2_1] The following files were already present in the environment: - include/iconv.h - include/libcharset.h - include/localcharset.h - lib/libcharset.a - lib/libcharset.so - lib/libcharset.so.1 - lib/libcharset.so.1.0.0 - lib/libiconv.a - lib/libiconv.so - lib/libiconv.so.2 - lib/libiconv.so.2.7.0 - share/locale/af/LC_MESSAGES/libiconv.mo - share/locale/be/LC_MESSAGES/libiconv.mo - share/locale/bg/LC_MESSAGES/libiconv.mo - share/locale/ca/LC_MESSAGES/libiconv.mo - share/locale/cs/LC_MESSAGES/libiconv.mo - share/locale/da/LC_MESSAGES/libiconv.mo - share/locale/de/LC_MESSAGES/libiconv.mo - share/locale/el/LC_MESSAGES/libiconv.mo - share/locale/eo/LC_MESSAGES/libiconv.mo - share/locale/es/LC_MESSAGES/libiconv.mo - share/locale/et/LC_MESSAGES/libiconv.mo - share/locale/fi/LC_MESSAGES/libiconv.mo - share/locale/fr/LC_MESSAGES/libiconv.mo - share/locale/ga/LC_MESSAGES/libiconv.mo - share/locale/gl/LC_MESSAGES/libiconv.mo - share/locale/hr/LC_MESSAGES/libiconv.mo - share/locale/hu/LC_MESSAGES/libiconv.mo - share/locale/id/LC_MESSAGES/libiconv.mo - share/locale/it/LC_MESSAGES/libiconv.mo - share/locale/ja/LC_MESSAGES/libiconv.mo - share/locale/ka/LC_MESSAGES/libiconv.mo - share/locale/ko/LC_MESSAGES/libiconv.mo - share/locale/lt/LC_MESSAGES/libiconv.mo - share/locale/nl/LC_MESSAGES/libiconv.mo - share/locale/pl/LC_MESSAGES/libiconv.mo - share/locale/pt_BR/LC_MESSAGES/libiconv.mo - share/locale/rm/LC_MESSAGES/libiconv.mo - share/locale/ro/LC_MESSAGES/libiconv.mo - share/locale/ru/LC_MESSAGES/libiconv.mo - share/locale/sk/LC_MESSAGES/libiconv.mo - share/locale/sl/LC_MESSAGES/libiconv.mo - share/locale/sq/LC_MESSAGES/libiconv.mo - share/locale/sr/LC_MESSAGES/libiconv.mo - share/locale/sv/LC_MESSAGES/libiconv.mo - share/locale/tr/LC_MESSAGES/libiconv.mo - share/locale/uk/LC_MESSAGES/libiconv.mo - share/locale/vi/LC_MESSAGES/libiconv.mo - share/locale/wa/LC_MESSAGES/libiconv.mo - share/locale/zh_CN/LC_MESSAGES/libiconv.mo - share/locale/zh_TW/LC_MESSAGES/libiconv.mo
Testing
warning libmamba [libffi-3.4.6-h2dba641_1] The following files were already present in the environment: - include/ffi.h - include/ffitarget.h - lib/libffi.a - lib/libffi.so - lib/libffi.so.8 - lib/libffi.so.8.1.4 - lib/pkgconfig/libffi.pc - share/info/libffi.info - share/man/man3/ffi.3 - share/man/man3/ffi_call.3 - share/man/man3/ffi_prep_cif.3 - share/man/man3/ffi_prep_cif_var.3
Testing
warning libmamba [libexpat-2.7.0-h5888daf_0] The following files were already present in the environment: - lib/libexpat.so.1 - lib/libexpat.so.1.10.1
Testing
warning libmamba [c-ares-1.34.5-hb9d3cd8_0] The following files were already present in the environment: - bin/adig - bin/ahost - include/ares.h - include/ares_build.h - include/ares_dns.h - include/ares_dns_record.h - include/ares_nameser.h - include/ares_version.h - lib/cmake/c-ares/c-ares-config-version.cmake - lib/cmake/c-ares/c-ares-config.cmake - lib/cmake/c-ares/c-ares-targets-release.cmake - lib/cmake/c-ares/c-ares-targets.cmake - lib/libcares.so - lib/libcares.so.2 - lib/libcares.so.2.19.4 - lib/pkgconfig/libcares.pc - share/man/man1/adig.1 - share/man/man1/ahost.1 - share/man/man3/ares_cancel.3 - share/man/man3/ares_create_query.3 - share/man/man3/ares_destroy.3 - share/man/man3/ares_destroy_options.3 - share/man/man3/ares_dns_class_fromstr.3 - share/man/man3/ares_dns_class_t.3 - share/man/man3/ares_dns_class_tostr.3 - share/man/man3/ares_dns_datatype_t.3 - share/man/man3/ares_dns_flags_t.3 - share/man/man3/ares_dns_mapping.3 - share/man/man3/ares_dns_opcode_t.3 - share/man/man3/ares_dns_opcode_tostr.3 - share/man/man3/ares_dns_opt_datatype_t.3 - share/man/man3/ares_dns_opt_get_datatype.3 - share/man/man3/ares_dns_opt_get_name.3 - share/man/man3/ares_dns_parse.3 - share/man/man3/ares_dns_rcode_t.3 - share/man/man3/ares_dns_rcode_tostr.3 - share/man/man3/ares_dns_rec_type_fromstr.3 - share/man/man3/ares_dns_rec_type_t.3 - share/man/man3/ares_dns_rec_type_tostr.3 - share/man/man3/ares_dns_record.3 - share/man/man3/ares_dns_record_create.3 - share/man/man3/ares_dns_record_destroy.3 - share/man/man3/ares_dns_record_duplicate.3 - share/man/man3/ares_dns_record_get_flags.3 - share/man/man3/ares_dns_record_get_id.3 - share/man/man3/ares_dns_record_get_opcode.3 - share/man/man3/ares_dns_record_get_rcode.3 - share/man/man3/ares_dns_record_query_add.3 - share/man/man3/ares_dns_record_query_cnt.3 - share/man/man3/ares_dns_record_query_get.3 - share/man/man3/ares_dns_record_query_set_name.3 - share/man/man3/ares_dns_record_query_set_type.3 - share/man/man3/ares_dns_record_rr_add.3 - share/man/man3/ares_dns_record_rr_cnt.3 - share/man/man3/ares_dns_record_rr_del.3 - share/man/man3/ares_dns_record_rr_get.3 - share/man/man3/ares_dns_record_rr_get_const.3 - share/man/man3/ares_dns_record_set_id.3 - share/man/man3/ares_dns_rr.3 - share/man/man3/ares_dns_rr_add_abin.3 - share/man/man3/ares_dns_rr_del_abin.3 - share/man/man3/ares_dns_rr_del_opt_byid.3 - share/man/man3/ares_dns_rr_get_abin.3 - share/man/man3/ares_dns_rr_get_abin_cnt.3 - share/man/man3/ares_dns_rr_get_addr.3 - share/man/man3/ares_dns_rr_get_addr6.3 - share/man/man3/ares_dns_rr_get_bin.3 - share/man/man3/ares_dns_rr_get_class.3 - share/man/man3/ares_dns_rr_get_keys.3 - share/man/man3/ares_dns_rr_get_name.3 - share/man/man3/ares_dns_rr_get_opt.3 - share/man/man3/ares_dns_rr_get_opt_byid.3 - share/man/man3/ares_dns_rr_get_opt_cnt.3 - share/man/man3/ares_dns_rr_get_str.3 - share/man/man3/ares_dns_rr_get_ttl.3 - share/man/man3/ares_dns_rr_get_type.3 - share/man/man3/ares_dns_rr_get_u16.3 - share/man/man3/ares_dns_rr_get_u32.3 - share/man/man3/ares_dns_rr_get_u8.3 - share/man/man3/ares_dns_rr_key_datatype.3 - share/man/man3/ares_dns_rr_key_t.3 - share/man/man3/ares_dns_rr_key_to_rec_type.3 - share/man/man3/ares_dns_rr_key_tostr.3 - share/man/man3/ares_dns_rr_set_addr.3 - share/man/man3/ares_dns_rr_set_addr6.3 - share/man/man3/ares_dns_rr_set_bin.3 - share/man/man3/ares_dns_rr_set_opt.3 - share/man/man3/ares_dns_rr_set_str.3 - share/man/man3/ares_dns_rr_set_u16.3 - share/man/man3/ares_dns_rr_set_u32.3 - share/man/man3/ares_dns_rr_set_u8.3 - share/man/man3/ares_dns_section_t.3 - share/man/man3/ares_dns_section_tostr.3 - share/man/man3/ares_dns_write.3 - share/man/man3/ares_dup.3 - share/man/man3
Testing
warning libmamba [libgcc-15.1.0-h767d61c_2] 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
Testing
warning libmamba [_openmp_mutex-4.5-2_gnu] The following files were already present in the environment: - lib/libgomp.so.1
Testing
warning libmamba [tzdata-2025b-h78e105d_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/Coyhaique - share/zoneinfo/America/Creston - share/zoneinfo/America/Cuiaba - share/zoneinfo/America/Curacao - share/zoneinfo/Amer
Testing
warning libmamba [libgomp-15.1.0-h767d61c_2] 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
Testing
warning libmamba [ld_impl_linux-64-2.43-h712a8e2_4] 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
Testing
warning libmamba [ca-certificates-2025.4.26-hbd8a1cb_0] The following files were already present in the environment: - ssl/cacert.pem - ssl/cert.pem
Testing
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'.
Testing
/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 25.9. 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(