Feat filter bam file with custom flags (#217) #1175
CChahrourAnnotations
90 warnings
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Test (design, atac)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/cache@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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Test (design, atac)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
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Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
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Test (design, atac)
/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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Test (design, atac)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
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Test (config, chip)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/cache@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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Test (config, chip)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
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Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
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Test (config, chip)
/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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Test (config, chip)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
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Test (config, atac)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/cache@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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Test (config, atac)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
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Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
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Test (config, atac)
/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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Test (config, atac)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
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Test (design, chip)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/cache@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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Test (design, chip)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
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Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
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Test (design, chip)
/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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Test (design, chip)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
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Test (config, rna-rx)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/cache@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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Test (config, rna-rx)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
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Test (config, rna-rx)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
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Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
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Test (config, rna-rx)
/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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Test (config, chip-rx)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/cache@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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Test (config, chip-rx)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
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Test (config, chip-rx)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
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Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
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Test (config, chip-rx)
/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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Test (design, snp)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/cache@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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Test (design, snp)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
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Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
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Test (design, snp)
/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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Test (design, snp)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
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Test (config, snp)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/cache@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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Test (config, snp)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
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Test (config, snp)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
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Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
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Test (config, snp)
/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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Test (config, rna)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/cache@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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Test (config, rna)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
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Test (config, rna)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
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Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
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Test (config, rna)
/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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Test (design, rna)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/cache@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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Test (design, rna)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
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Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
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Test (design, rna)
/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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Test (design, rna)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
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Test (design, chip-rx)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/cache@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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Test (design, chip-rx)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
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Test (design, chip-rx)
/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)
|
|
Test (design, chip-rx)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
|
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Test (design, rna-rx)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/cache@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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Test (design, rna-rx)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
|
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Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
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Test (design, rna-rx)
/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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Test (design, rna-rx)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
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Test (pipeline, snp)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/cache@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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Test (pipeline, snp)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
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Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
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Test (pipeline, snp)
/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)
|
|
Test (pipeline, snp)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
|
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Test (pipeline, rna)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/cache@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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Test (pipeline, rna)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
|
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Test (pipeline, rna)
/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)
|
|
Test (pipeline, rna)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
|
|
Test (pipeline, chip-rx)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/cache@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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Test (pipeline, chip-rx)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
|
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Test (pipeline, chip-rx)
/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)
|
|
Test (pipeline, chip-rx)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
|
|
Test (pipeline, atac)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/cache@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
|
|
Test (pipeline, atac)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
|
|
Test (pipeline, atac)
/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)
|
|
Test (pipeline, atac)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
|
|
Test (pipeline, chip)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/cache@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
|
|
Test (pipeline, chip)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
|
|
Test (pipeline, chip)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
|
|
Test (pipeline, chip)
/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)
|
|
Test (pipeline, rna-rx)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/cache@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
|
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Test (pipeline, rna-rx)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
|
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Test (pipeline, rna-rx)
/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)
|
|
Test (pipeline, rna-rx)
'Mambaforge' variants are now equivalent to 'Miniforge3'. In the future, we will ignore with a warning and use 'Miniforge3'. Eventually, using 'Mambaforge' will throw an error. Please change to 'Miniforge3' at your earliest convenience.
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