Closed fasterius closed 11 months ago
mirpedrol
commented
11 months ago Hello @fasterius, I can't reproduce your error with the commands you provided. Could you try running nf-core --verbose lint and share the output here, to see if we can get more information? Thank you
fasterius
commented
11 months ago Absolutely! Here it is:
[erikfmbp: ~/projects/nf-core-spatialtranscriptomics] ((HEAD detached at e8b627a))$ nf-core --verbose lint
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.11.1 - https://nf-co.re
DEBUG Failed checking if running in CYGWIN due to: FileNotFoundError(2, 'No such file or directory') util.py:439
DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/Users/erikfasterius/projects/nf-core-spatialtranscriptomics, stdin=<valid stream>, shell=False, cmd.py:978
universal_newlines=False)
DEBUG Using config file: .nf-core.yml utils.py:1034
DEBUG Got '.' as path utils.py:230
DEBUG Found a config cache, loading: /Users/erikfasterius/.nextflow/nf-core/wf-config-cache-a2752e495d012ade6e9c1d7bd.json utils.py:264
DEBUG Popen(['git', 'version'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'fetch', '-v', '--progress', '--', 'origin'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=True) cmd.py:978
DEBUG Popen(['git', 'checkout', 'master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Using config file: /Users/erikfasterius/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1034
DEBUG Using config file: .nf-core.yml utils.py:1034
DEBUG Got '.' as path utils.py:230
DEBUG Found a config cache, loading: /Users/erikfasterius/.nextflow/nf-core/wf-config-cache-a2752e495d012ade6e9c1d7bd.json utils.py:264
DEBUG Registry set to quay.io __init__.py:140
DEBUG Using config file: .nf-core.yml utils.py:1034
INFO Testing pipeline: . __init__.py:271
DEBUG Running lint test: files_exist __init__.py:334
DEBUG Running lint test: nextflow_config __init__.py:334
DEBUG Running lint test: files_unchanged __init__.py:334
DEBUG No tools config file found: .nf-core.yml utils.py:1025
DEBUG Using config file: /var/folders/55/xdyh71s56ms7cs0z_3x0kfhm0000gp/T/tmp6wnr82nr/nf-core-spatialtranscriptomics/.nf-core.yml utils.py:1034
DEBUG Skipping lint test 'actions_ci' __init__.py:330
DEBUG Running lint test: actions_awstest __init__.py:334
DEBUG Running lint test: actions_awsfulltest __init__.py:334
DEBUG Running lint test: readme __init__.py:334
DEBUG Running lint test: pipeline_todos __init__.py:334
DEBUG Running lint test: pipeline_name_conventions __init__.py:334
DEBUG Running lint test: template_strings __init__.py:334
DEBUG Running lint test: schema_lint __init__.py:334
DEBUG Got '.' as path utils.py:230
DEBUG Found a config cache, loading: /Users/erikfasterius/.nextflow/nf-core/wf-config-cache-a2752e495d012ade6e9c1d7bd.json utils.py:264
DEBUG Running lint test: schema_params __init__.py:334
DEBUG Got '.' as path utils.py:230
DEBUG Found a config cache, loading: /Users/erikfasterius/.nextflow/nf-core/wf-config-cache-a2752e495d012ade6e9c1d7bd.json utils.py:264
DEBUG Running lint test: system_exit __init__.py:334
DEBUG Running lint test: schema_description __init__.py:334
DEBUG Got '.' as path utils.py:230
DEBUG Found a config cache, loading: /Users/erikfasterius/.nextflow/nf-core/wf-config-cache-a2752e495d012ade6e9c1d7bd.json utils.py:264
DEBUG Running lint test: actions_schema_validation __init__.py:334
DEBUG Running lint test: merge_markers __init__.py:334
DEBUG Running lint test: modules_json __init__.py:334
DEBUG Running lint test: multiqc_config __init__.py:334
DEBUG Running lint test: modules_structure __init__.py:334
DEBUG Connected to URL: https://depot.galaxyproject.org/singularity/scanpy:1.7.2--pyhdfd78af_0, status_code: 200 main_nf.py:332
DEBUG Connected to URL: https://quay.io/biocontainers/scanpy:1.7.2--pyhdfd78af_0, status_code: 200 main_nf.py:332
DEBUG Popen(['git', 'checkout', 'master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Using config file: /Users/erikfasterius/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1034
DEBUG Popen(['git', 'checkout', 'master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=<valid stream>, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'rev-list', '0e70547d116de782ec3825f1a449a56abb894482', '--', 'modules/nf-core/custom/dumpsoftwareversions'], cmd.py:978
cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False)
DEBUG Popen(['git', 'cat-file', '--batch'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=<valid stream>, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'rev-list', '0e70547d116de782ec3825f1a449a56abb894482', '--', 'modules/custom/dumpsoftwareversions'], cmd.py:978
cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False)
DEBUG Popen(['git', 'checkout', 'master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Using config file: /Users/erikfasterius/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1034
DEBUG Popen(['git', 'checkout', 'bba7e362e4afead70653f84d8700588ea28d0f9e'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, cmd.py:978
universal_newlines=False)
DEBUG Popen(['git', 'checkout', 'master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'checkout', 'master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Using config file: /Users/erikfasterius/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1034
DEBUG Popen(['git', 'checkout', 'master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=<valid stream>, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'rev-list', '0e70547d116de782ec3825f1a449a56abb894482', '--', 'modules/nf-core/fastqc'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, cmd.py:978
stdin=None, shell=False, universal_newlines=False)
DEBUG Popen(['git', 'cat-file', '--batch'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=<valid stream>, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'rev-list', '0e70547d116de782ec3825f1a449a56abb894482', '--', 'modules/fastqc'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, cmd.py:978
shell=False, universal_newlines=False)
DEBUG Popen(['git', 'checkout', 'master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Using config file: /Users/erikfasterius/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1034
DEBUG Popen(['git', 'checkout', '65ad3e0b9a4099592e1102e92e10455dc661cf53'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, cmd.py:978
universal_newlines=False)
DEBUG Popen(['git', 'checkout', 'master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'checkout', 'master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Using config file: /Users/erikfasterius/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1034
DEBUG Popen(['git', 'checkout', 'master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=<valid stream>, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'rev-list', '0e70547d116de782ec3825f1a449a56abb894482', '--', 'modules/nf-core/multiqc'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, cmd.py:978
stdin=None, shell=False, universal_newlines=False)
DEBUG Popen(['git', 'cat-file', '--batch'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=<valid stream>, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'rev-list', '0e70547d116de782ec3825f1a449a56abb894482', '--', 'modules/multiqc'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, cmd.py:978
shell=False, universal_newlines=False)
DEBUG Popen(['git', 'checkout', 'master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Using config file: /Users/erikfasterius/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1034
DEBUG Popen(['git', 'checkout', '4ab13872435962dadc239979554d13709e20bf29'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, cmd.py:978
universal_newlines=False)
DEBUG Popen(['git', 'checkout', 'master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'checkout', 'master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Using config file: /Users/erikfasterius/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1034
DEBUG Popen(['git', 'checkout', 'master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=<valid stream>, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'rev-list', '0e70547d116de782ec3825f1a449a56abb894482', '--', 'modules/nf-core/spaceranger/count'], cmd.py:978
cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False)
DEBUG Popen(['git', 'cat-file', '--batch'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=<valid stream>, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'rev-list', '0e70547d116de782ec3825f1a449a56abb894482', '--', 'modules/spaceranger/count'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, cmd.py:978
stdin=None, shell=False, universal_newlines=False)
DEBUG Applying patch to modules/nf-core/spaceranger/count/meta.yml modules_differ.py:447
DEBUG Applying patch to modules/nf-core/spaceranger/count/main.nf modules_differ.py:447
DEBUG Popen(['git', 'checkout', 'master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Using config file: /Users/erikfasterius/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1034
DEBUG Popen(['git', 'checkout', '3f5420aa22e00bd030a2556dfdffc9e164ec0ec5'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, cmd.py:978
universal_newlines=False)
DEBUG Popen(['git', 'checkout', 'master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'checkout', 'master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Using config file: /Users/erikfasterius/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1034
DEBUG Popen(['git', 'checkout', 'master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=<valid stream>, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'rev-list', '0e70547d116de782ec3825f1a449a56abb894482', '--', 'modules/nf-core/untar'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, cmd.py:978
stdin=None, shell=False, universal_newlines=False)
DEBUG Popen(['git', 'cat-file', '--batch'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=<valid stream>, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'rev-list', '0e70547d116de782ec3825f1a449a56abb894482', '--', 'modules/untar'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, cmd.py:978
shell=False, universal_newlines=False)
DEBUG Popen(['git', 'checkout', 'master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Using config file: /Users/erikfasterius/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1034
DEBUG Popen(['git', 'checkout', '3f5420aa22e00bd030a2556dfdffc9e164ec0ec5'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, cmd.py:978
universal_newlines=False)
DEBUG Popen(['git', 'checkout', 'master'], cwd=/Users/erikfasterius/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:978
DEBUG Printing final results __init__.py:365
DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10
DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10
DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13
DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14
DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102
DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10
DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35
DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13
DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10
DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10
DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10
DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10
DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13
DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14
DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102
DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10
DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35
DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13
DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10
DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10
DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10
DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10
DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13
DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14
DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102
DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10
DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35
DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13
DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10
DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10
╭─ [?] 3 Pipeline Tests Ignored ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ │
│ files_exist: File is ignored: conf/igenomes.config │
│ files_unchanged: File ignored due to lint config: .gitattributes │
│ actions_ci: actions_ci │
│ │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10
DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10
DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13
DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14
DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102
DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10
DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35
DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13
DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10
DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10
DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10
DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10
DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13
DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14
DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102
DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10
DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35
DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13
DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10
DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10
DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10
DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10
DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13
DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14
DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102
DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10
DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35
DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13
DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10
DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10
DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10
DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10
DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13
DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14
DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102
DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10
DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35
DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13
DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10
DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10
DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10
DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10
DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13
DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14
DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102
DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10
DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35
DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13
DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10
DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10
DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10
DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10
DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13
DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14
DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102
DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10
DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35
DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13
DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10
DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10
DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10
DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10
DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13
DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14
DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102
DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10
DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35
DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13
DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10
DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10
╭─ [!] 7 Pipeline Test Warnings ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ │
│ readme: README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release). │
│ pipeline_todos: TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. │
│ pipeline_todos: TODO string in output.md: More details for each analytical step should probably be added, │
│ pipeline_todos: TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required │
│ pipeline_todos: TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release │
│ pipeline_todos: TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline │
│ schema_params: Schema param st_spatial_de_top_hvg not found from nextflow config │
│ │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10
DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10
DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13
DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14
DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102
DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10
DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35
DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13
DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10
DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10
DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10
DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10
DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13
DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14
DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102
DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10
DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35
DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13
DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10
DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10
DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10
DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10
DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13
DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14
DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102
DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10
DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35
DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13
DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10
DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10
DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10
DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10
DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13
DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14
DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102
DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10
DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35
DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13
DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10
DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10
╭─ [✗] 4 Pipeline Tests Failed ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ │
│ schema_params: Param st_load_min_counts from nextflow config not found in nextflow_schema.json │
│ schema_params: Param st_load_min_cells from nextflow config not found in nextflow_schema.json │
│ schema_params: Param st_spatial_de_top_hgv from nextflow config not found in nextflow_schema.json │
│ schema_params: Default value for param st_spatial_de_top_hvg invalid: Not in pipeline parameters. Check nextflow.config. │
│ │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
DEBUG Printing final results __init__.py:202
DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10
DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10
DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13
DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14
DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102
DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10
DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35
DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13
DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10
DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10
DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10
DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10
DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13
DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14
DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102
DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10
DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35
DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13
DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10
DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10
DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10
DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10
DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13
DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14
DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102
DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10
DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35
DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13
DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10
DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10
DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10
DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10
DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13
DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14
DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102
DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10
DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35
DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13
DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10
DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10
DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10
DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10
DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13
DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14
DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102
DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10
DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35
DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13
DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10
DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10
DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10
DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10
DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13
DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14
DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102
DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10
DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35
DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13
DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10
DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10
DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10
DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10
DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13
DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14
DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102
DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10
DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35
DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13
DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10
DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10
DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10
DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10
DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13
DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14
DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102
DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10
DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35
DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13
DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10
DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10
DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10
DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10
DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13
DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14
DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102
DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10
DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35
DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13
DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10
DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10
DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10
DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10
DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13
DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14
DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102
DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10
DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35
DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13
DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10
DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10
╭─ [!] 5 Module Test Warnings ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ ╷ ╷ │
│ Module name │ File path │ Test message │
│╶─────────────────────────────┼──────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────────────────────────────────────────────╴│
│ st_clustering │ modules/local/st_clustering.nf │ Container versions do not match │
│ st_qc_and_normalisation │ modules/local/st_qc_and_normalisation.nf │ Container versions do not match │
│ st_spatial_de │ modules/local/st_spatial_de.nf │ Container versions do not match │
│ fastqc │ modules/nf-core/fastqc │ New version available │
│ multiqc │ modules/nf-core/multiqc │ New version available │
│ ╵ ╵ │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭───────────────────────╮
│ LINT RESULTS SUMMARY │
├───────────────────────┤
│ [✔] 227 Tests Passed │
│ [?] 3 Tests Ignored │
│ [!] 12 Test Warnings │
│ [✗] 4 Tests Failed │
╰───────────────────────╯I'm assuming that since it only fails on my system there's something weird going on on my end. Not sure how to read the DEBUG output though.
mirpedrol
commented
11 months ago Could you try removing the cache with rm $HOME/.nextflow/nf-core/wf-config-cache-a2752e495d012ade6e9c1d7bd.json?
fasterius
commented
11 months ago Yup, that works! So there was some kind of caching. I cannot find this in the documentation of nf-core/tools, but maybe I'm just missing it. Or is this to do with some interaction between linting and Nextflow's cache? Probably just my lack of knowledge that was the real issue here 😅 here.
Description of the bug
I previously had the
conf/analysis.configthat was sourced bynextflow.config, which contained some unused parameters. After removal of these parameters the linting started failing with the following errors:The parameters are not found anywhere in the pipeline's code anymore, and
nextflow configdoes not show them either. I assumed there was some kind of caching going on in the linting, but could not find anything in the documentation. Re-installingnf-core toolsitself didn't fix anything either. Running the pipeline itself works just fine and all the other parameters fromanalysis.configare picked up by the execution.After moving the externally sourced config to the
nextflow.configitself the problem went away, but I have no idea why. Did I miss that one shouldn't put different groups of parameter in external configs?Command used and terminal output
System information
Nextflow version: 23.04.4.5881 Hardware: MacBook Pro Executor: local OS: MacOS Version of nf-core/tools: 2.11.1 Python version: 3.12.1