Full test#6
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Replace local file paths with direct URLs from PDM database: - Eliminates need to manually download FASTQs via download_data.sh - Nextflow will automatically fetch files from URLs - Simplifies full_test profile usage for users URLs point to PDM database for samples: - 319-R-AH8 - 319-R-AH6T26
Documentation changes: - Remove mention of manual download_data.sh requirement - Add examples showing URL support in samplesheets - Clarify that data is automatically fetched from PDM database - Show examples for both local files and URLs (http/s3/ftp) Makes it clear users can use URLs directly without manual downloads.
The test_full profile was failing because it had placeholder paths for reference genomes that dont exist. Changes: - Remove placeholder paths for hg38_fasta and nsg_fasta in test_full - Make reference genomes required parameters (must be provided by user) - Add clear documentation in config file with usage example - Update README to show required parameters for full test - Clarify that reference genomes are not bundled due to size Users must now provide their own reference genome paths: --hg38_fasta s3://bucket/GRCh38.fa --nsg_fasta s3://bucket/mm10_nsg.fa Fixes workflow run 2BFlAeqBicjcnw
- Add default reference genome paths from AWS iGenomes (s3://ngi-igenomes) - Set hg38_fasta to GRCh38 NCBI build - Set nsg_fasta to mm10 UCSC build - Makes test_full profile fully self-contained and runnable without additional parameters - Updated README to document the new default configuration - Users can still override with custom reference paths if needed (e.g., for NSG-adapted genome) This change makes the test_full profile much more user-friendly and enables testing in cloud environments (AWS, Seqera Platform) without local reference setup.
- Add stageAs directive to rename input FASTA files to unique names - Prevents collision when both reference genomes are named 'genome.fa' - Stages human reference as 'human_reference.fa' and mouse as 'mouse_reference.fa' This fixes the error: 'Process XENGSORT_INDEX input file name collision -- There are multiple input files for each of the following file names: genome.fa' Resolves issues with test_full profile using iGenomes references.
- Change from local file paths to GitHub raw URLs - Makes test_minimal match main branch's tests/ directory structure - URLs point to main branch test data files - Enables remote data fetching for test_minimal profile This aligns test_minimal with the main branch's testing approach where test data is fetched from GitHub rather than using local paths.
…s signs to nf-test.config
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