Closed nschcolnicov closed 7 months ago
The issue is described here: https://github.com/nf-core/rnavar/issues/126
I tested it with the command: nextflow run ../../main.nf -profile docker -c config.config --outdir . --annotate_tools merge -resume
The config.config file contains the same values as the test profile but without the snpeff_cache and vep_cache being set to null:
params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' // Limit resources so that this can run on GitHub Actions max_cpus = 2 max_memory = '6.GB' max_time = '6.h' // Input data input = "${projectDir}/tests/csv/1.0/fastq_single.csv" // Genome references genome = 'WBcel235' fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta' dict = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.dict' gtf = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.gtf' // Known genome resources (optional) dbsnp = 'https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz' dbsnp_tbi = 'https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi' known_indels = 'https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz' known_indels_tbi = 'https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi' // STAR index (optional) star_index = 'https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/genome/index/star/star.tar.gz' // Annotation snpeff_db = 105 snpeff_genome = 'WBcel235' vep_cache_version = 110 vep_genome = 'WBcel235' vep_species = 'caenorhabditis_elegans' }
nf-core lint
nextflow run . -profile test,docker --outdir <OUTDIR>
docs/usage.md
docs/output.md
CHANGELOG.md
README.md
Posted for pipeline commit 3de9b74
+| ✅ 188 tests passed |+ !| ❗ 4 tests had warnings |!
The issue is described here: https://github.com/nf-core/rnavar/issues/126
I tested it with the command: nextflow run ../../main.nf -profile docker -c config.config --outdir . --annotate_tools merge -resume
The config.config file contains the same values as the test profile but without the snpeff_cache and vep_cache being set to null:
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).