Open jfy133 opened 2 months ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit cc114f3
+| ✅ 335 tests passed |+
#| ❔ 2 tests were ignored |#
!| ❗ 21 tests had warnings |!
Damage profiler:
Not sure which output idr (final_bams
):
Qualimap:
MultiQC:
fastp:
fastqc:
bed
, preseq
, and fastqc
processes?Existing tests to make sure we account for with new configs:
- "-profile test,docker --preprocessing_tool fastp --preprocessing_adapterlist 'https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/fastp/adapters.fasta'"
- "-profile test,docker --preprocessing_tool adapterremoval --preprocessing_adapterlist 'https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/adapterremoval/adapterremoval_adapterlist.txt' --sequencing_qc_tool falco --run_genotyping --genotyping_tool 'freebayes' --genotyping_source 'raw'"
- "-profile test,docker --mapping_tool bwamem --run_mapdamage_rescaling --run_pmd_filtering --run_trim_bam --run_genotyping --genotyping_tool 'ug' --genotyping_source 'trimmed'"
- "-profile test,docker --mapping_tool bowtie2 --damagecalculation_tool mapdamage --damagecalculation_mapdamage_downsample 100 --run_genotyping --genotyping_tool 'hc' --genotyping_source 'raw'"
- "-profile test,docker --skip_preprocessing --convert_inputbam"
- "-profile test_humanbam,docker --run_mtnucratio --run_contamination_estimation_angsd --snpcapture_bed 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz' --run_genotyping --genotyping_tool 'pileupcaller' --genotyping_source 'raw'"
- "-profile test_humanbam,docker --run_sexdeterrmine --run_genotyping --genotyping_tool 'angsd' --genotyping_source 'raw'"
- "-profile test_multiref,docker" ## TODO add damage manipulation here instead once it goes multiref
… test profile
Initial set up, testing command
nf-test test --tag test --profile test,docker
PR checklist
scrape_software_versions.py
nf-core lint .
).nextflow run . -profile test,docker
).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).