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Igv reports #5263
Igv reports #5263
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I tested this PR with docker, it passed.
I checked the output files in the .nf-test/ directory and versions.yaml
is fine, and the HTML document looks ok.
I wonder if the name should be igv-reports
as it is in bioconda (see [naming conventions[(https://nf-co.re/docs/contributing/modules)).
UPDATE The linter clearly does not allow to add punctuation marks... I wonder if we can make it clearer in the docs?
✅ LGTM (but I'm new, so I'll let someone else double check :) )
* add inital igvreports module * add full input and tests --------- Co-authored-by: Andrea Telatin <15690844+telatin@users.noreply.github.com>
* master: Added contrast limited adaptive histogram equalization module (nf-core#5268) Leviosam2 index (nf-core#5316) Add subworkflow mapAD (nf-core#5239) Remove AMRFinderPlus DB update on each invocation (nf-core#5232) Revert "add paths in output directive in cellranger cout module" (nf-core#5306) Revert "update kallistobustools count output list" (nf-core#5307) Igv reports (nf-core#5263) Remove unnecessary .view() in subworkflows/nf-core/vcf_phase_shapeit5 & tests/modules/nf-core/shapeit5/ligate/main.nf (nf-core#5280) Add wittyer as module (nf-core#5171) Bamstats (nf-core#4474) gatk4_asereadcounter add updated meta and nf-tests (nf-core#5164) 4557 new module kaijumergeoutputs + stub Kraken2/Kraken2 (nf-core#5249) add cram/index support to bwamem2 (nf-core#5248) Add README to modules build with Docker (nf-core#4935) update paths for VEP (nf-core#5281) nf-test bases2fastq (nf-core#5272) Add module seqfu/stats (nf-core#5275)
* master: Added contrast limited adaptive histogram equalization module (nf-core#5268) Leviosam2 index (nf-core#5316) Add subworkflow mapAD (nf-core#5239) Remove AMRFinderPlus DB update on each invocation (nf-core#5232) Revert "add paths in output directive in cellranger cout module" (nf-core#5306) Revert "update kallistobustools count output list" (nf-core#5307) Igv reports (nf-core#5263) Remove unnecessary .view() in subworkflows/nf-core/vcf_phase_shapeit5 & tests/modules/nf-core/shapeit5/ligate/main.nf (nf-core#5280) Add wittyer as module (nf-core#5171) Bamstats (nf-core#4474) gatk4_asereadcounter add updated meta and nf-tests (nf-core#5164) 4557 new module kaijumergeoutputs + stub Kraken2/Kraken2 (nf-core#5249) add cram/index support to bwamem2 (nf-core#5248) Add README to modules build with Docker (nf-core#4935) update paths for VEP (nf-core#5281) nf-test bases2fastq (nf-core#5272) Add module seqfu/stats (nf-core#5275) Added gt/gff3validator (nf-core#4718) Added liftoff (nf-core#5209)
* add inital igvreports module * add full input and tests --------- Co-authored-by: Andrea Telatin <15690844+telatin@users.noreply.github.com>
* add inital igvreports module * add full input and tests --------- Co-authored-by: Andrea Telatin <15690844+telatin@users.noreply.github.com>
* add inital igvreports module * add full input and tests --------- Co-authored-by: Andrea Telatin <15690844+telatin@users.noreply.github.com>
PR checklist
Add nf-core module for the igv-reports tool.
Closes #2173
versions.yml
file.label
nf-core modules test <MODULE> --profile docker
nf-core modules test <MODULE> --profile singularity
nf-core modules test <MODULE> --profile conda
nf-core subworkflows test <SUBWORKFLOW> --profile docker
nf-core subworkflows test <SUBWORKFLOW> --profile singularity
nf-core subworkflows test <SUBWORKFLOW> --profile conda