From 7a4f82f74d13f1a53ae0c5bebf58701ba54927be Mon Sep 17 00:00:00 2001 From: Saul Pierotti Date: Wed, 2 Oct 2024 16:22:00 +0100 Subject: [PATCH] bug in test --- README.md | 15 ++++++++++++++- modules/local/r/get_min_p_distribution.nf | 2 +- 2 files changed, 15 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 1b9e462..8d185c5 100644 --- a/README.md +++ b/README.md @@ -14,7 +14,7 @@ Both models are specified by the user with the [R formula interface](https://www **Disclaimer**: this pipeline uses the nf-core template but it is not part of nf-core itself. -![birneylab/stitchimpute_metro_map](docs/images/birneylab_flexlmm_drawing.png) +![birneylab/flexlmm_metro_map](docs/images/birneylab_flexlmm_drawing.png) 1. Convert vcf genotypes to `pgen` format ([`plink2`](https://www.cog-genomics.org/plink/2.0/)) 1. Compute the relatedness matrix for the whole genome and each LOCO subset ([`plink2`](https://www.cog-genomics.org/plink/2.0/)) @@ -139,6 +139,19 @@ nextflow run birneylab/flexlmm \ > **Warning**: > It is highly recommended to use the docker or singularity profile. Some processes do not have a working conda configuration. +## Testing +To run the pipeline on minimal test data, just execute the following: + +``` +nextflow run birneylab/flexlmm -profile test --outdir +``` +This minimal command requires Docker to be available in your system. +If you prefer, you can run the pipeline using conda or Singularity (choose one of them) instead with: + +``` +nextflow run birneylab/flexlmm -profile test, --outdir +``` + ## Pipeline output For more details about the output files and reports, please refer to the diff --git a/modules/local/r/get_min_p_distribution.nf b/modules/local/r/get_min_p_distribution.nf index f4f413f..9966013 100644 --- a/modules/local/r/get_min_p_distribution.nf +++ b/modules/local/r/get_min_p_distribution.nf @@ -63,7 +63,7 @@ process GET_MIN_P_DISTRIBUTION { stopifnot(length(p_vec) == ${nperms}) stopifnot(perm_vec == 1:${nperms}) stopifnot(length(n_snps_vec) == ${nperms}) - stopifnot(all(p_vec <= 1)) + stopifnot(all(p_vec <= 1 | p_vec == 2)) stopifnot(all(p_vec >= 0)) stopifnot(all(!is.na(n_snps_vec))) stopifnot(length(unique(n_snps_vec)) == 1)