bug in test

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 <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,<conda|singularity> --outdir <OUTDIR>
+```
+
 ## Pipeline output
 
 For more details about the output files and reports, please refer to the

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)