Merge branch 'dev' into dev

nf-core · Mar 20, 2024 · 6138fa6 · 6138fa6
2 parents 7a1cabe + 462be6d
commit 6138fa6
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Showing 6 changed files with 8 additions and 15 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,7 +11,8 @@ Initial release of nf-core/phaseimpute, created with the [nf-core](https://nf-co
 
 ### `Changed`
 
-[#15](https://github.com/nf-core/phaseimpute/pull/15) - Changed test csv files to point to nf-core repository
+- [#15](https://github.com/nf-core/phaseimpute/pull/15) - Changed test csv files to point to nf-core repository
+- [#16](https://github.com/nf-core/phaseimpute/pull/16) - Removed outdir from test config files
 
 ### `Fixed`
 

diff --git a/README.md b/README.md
@@ -90,9 +90,10 @@ nf-core/phaseimpute was originally written by Louis Le Nézet.
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
-- Anabella Trigilla
+- Anabella Trigila
 - Saul Pierotti
 - Eugenia Fontecha
+- Matias Romero Victorica
 
 ## Contributions and Support
 

diff --git a/conf/test.config b/conf/test.config
@@ -20,8 +20,6 @@ params {
     max_time   = '6.h'
 
     // Input data
-    // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
-    // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input  = "${projectDir}/tests/csv/bam.csv"
 
     // Genome references

diff --git a/conf/test_full.config b/conf/test_full.config
@@ -32,6 +32,5 @@ params {
     input                  = "tests/csv/sample_sim.csv"
     panel                  = "tests/csv/panel.csv"
     input_region_string    = "all"
-    outdir                 = "results/test_full"
     step                   = "simulate"
 }
diff --git a/conf/test_sim.config b/conf/test_sim.config
@@ -23,7 +23,6 @@ params {
     input                = "tests/csv/sample_sim.csv"
     input_region_file    = "tests/csv/regionsheet.csv"
     depth                = [1, 2]
-    outdir               = "results/test_sim"
     genome               = "GRCh38"
 
     map                  = "/groups/dog/llenezet/test-datasets/data/genetic_maps.b38/chr21.b38.gmap.gz"

diff --git a/modules.json b/modules.json
@@ -14,12 +14,7 @@
                     "bcftools/index": {
                         "branch": "master",
                         "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
-                        "installed_by": [
-                            "modules",
-                            "multiple_impute_glimpse2",
-                            "vcf_impute_glimpse",
-                            "vcf_phase_shapeit5"
-                        ]
+                        "installed_by": ["multiple_impute_glimpse2", "vcf_impute_glimpse", "vcf_phase_shapeit5"]
                     },
                     "bcftools/mpileup": {
                         "branch": "master",
@@ -56,7 +51,7 @@
                     "glimpse/chunk": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules", "vcf_impute_glimpse"]
+                        "installed_by": ["vcf_impute_glimpse"]
                     },
                     "glimpse/ligate": {
                         "branch": "master",
@@ -141,7 +136,7 @@
                 "nf-core": {
                     "multiple_impute_glimpse2": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {
@@ -166,7 +161,7 @@
                     },
                     "vcf_phase_shapeit5": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
                         "installed_by": ["subworkflows"]
                     }
                 }