Merge pull request #19 from eugeniafontecha/dev

Reference panel accepts a csv

CHANGELOG.md

@@ -13,6 +13,7 @@ Initial release of nf-core/phaseimpute, created with the [nf-core](https://nf-co
 
 - [#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
+- [#19](https://github.com/nf-core/phaseimpute/pull/19) - Changed reference panel to accept a csv, update modules and subworkflows (glimpse1/2 and shapeit5)
 
 ### `Fixed`
 

assets/schema_input_panel.json

@@ -15,22 +15,22 @@
             },
             "vcf": {
                 "type": "string",
-                "pattern": "^\\S+\\.vcf$",
+                "pattern": "^\\S+\\.(vcf|bcf)(\\.gz)?$",
                 "errorMessage": "Panel vcf file must be provided, cannot contain spaces and must have extension '.vcf'"
             },
             "index": {
                 "type": "string",
-                "pattern": "^\\S+\\.vcf\\.(tbi|csi)$",
+                "pattern": "^\\S+\\.(vcf|bcf)(\\.gz)?\\.(tbi|csi)$",
                 "errorMessage": "Panel vcf index file must be provided, cannot contain spaces and must have extension '.vcf.tbi' or '.vcf.csi'"
             },
             "sites": {
                 "type": "string",
-                "pattern": "^\\S+\\.sites$",
+                "pattern": "^\\S+\\.sites(\\.bcf)?$",
                 "errorMessage": "Panel sites file must be provided, cannot contain spaces and must have extension '.sites'"
             },
             "tsv": {
                 "type": "string",
-                "pattern": "^\\S+\\.tsv$",
+                "pattern": "^\\S+\\.tsv(\\.gz)?$",
                 "errorMessage": "Panel tsv file must be provided, cannot contain spaces and must have extension '.tsv'"
             },
             "legend": {

conf/test.config

@@ -24,7 +24,7 @@ params {
 
     // Genome references
     fasta    = "https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/reference_genome/21_22/hs38DH.chr21_22.fa"
-    panel    = "https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/panel/21_22/1000GP.chr21_22.s.norel.bcf"
+    panel    = "${projectDir}/tests/csv/panel.csv"
     phased   = true
 
     // Impute parameters

modules.json

@@ -50,17 +50,17 @@
                     },
                     "glimpse/chunk": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "7e56daae390ff896b292ddc70823447683a79936",
                         "installed_by": ["vcf_impute_glimpse"]
                     },
                     "glimpse/ligate": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "7e56daae390ff896b292ddc70823447683a79936",
                         "installed_by": ["vcf_impute_glimpse"]
                     },
                     "glimpse/phase": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "7e56daae390ff896b292ddc70823447683a79936",
                         "installed_by": ["vcf_impute_glimpse"]
                     },
                     "glimpse2/chunk": {
@@ -70,7 +70,7 @@
                     },
                     "glimpse2/ligate": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "ee7fee68281944b002bd27a8ff3f19200b4d3fad",
                         "installed_by": ["multiple_impute_glimpse2"]
                     },
                     "glimpse2/phase": {
@@ -112,7 +112,7 @@
                     },
                     "shapeit5/ligate": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "dcf17cc0ed8fd5ea57e61a13e0147cddb5c1ee30",
                         "installed_by": ["vcf_phase_shapeit5"]
                     },
                     "shapeit5/phasecommon": {
@@ -136,7 +136,7 @@
                 "nf-core": {
                     "multiple_impute_glimpse2": {
                         "branch": "master",
-                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {
@@ -156,12 +156,12 @@
                     },
                     "vcf_impute_glimpse": {
                         "branch": "master",
-                        "git_sha": "8dab3bf2aaa912730419080e96d2a7d98911db48",
+                        "git_sha": "7e56daae390ff896b292ddc70823447683a79936",
                         "installed_by": ["subworkflows"]
                     },
                     "vcf_phase_shapeit5": {
                         "branch": "master",
-                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "git_sha": "dcf17cc0ed8fd5ea57e61a13e0147cddb5c1ee30",
                         "installed_by": ["subworkflows"]
                     }
                 }