Merge pull request #161 from LouisLeNezet/config

Update VCF_SPLIT_BCFTOOLS

CHANGELOG.md

@@ -74,6 +74,7 @@ Special thanks to [Matthias Hörtenhuber](https://github.com/mashehu) and [Mazza
 - [#117](https://github.com/nf-core/phaseimpute/pull/117) - Fix directories in CSV.
 - [#151](https://github.com/nf-core/phaseimpute/pull/151) - Fix `Type not supported: class org.codehaus.groovy.runtime.GStringImpl` error due to `String` test in `getFileExtension()`.
 - [#153](https://github.com/nf-core/phaseimpute/pull/153) - Fix getFileExtension function. Fix image in `usage.md`. Fix small warnings and errors with updated language server. `def` has been added when necessary, `:` use instead of `,` in assertions, `_` added to variables not used in closures, `for` loop replaced by `.each{}`, remove unused code / input.
+- [#161](https://github.com/nf-core/phaseimpute/pull/161) - Fix `VCF_SPLIT_BCFTOOLS` when only one sample present by updating `BCFTOOLS_PLUGINSPLIT` and adding `BCFTOOLS_QUERY` to get truth samples names for renaming the resulting files.
 
 ### `Dependencies`
 

conf/modules.config

@@ -88,7 +88,6 @@ process {
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_SPLIT_BCFTOOLS:BCFTOOLS_PLUGINSPLIT' {
         tag = { "${meta.id} Batch ${meta.batch} ${meta.tools}" }
         ext.args   = ["--output-type z", "--write-index=tbi"].join(' ')
-        ext.prefix = { "${meta.id}_${meta.batch}" }
         publishDir = [
             path: { "${params.outdir}/imputation/${meta.tools}/samples/" },
             mode: params.publish_dir_mode,

conf/steps/validation.config

@@ -64,21 +64,30 @@ process {
         ext.args   = ["--ligate", "--output-type z", "--write-index=tbi"].join(' ')
     }
 
+    // Compute sample files for renaming
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BCFTOOLS_QUERY' {
+        tag = { "${meta.id} Batch ${meta.batch} ${meta.tools}" }
+        ext.args = '--list-samples'
+        publishDir = [enabled: false]
+    }
+
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:GAWK' {
+        tag = { "${meta.id} Batch ${meta.batch} ${meta.tools}" }
+        ext.prefix = { "${meta.id}_samples"}
+        ext.args2 = "'BEGIN { OFS = \"\\t\" } { print \$1, \"-\", \$1\".truth\" }'"
+        publishDir = [enabled: false]
+    }
+
     // Split by samples
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:SPLIT_TRUTH:.*' {
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:SPLIT_TRUTH:BCFTOOLS_PLUGINSPLIT' {
+        ext.args   = ["--output-type z", "--write-index=tbi"].join(' ')
         publishDir = [
             path: { "${params.outdir}/validation/samples" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:SPLIT_TRUTH:BCFTOOLS_PLUGINSPLIT' {
-        ext.args   = ["--output-type z", "--write-index=tbi"].join(' ')
-        ext.prefix = { "${meta.id}" }
-        ext.suffix = ".truth"
-    }
-
     // Validation subworkflow
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CONCORDANCE_GLIMPSE2:.*' {
         publishDir = [
@@ -106,6 +115,6 @@ process {
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CONCORDANCE_GLIMPSE2:GAWK' {
         ext.args2  = "'(NR == 1) || (FNR > 1)'" // Skip header line
         ext.suffix = { "txt" }
-        tag = {"Test Quality"}
+        tag = {"${meta.id}"}
     }
 }

modules.json

@@ -46,10 +46,15 @@
                     },
                     "bcftools/pluginsplit": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "14c910af1f9c20c65e5df9325a1e4d3939d524d1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/bcftools/pluginsplit/bcftools-pluginsplit.diff"
                     },
+                    "bcftools/query": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "bcftools/stats": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",