Fix smoove output when using --output_callers (#89)

* fix smoove output * fix copy paste error * fix smoove tests * update changelog
nf-cmgg · Apr 29, 2024 · e71fddc · e71fddc
1 parent 4313b86
commit e71fddc
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,6 +19,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+1. The smoove outputs are now correct when using `--output_callers`
+
 ## v0.1.0 - [3 April 2024] - Amazing Atomium
 
 Initial release of nf-cmgg/structural, created with the [nf-core](https://nf-co.re/) template.

diff --git a/conf/modules.config b/conf/modules.config
@@ -194,7 +194,8 @@ process {
                 ]]
             }
 
-            withName: "^.*:BAM_VARIANT_CALLING_SMOOVE:TABIX_TABIX\$" {
+            withName: "^.*:BAM_VARIANT_CALLING_SMOOVE:TABIX_CALLER\$" {
+                ext.when = output_callers || (!params.annotate && foundSvCallers.size() == 1 && (count_types == 1 || !params.concat_output))
                 publishDir = [[
                     enabled: !params.annotate && foundSvCallers.size() == 1 && (count_types == 1 || !params.concat_output),
                     overwrite: true,

diff --git a/subworkflows/local/bam_variant_calling_smoove/main.nf b/subworkflows/local/bam_variant_calling_smoove/main.nf
@@ -1,11 +1,12 @@
 //
-// Run Delly
+// Run Smoove
 //
 
-include { SMOOVE_CALL        } from '../../../modules/nf-core/smoove/call/main'
-include { BCFTOOLS_SORT      } from '../../../modules/nf-core/bcftools/sort/main'
-include { TABIX_TABIX        } from '../../../modules/nf-core/tabix/tabix/main'
-include { SVYNC              } from '../../../modules/nf-core/svync/main'
+include { SMOOVE_CALL                   } from '../../../modules/nf-core/smoove/call/main'
+include { BCFTOOLS_SORT                 } from '../../../modules/nf-core/bcftools/sort/main'
+include { TABIX_TABIX                   } from '../../../modules/nf-core/tabix/tabix/main'
+include { TABIX_TABIX as TABIX_CALLER   } from '../../../modules/nf-core/tabix/tabix/main'
+include { SVYNC                         } from '../../../modules/nf-core/svync/main'
 
 workflow BAM_VARIANT_CALLING_SMOOVE {
     take:
@@ -41,6 +42,11 @@ workflow BAM_VARIANT_CALLING_SMOOVE {
     )
     ch_versions = ch_versions.mix(BCFTOOLS_SORT.out.versions.first())
 
+    TABIX_CALLER(
+        BCFTOOLS_SORT.out.vcf
+    )
+    ch_versions = ch_versions.mix(TABIX_CALLER.out.versions.first())
+
     BCFTOOLS_SORT.out.vcf
         .map(
             { meta, vcf ->

diff --git a/tests/pipeline/all_types/all.nf.test b/tests/pipeline/all_types/all.nf.test
@@ -28,15 +28,9 @@ nextflow_pipeline {
 
                     path("$outputDir")
                         .list()
-                        .findAll {
-                            !it.toString().endsWith("pipeline_info")
-                        }
-                        .collect {
-                            it.list().collect { it.toString().split("/")[-1] }
-                        },
-                    path("$outputDir").list().collect{
-                        it.toString().split("/")[-1]
-                    }
+                        .findAll { !it.toString().endsWith("pipeline_info") }
+                        .collect { getRecursiveFileNames(it, "${outputDir}") }
+                        .flatten()
                 ).match("all")}
             )
         }
@@ -64,19 +58,50 @@ nextflow_pipeline {
 
                     path("$outputDir")
                         .list()
-                        .findAll {
-                            !it.toString().endsWith("pipeline_info")
-                        }
-                        .collect {
-                            it.list().collect { it.toString().split("/")[-1] }
-                        },
-                    path("$outputDir").list().collect{
-                        it.toString().split("/")[-1]
-                    }
+                        .findAll { !it.toString().endsWith("pipeline_info") }
+                        .collect { getRecursiveFileNames(it, "${outputDir}") }
+                        .flatten()
                 ).match("concat")}
             )
         }
 
     }
 
+    test("output callers") {
+
+        when {
+            params {
+                outdir = "${outputDir}"
+                callers = "all"
+                max_cpus   = 2
+                max_memory = '6.GB'
+                max_time   = '6.h'
+                output_callers = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.stdout,
+
+                    path("$outputDir")
+                        .list()
+                        .findAll { !it.toString().endsWith("pipeline_info") }
+                        .collect { getRecursiveFileNames(it, "${outputDir}") }
+                        .flatten()
+                ).match("output callers")}
+            )
+        }
+
+    }
+
+}
+
+def getRecursiveFileNames(fileOrDir, outputDir) {
+    if(file(fileOrDir.toString()).isDirectory()) {
+        return fileOrDir.list().collect { getRecursiveFileNames(it, outputDir) }
+    }
+    return fileOrDir.toString().replace("${outputDir}/", "")
 }