ADD tabix index for indexcov (#6121)

* add tabix index for indexcov * Update snapshot * Pin htslib --------- Co-authored-by: Simon Pearce <[email protected]>
nf-core · Aug 22, 2024 · 1667117 · 1667117
1 parent 51076a8
commit 1667117
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Showing 4 changed files with 158 additions and 260 deletions.
diff --git a/modules/nf-core/goleft/indexcov/environment.yml b/modules/nf-core/goleft/indexcov/environment.yml
@@ -5,3 +5,4 @@ channels:
   - defaults
 dependencies:
   - bioconda::goleft=0.2.4
+  - bioconda::htslib=1.12
diff --git a/modules/nf-core/goleft/indexcov/main.nf b/modules/nf-core/goleft/indexcov/main.nf
@@ -12,13 +12,14 @@ process GOLEFT_INDEXCOV {
     tuple val(meta2), path(fai)
 
     output:
-    tuple val(meta), path("${prefix}/*")      , emit: output
-    tuple val(meta), path("${prefix}/*ped")   , emit: ped , optional: true
-    tuple val(meta), path("${prefix}/*bed.gz"), emit: bed , optional: true
-    tuple val(meta), path("${prefix}/*roc")   , emit: roc , optional: true
-    tuple val(meta), path("${prefix}/*html")  , emit: html, optional: true
-    tuple val(meta), path("${prefix}/*png")   , emit: png , optional: true
-    path "versions.yml"                      , emit: versions
+    tuple val(meta), path("${prefix}/*")          , emit: output
+    tuple val(meta), path("${prefix}/*ped")       , emit: ped , optional: true
+    tuple val(meta), path("${prefix}/*bed.gz")    , emit: bed , optional: true
+    tuple val(meta), path("${prefix}/*bed.gz.tbi"), emit: bed_index , optional: true
+    tuple val(meta), path("${prefix}/*roc")       , emit: roc , optional: true
+    tuple val(meta), path("${prefix}/*html")      , emit: html, optional: true
+    tuple val(meta), path("${prefix}/*png")       , emit: png , optional: true
+    path "versions.yml"                           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -37,21 +38,28 @@ process GOLEFT_INDEXCOV {
         $args \\
         ${input_files.join(" ")}
 
+    if [ -f "${prefix}/${prefix}-indexcov.bed.gz" ] ; then
+        tabix -p bed "${prefix}/${prefix}-indexcov.bed.gz"
+    fi
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         goleft: \$(goleft --version 2>&1 | head -n 1 | sed 's/^.*goleft Version: //')
+        tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
     END_VERSIONS
     """
     stub:
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir "${prefix}"
-    touch "${prefix}/${prefix}-indexcov.bed.gz"
+    echo "" | gzip > "${prefix}/${prefix}-indexcov.bed.gz"
+    touch "${prefix}/${prefix}-indexcov.bed.gz.tbi"
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         goleft: \$(goleft --version 2>&1 | head -n 1 | sed 's/^.*goleft Version: //')
+        tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/goleft/indexcov/tests/main.nf.test b/modules/nf-core/goleft/indexcov/tests/main.nf.test
@@ -18,11 +18,11 @@ nextflow_process {
                     [ id:'test' ], // meta map
                     [
                         file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.sorted.bam", checkIfExists: true),
-                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true)                                                                                       
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true)
                     ],
                     [
                         file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai", checkIfExists: true),
-                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true)                                                                                       
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true)
                     ],
                 ])
 
@@ -39,7 +39,15 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out.ped,
+                    process.out.bed,
+                    file(process.out.bed_index[0][1]).name,
+                    process.out.roc,
+                    process.out.html,
+                    process.out.png,
+                    process.out.versions
+                    ).match() }
             )
         }
 
@@ -76,7 +84,15 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out.ped,
+                    process.out.bed,
+                    file(process.out.bed_index[0][1]).name,
+                    process.out.roc,
+                    process.out.html,
+                    process.out.png,
+                    process.out.versions
+                    ).match() }
             )
         }
 
@@ -105,7 +121,8 @@ nextflow_process {
 
         then {
             assertAll(
-                { assert process.success }
+                { assert process.success },
+                { assert snapshot(process.out).match() }
             )
         }