Update stubs for samtools flagstat (nf-core#3657)

Update stubs Co-authored-by: Ram Nanduri <ram@MTLUCMDS1.lund.skane.se>
limrp · Jul 28, 2023 · 5281289 · 5281289
1 parent 2347ffa
commit 5281289
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diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf
@@ -32,4 +32,15 @@ process SAMTOOLS_FLAGSTAT {
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.flagstat
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/tests/modules/nf-core/samtools/flagstat/main.nf b/tests/modules/nf-core/samtools/flagstat/main.nf
@@ -13,3 +13,14 @@ workflow test_samtools_flagstat {
 
     SAMTOOLS_FLAGSTAT ( input )
 }
+
+
+workflow test_samtools_flagstat_stub {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+    ]
+
+    SAMTOOLS_FLAGSTAT ( input )
+}
diff --git a/tests/modules/nf-core/samtools/flagstat/test.yml b/tests/modules/nf-core/samtools/flagstat/test.yml
@@ -7,3 +7,12 @@
     - path: output/samtools/test.flagstat
       md5sum: 4f7ffd1e6a5e85524d443209ac97d783
     - path: output/samtools/versions.yml
+
+- name: samtools faidx test_samtools_flagstat_stub
+  command: nextflow run ./tests/modules/nf-core/samtools/flagstat -entry test_samtools_flagstat_stub -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/flagstat/nextflow.config -stub
+  tags:
+    - samtools/flagstat
+    - samtools
+  files:
+    - path: output/samtools/test.flagstat
+    - path: output/samtools/versions.yml