Make mosdepth stub use gzip for .gz files (#5410)

Switch to using proper gzip command to generate empty gz files. Update snapshot and tests
nf-core · Mar 28, 2024 · 30d3ca4 · 30d3ca4
1 parent b046a28
commit 30d3ca4
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Showing 3 changed files with 295 additions and 68 deletions.
diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf
@@ -63,13 +63,13 @@ process MOSDEPTH {
     touch ${prefix}.region.dist.txt
     touch ${prefix}.summary.txt
     touch ${prefix}.per-base.d4
-    touch ${prefix}.per-base.bed.gz
+    echo "" | gzip > ${prefix}.per-base.bed.gz
     touch ${prefix}.per-base.bed.gz.csi
-    touch ${prefix}.regions.bed.gz
+    echo "" | gzip > ${prefix}.regions.bed.gz
     touch ${prefix}.regions.bed.gz.csi
-    touch ${prefix}.quantized.bed.gz
+    echo "" | gzip > ${prefix}.quantized.bed.gz
     touch ${prefix}.quantized.bed.gz.csi
-    touch ${prefix}.thresholds.bed.gz
+    echo "" | gzip > ${prefix}.thresholds.bed.gz
     touch ${prefix}.thresholds.bed.gz.csi
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/modules/nf-core/mosdepth/tests/main.nf.test b/modules/nf-core/mosdepth/tests/main.nf.test
@@ -237,21 +237,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    file(process.out.global_txt[0][1]).name,
-                    file(process.out.summary_txt[0][1]).name,
-                    file(process.out.regions_txt[0][1]).name,
-                    file(process.out.per_base_d4[0][1]).name,
-                    file(process.out.per_base_bed[0][1]).name,
-                    file(process.out.per_base_csi[0][1]).name,
-                    file(process.out.regions_bed[0][1]).name,
-                    file(process.out.regions_csi[0][1]).name,
-                    file(process.out.quantized_bed[0][1]).name,
-                    file(process.out.quantized_csi[0][1]).name,
-                    file(process.out.thresholds_bed[0][1]).name,
-                    file(process.out.thresholds_csi[0][1]).name,
-                    process.out.versions
-                ).match() }
+                { assert snapshot(process.out).match() }
             )
         }