Try for stable snapshotting strategy in fastq_subsample_fq_salmon, fa…

…stq_download_prefetch_fasterqdump_sratools (nf-core#4714) * Dummy change to see what nf-test does for this subworkflow * Amend fastq.gz testing strategy * Revert "Dummy change to see what nf-test does for this subworkflow" This reverts commit 6f96c42. * Also fix snapshots from fastq_download_prefetch_fasterqdump_sratools * Remove old assertions * Fix snapshots for version --------- Co-authored-by: Maxime U Garcia <[email protected]>
maxulysse · Jan 11, 2024 · bdfd7bc · bdfd7bc
1 parent 84b334a
commit bdfd7bc
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Showing 4 changed files with 114 additions and 67 deletions.
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
@@ -28,9 +28,18 @@ nextflow_workflow {
         }
 
         then {
+            def pelines1 = path(workflow.out.reads[0][1][0]).linesGzip
+            def pelines2 = path(workflow.out.reads[0][1][1]).linesGzip
+            def selines = path(workflow.out.reads[1][1]).linesGzip
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(workflow.out).match() }
+                { assert snapshot(pelines1[0..5]).match("test_pe_reads_1_lines") },
+                { assert snapshot(pelines1.size()).match("test_pe_reads_1_size") },
+                { assert snapshot(pelines2[0..5]).match("test_pe_reads_2_lines") },
+                { assert snapshot(pelines2.size()).match("test_pe_reads_2_size") },
+                { assert snapshot(selines[0..5]).match("test_se_reads_lines") },
+                { assert snapshot(selines.size()).match("test_se_reads_size") },
+                { assert snapshot(workflow.out.versions).match("versions") }
             )
         }
     }

diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
diff --git a/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test b/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test
@@ -47,9 +47,14 @@ nextflow_workflow {
         }
 
         then {
+            def readlines1 = path(workflow.out.reads[0][1][0]).linesGzip
+            def readlines2 = path(workflow.out.reads[0][1][1]).linesGzip
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(workflow.out.reads).match("reads") },
+                { assert snapshot(readlines1[0..5]).match("test_reads_1_lines") },
+                { assert snapshot(readlines1.size()).match("test_reads_1_size") },
+                { assert snapshot(readlines2[0..5]).match("test_reads_2_lines") },
+                { assert snapshot(readlines2.size()).match("test_reads_2_size") },
                 { assert snapshot(workflow.out.versions).match("versions") },
 
                 { assert workflow.out.index },

diff --git a/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test.snap