Store test files in data directory instead of inline

Author: robsyme

modules/local/rsem_merge_counts/tests/main.nf.test

@@ -12,57 +12,8 @@ nextflow_process {
         when {
             process {
                 """
-                def gene_headers = ['gene_id', 'transcript_id(s)', 'length', 'effective_length', 'expected_count', 'TPM', 'FPKM'].join('\t')
-                def isoform_headers = ['transcript_id', 'gene_id', 'length', 'effective_length', 'expected_count', 'TPM', 'FPKM', 'IsoPct'].join('\t')
-
-                geneData = [
-                    'genes/RAP1_IAA_30M_REP1.genes.results': [
-                        'Gfp_transgene	Gfp_transgene	729.00	562.01	0.00	0.00	0.00',
-                        'HRA1	HRA1	564.00	397.05	0.00	0.00	0.00',
-                        'YAL001C	YAL001C	3483.00	3316.01	55.00	762.38	490.51',
-                    ],
-                    'genes/RAP1_UNINDUCED_REP1.genes.results': [
-                        'Gfp_transgene	Gfp_transgene	729.00	630.96	0.00	0.00	0.00',
-                        'HRA1	HRA1	564.00	465.96	0.00	0.00	0.00',
-                        'YAL001C	YAL001C	3483.00	3384.96	69.00	937.05	581.61',
-                    ],
-                    'genes/RAP1_UNINDUCED_REP2.genes.results': [
-                        'Gfp_transgene	Gfp_transgene	729.00	630.86	0.00	0.00	0.00',
-                        'HRA1	HRA1	564.00	465.86	0.00	0.00	0.00',
-                        'YAL001C	YAL001C	3483.00	3384.86	110.00	783.22	460.39',
-                    ]
-                ]
-
-                isoformData = [
-                    'isoforms/RAP1_IAA_30M_REP1.isoforms.results': [
-                        'Gfp_transgene	Gfp_transgene	729	562.01	0.00	0.00	0.00	0.00',
-                        'HRA1	HRA1	564	397.05	0.00	0.00	0.00	0.00',
-                        'YAL001C	YAL001C	3483	3316.01	55.00	762.38	490.51	100.00',
-                    ],
-                    'isoforms/RAP1_UNINDUCED_REP1.isoforms.results': [
-                        'Gfp_transgene	Gfp_transgene	729	630.96	0.00	0.00	0.00	0.00',
-                        'HRA1	HRA1	564	465.96	0.00	0.00	0.00	0.00',
-                        'YAL001C	YAL001C	3483	3384.96	69.00	937.05	581.61	100.00',
-                    ],
-                    'isoforms/RAP1_UNINDUCED_REP2.isoforms.results': [
-                        'Gfp_transgene	Gfp_transgene	729	630.86	0.00	0.00	0.00	0.00',
-                        'HRA1	HRA1	564	465.86	0.00	0.00	0.00	0.00',
-                        'YAL001C	YAL001C	3483	3384.86	110.00	783.22	460.39	100.00',
-                    ],
-                ]
-
-                for (map in [geneData, isoformData]) {
-                    for (entry in map) {
-                        def filename = entry.key
-                        def filedata = entry.value.join("\\n")
-                        tmpfile = file("${workDir}/\${filename}")
-                        tmpfile.getParent().mkdirs()
-                        tmpfile.text = filedata
-                    }
-                }
-
-                input[0] = geneData.collect{filename,_ -> file("${workDir}/\${filename}")}
-                input[1] = isoformData.collect{filename,_ -> file("${workDir}/\${filename}")}
+                input[0] = file("${moduleTestDir}/data/genes/*")
+                input[1] = file("${moduleTestDir}/data/isoforms/*")
                 """
             }
         }

modules/local/rsem_merge_counts/tests/main.nf.test.snap

@@ -3,31 +3,31 @@
         "content": [
             {
                 "0": [
-                    "rsem.merged.gene_counts.tsv:md5,23164d60dbb95179310ecfa81eb53f21"
+                    "rsem.merged.gene_counts.tsv:md5,7d1da94077dc2f90cfb2c793ca5b7446"
                 ],
                 "1": [
-                    "rsem.merged.gene_tpm.tsv:md5,e02f8a05d35010db454d79846935a973"
+                    "rsem.merged.gene_tpm.tsv:md5,39bad606eb012456bba1d995fe0feb5f"
                 ],
                 "2": [
-                    "rsem.merged.transcript_counts.tsv:md5,23164d60dbb95179310ecfa81eb53f21"
+                    "rsem.merged.transcript_counts.tsv:md5,e40bba0aafc5904361513b3513c217ad"
                 ],
                 "3": [
-                    "rsem.merged.transcript_tpm.tsv:md5,e02f8a05d35010db454d79846935a973"
+                    "rsem.merged.transcript_tpm.tsv:md5,abbaac45f9938716c58d604299ea284e"
                 ],
                 "4": [
                     "versions.yml:md5,48ca3e12c91829af8019462b3f6aa29c"
                 ],
                 "counts_gene": [
-                    "rsem.merged.gene_counts.tsv:md5,23164d60dbb95179310ecfa81eb53f21"
+                    "rsem.merged.gene_counts.tsv:md5,7d1da94077dc2f90cfb2c793ca5b7446"
                 ],
                 "counts_transcript": [
-                    "rsem.merged.transcript_counts.tsv:md5,23164d60dbb95179310ecfa81eb53f21"
+                    "rsem.merged.transcript_counts.tsv:md5,e40bba0aafc5904361513b3513c217ad"
                 ],
                 "tpm_gene": [
-                    "rsem.merged.gene_tpm.tsv:md5,e02f8a05d35010db454d79846935a973"
+                    "rsem.merged.gene_tpm.tsv:md5,39bad606eb012456bba1d995fe0feb5f"
                 ],
                 "tpm_transcript": [
-                    "rsem.merged.transcript_tpm.tsv:md5,e02f8a05d35010db454d79846935a973"
+                    "rsem.merged.transcript_tpm.tsv:md5,abbaac45f9938716c58d604299ea284e"
                 ],
                 "versions": [
                     "versions.yml:md5,48ca3e12c91829af8019462b3f6aa29c"
@@ -38,6 +38,6 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-03-09T17:03:14.647859"
+        "timestamp": "2024-03-09T17:13:37.377348"
     }
 }