Updated test cases

- increaed memory per process: Caused stalling of pipeline with only 1GB - Changed input channels to values for "raw", "conensus" and "final" - Updated snapshots accordingly
genepi · Jun 18, 2024 · 7f5d96e · 7f5d96e
1 parent 78c6dad
commit 7f5d96e
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Showing 14 changed files with 1,130 additions and 52 deletions.
diff --git a/env/Dockerfile b/env/Dockerfile
@@ -19,5 +19,3 @@ RUN conda update -y conda && \
 
 WORKDIR "/opt"
 RUN wget https://github.com/seppinho/mutserve/releases/download/v2.0.0-rc13.lpa/mutserve_LPA_adapted.jar
-
-
diff --git a/tests/lib/processes/cluster.nf.test b/tests/lib/processes/cluster.nf.test
@@ -17,7 +17,7 @@ nextflow_process {
                     ["barcode06", "raw", "$baseDir/tests/input/cluster/barcode06/detected_umis.fastq"],
                     ["barcode07", "raw", "$baseDir/tests/input/cluster/barcode07/detected_umis.fastq"]
                 )
-                input[1] = Channel.of("raw", "raw", "raw", "raw", "raw", "raw")
+                input[1] ="raw"
                 """
             }
         }

diff --git a/tests/lib/processes/detect_umi_fastq.nf.test b/tests/lib/processes/detect_umi_fastq.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
                     ["barcode04", "raw", "$baseDir/tests/input/detect_umi/barcode04/lpa2645_filtered.fastq"],
                     ["barcode05", "raw", "$baseDir/tests/input/detect_umi/barcode05/lpa2645_filtered.fastq"],
                 )
-                input[1] = Channel.of("raw", "raw", "raw", "raw")
+                input[1] = "raw"
                 input[2] = file("$baseDir/bin/extract_umis.py")
                 """
             }
@@ -41,7 +41,7 @@ nextflow_process {
                     ["barcode04", "raw", "$baseDir/tests/input/detect_umi/barcode04/lpa2645_filtered.fastq"],
                     ["barcode05", "raw", "$baseDir/tests/input/detect_umi/barcode05/lpa2645_filtered.fastq"],
                 )
-                input[1] = Channel.of("raw", "raw", "raw", "raw")
+                input[1] = "raw"
                 input[2] = file("$baseDir/bin/extract_umis.py")
                 """
             }

diff --git a/tests/lib/processes/freebayes.nf.test b/tests/lib/processes/freebayes.nf.test
@@ -14,7 +14,7 @@ nextflow_process {
             process {
                 """
                 input[0] = Channel.of(["barcode03", "final", "$baseDir/tests/input/variant_calling/barcode03/final.bam", "$baseDir/tests/input/variant_calling/barcode03/final.bam.bai"])
-                input[1] = Channel.of("final")
+                input[1] = "final"
                 input[2] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta")
                 input[3] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta.fai")
                 """
@@ -41,7 +41,7 @@ nextflow_process {
                     ["barcode04", "final", "$baseDir/tests/input/variant_calling/barcode04/final.bam", "$baseDir/tests/input/variant_calling/barcode04/final.bam.bai"],
                     ["barcode05", "final", "$baseDir/tests/input/variant_calling/barcode05/final.bam", "$baseDir/tests/input/variant_calling/barcode05/final.bam.bai"]
                     )
-                input[1] = Channel.of("final", "final", "final")
+                input[1] = "final"
                 input[2] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta")
                 input[3] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta.fai")
                 """

diff --git a/tests/lib/processes/freebayes.nf.test.snap b/tests/lib/processes/freebayes.nf.test.snap
@@ -3,38 +3,38 @@
         "content": [
             {
                 "0": [
-                    "final.vcf:md5,88efc7556e75a4896acb25af4fd891ea",
-                    "final.vcf:md5,8d2f225076db263df46ea74c3444d8a1",
-                    "final.vcf:md5,c1ef037ccb4f791326fda68ef02ab497"
+                    "final.vcf:md5,bf6dfb83c6e0762789976816b72af4e6",
+                    "final.vcf:md5,c15c281e18b741734eb928f7112a02a4",
+                    "final.vcf:md5,c9eb084d495bd1facf2a9049cb439c86"
                 ],
                 "variants": [
-                    "final.vcf:md5,88efc7556e75a4896acb25af4fd891ea",
-                    "final.vcf:md5,8d2f225076db263df46ea74c3444d8a1",
-                    "final.vcf:md5,c1ef037ccb4f791326fda68ef02ab497"
+                    "final.vcf:md5,bf6dfb83c6e0762789976816b72af4e6",
+                    "final.vcf:md5,c15c281e18b741734eb928f7112a02a4",
+                    "final.vcf:md5,c9eb084d495bd1facf2a9049cb439c86"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.10.0"
         },
-        "timestamp": "2024-03-11T12:43:44.072561"
+        "timestamp": "2024-06-18T12:20:32.632422"
     },
     "Should run without failures": {
         "content": [
             {
                 "0": [
-                    "final.vcf:md5,c1ef037ccb4f791326fda68ef02ab497"
+                    "final.vcf:md5,c9eb084d495bd1facf2a9049cb439c86"
                 ],
                 "variants": [
-                    "final.vcf:md5,c1ef037ccb4f791326fda68ef02ab497"
+                    "final.vcf:md5,c9eb084d495bd1facf2a9049cb439c86"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.10.0"
         },
-        "timestamp": "2024-03-11T12:43:32.975611"
+        "timestamp": "2024-06-18T12:20:22.431414"
     }
 }
diff --git a/tests/lib/processes/lofreq.nf.test b/tests/lib/processes/lofreq.nf.test
@@ -14,7 +14,7 @@ nextflow_process {
             process {
                 """
                 input[0] = Channel.of(["barcode03", "final", "$baseDir/tests/input/variant_calling/barcode03/final.bam", "$baseDir/tests/input/variant_calling/barcode03/final.bam.bai"])
-                input[1] = Channel.of("final")
+                input[1] = "final"
                 input[2] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta")
                 input[3] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta.fai")
                 """
@@ -41,7 +41,7 @@ nextflow_process {
                     ["barcode04", "final", "$baseDir/tests/input/variant_calling/barcode04/final.bam", "$baseDir/tests/input/variant_calling/barcode04/final.bam.bai"],
                     ["barcode05", "final", "$baseDir/tests/input/variant_calling/barcode05/final.bam", "$baseDir/tests/input/variant_calling/barcode05/final.bam.bai"]
                     )
-                input[1] = Channel.of("final", "final", "final")
+                input[1] = "final"
                 input[2] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta")
                 input[3] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta.fai")
                 """

diff --git a/tests/lib/processes/lofreq.nf.test.snap b/tests/lib/processes/lofreq.nf.test.snap
@@ -3,38 +3,38 @@
         "content": [
             {
                 "0": [
-                    "final.vcf:md5,1834d639e6fd638fb43dc15430b2c507",
-                    "final.vcf:md5,527bcb8a79c99a9cf4deb47b54b0d068",
-                    "final.vcf:md5,7d03b1b5af994b65dce89c71f09771b3"
+                    "final.vcf:md5,13437d43022bd6b7a171daed88c010c4",
+                    "final.vcf:md5,1b57a477112f541443d246db37138216",
+                    "final.vcf:md5,810ba2f38eb3bda15699654945daa21a"
                 ],
                 "variants": [
-                    "final.vcf:md5,1834d639e6fd638fb43dc15430b2c507",
-                    "final.vcf:md5,527bcb8a79c99a9cf4deb47b54b0d068",
-                    "final.vcf:md5,7d03b1b5af994b65dce89c71f09771b3"
+                    "final.vcf:md5,13437d43022bd6b7a171daed88c010c4",
+                    "final.vcf:md5,1b57a477112f541443d246db37138216",
+                    "final.vcf:md5,810ba2f38eb3bda15699654945daa21a"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.10.0"
         },
-        "timestamp": "2024-03-11T15:08:10.610508"
+        "timestamp": "2024-06-18T12:20:15.213263"
     },
     "Should run without failures": {
         "content": [
             {
                 "0": [
-                    "final.vcf:md5,1834d639e6fd638fb43dc15430b2c507"
+                    "final.vcf:md5,13437d43022bd6b7a171daed88c010c4"
                 ],
                 "variants": [
-                    "final.vcf:md5,1834d639e6fd638fb43dc15430b2c507"
+                    "final.vcf:md5,13437d43022bd6b7a171daed88c010c4"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.10.0"
         },
-        "timestamp": "2024-03-11T15:07:59.738964"
+        "timestamp": "2024-06-18T12:20:05.981639"
     }
 }
diff --git a/tests/lib/processes/map_reads.nf.test b/tests/lib/processes/map_reads.nf.test
@@ -14,7 +14,7 @@ nextflow_process {
                     ["barcode04", "raw", "$baseDir/tests/input/mapping/barcode04/raw/lpa2645_filtered.fastq"], 
                     ["barcode05", "raw", "$baseDir/tests/input/mapping/barcode05/raw/lpa2645_filtered.fastq"], 
                     )
-                input[1] = Channel.from("raw", "raw", "raw")
+                input[1] = "raw"
                 input[2] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta")
                 """
             }
@@ -37,7 +37,7 @@ nextflow_process {
                     ["barcode04", "consensus", "$baseDir/tests/input/mapping/barcode04/consensus/masked_consensus.fastq"], 
                     ["barcode05", "consensus", "$baseDir/tests/input/mapping/barcode05/consensus/masked_consensus.fastq"], 
                     )
-                input[1] = Channel.from("consensus", "consensus", "consensus")
+                input[1] = "consensus"
                 input[2] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta")
                 """
             }
@@ -60,7 +60,7 @@ nextflow_process {
                     ["barcode04", "final", "$baseDir/tests/input/mapping/barcode04/final/final.fastq"], 
                     ["barcode05", "final", "$baseDir/tests/input/mapping/barcode05/final/final.fastq"], 
                     )
-                input[1] = Channel.from("final", "final", "final")
+                input[1] = "final"
                 input[2] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta")
                 """
             }

diff --git a/tests/lib/processes/mutserve.nf.test b/tests/lib/processes/mutserve.nf.test
@@ -14,7 +14,7 @@ nextflow_process {
             process {
                 """
                 input[0] = Channel.of(["barcode03", "final", "$baseDir/tests/input/variant_calling/barcode03/final.bam", "$baseDir/tests/input/variant_calling/barcode03/final.bam.bai"])
-                input[1] = Channel.of("final")
+                input[1] = "final"
                 input[2] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.bed")
                 input[3] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta")
                 input[4] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta.fai")
@@ -42,7 +42,7 @@ nextflow_process {
                     ["barcode04", "final", "$baseDir/tests/input/variant_calling/barcode04/final.bam", "$baseDir/tests/input/variant_calling/barcode04/final.bam.bai"],
                     ["barcode05", "final", "$baseDir/tests/input/variant_calling/barcode05/final.bam", "$baseDir/tests/input/variant_calling/barcode05/final.bam.bai"]
                     )
-                input[1] = Channel.of("final", "final", "final")
+                input[1] = "final"
                 input[2] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.bed")
                 input[3] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta")
                 input[4] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta.fai")

diff --git a/tests/lib/processes/polish_cluster.nf.test b/tests/lib/processes/polish_cluster.nf.test
@@ -41,7 +41,7 @@ nextflow_process {
             process {
                 """
                 input[0] = REFORMAT_FILTER_CLUSTER.out.smolecule_cluster_fastqs.transpose()
-                input[1] = Channel.of("consensus", "consensus", "consensus", "consensus", "consensus")
+                input[1] = "Consensus"
                 """
             }
         }
Original file line number	Diff line number	Diff line change
Expand Up		@@ -19,5 +19,3 @@ RUN conda update -y conda && \

		WORKDIR "/opt"
		RUN wget https://github.com/seppinho/mutserve/releases/download/v2.0.0-rc13.lpa/mutserve_LPA_adapted.jar