Merge branch 'dev' into fix_params

modules.json

@@ -35,6 +35,11 @@
                         "git_sha": "ec155021a9104441bf6a9bae3b55d1b5b0bfdb3a",
                         "installed_by": ["modules"]
                     },
+                    "dupradar": {
+                        "branch": "master",
+                        "git_sha": "f632a6e25b05497477920183cff33ba72ab7b6fc",
+                        "installed_by": ["modules"]
+                    },
                     "fastp": {
                         "branch": "master",
                         "git_sha": "003920c7f9a8ae19b69a97171922880220bedf56",

modules/local/deseq2_qc/tests/data/countFile.tsv

@@ -0,0 +1,18 @@
+gene_id	gene_name	RAP1_IAA_30M_REP1	RAP1_UNINDUCED_REP1	RAP1_UNINDUCED_REP2	WT_REP1	WT_REP2
+Gfp_transgene_gene	Gfp_transgene_gene	0	0	0	0	0
+HRA1	HRA1	3.01943228500291	9.80701185810843	9.53274413980081	5.72894534769954	5.9648842559222
+snR18	snR18	2.15518528497702	20.2706605484032	10.1398196728994	5.78313737408605	5.79976683844901
+YAL001C	TFC3	56.5487189493641	70.7846010387686	113.108816589334	60.5178622417112	30.2958040068545
+YAL002W	VPS8	36.3862437592078	32.3965311942571	80.536128672497	63.6031126291227	25.2702744059695
+YAL003W	EFB1	598.396699649099	887.339579289614	1856.66699260635	1049.93553354283	665.403243069765
+YAL004W	YAL004W	388.410667489585	383.296795393227	203.744142706403	202.691892385957	251.440658667147
+YAL005C	SSA1	5647.27979655766	5715.94369645599	12575.108029018	7775.42737695585	3903.66710060582
+YAL007C	ERP2	44.6930487868818	60.9301400694571	143.68466075721	56.9486461946981	41.7805866183878
+YAL008W	FUN14	13.1986081960994	18.7996646072737	26.552459043029	9.4087625308538	2.82245410144267
+YAL009W	SPO7	13.5217762310537	15.8719804576371	20.113413795	8.67724034815225	4.82436501953514
+YAL010C	MDM10	10.9410758413598	12.0839661783069	36.2679562039924	29.7986383847897	9.94377960724503
+YAL011W	SWC3	12.0055027348268	24.9403272396788	35.9299792122994	19.9834911886444	18.0057148106317
+YAL012W	CYS3	242.877787996136	236.466395413312	547.58060621785	378.571834233094	226.984289418222
+YAL013W	DEP1	7.90662508175251	18.3153373366285	35.6289306191157	20.7248252538103	10.8672258295774
+YAL014C	SYN8	15.4361922388434	21.2042068878003	44.5485583043788	26.9652946879967	16.3840947562552
+YAL015C	NTG1	12.841137836752	12.2213888342821	28.5292052419374	7.89073247427083	5.92421903162791

modules/local/deseq2_qc/tests/data/deseq2_clustering_header.txt

@@ -0,0 +1,12 @@
+#id: 'deseq2_clustering'
+#section_name: 'DESeq2 sample similarity'
+#description: "is generated from clustering by Euclidean distances between
+#	       <a href='https://bioconductor.org/packages/release/bioc/html/DESeq2.html' target='_blank'>DESeq2</a>
+#              rlog values for each sample
+#              in the <a href='https://github.com/nf-core/rnaseq/blob/master/bin/deseq2_qc.r'><code>deseq2_qc.r</code></a> script."
+#plot_type: 'heatmap'
+#anchor: 'deseq2_clustering'
+#pconfig:
+#    title: 'DESeq2: Heatmap of the sample-to-sample distances'
+#    xlab: True
+#    reverseColors: True

modules/local/deseq2_qc/tests/data/deseq2_pca_header.txt

@@ -0,0 +1,11 @@
+#id: 'deseq2_pca'
+#section_name: 'DESeq2 PCA plot'
+#description: "PCA plot between samples in the experiment.
+#              These values are calculated using <a href='https://bioconductor.org/packages/release/bioc/html/DESeq2.html'>DESeq2</a>
+#              in the <a href='https://github.com/nf-core/rnaseq/blob/master/bin/deseq2_qc.r'><code>deseq2_qc.r</code></a> script."
+#plot_type: 'scatter'
+#anchor: 'deseq2_pca'
+#pconfig:
+#    title: 'DESeq2: Principal component plot'
+#    xlab: PC1
+#    ylab: PC2

modules/local/deseq2_qc/tests/main.nf.test

@@ -0,0 +1,36 @@
+nextflow_process {
+
+    name "Test Process DESEQ2_QC"
+    script "../main.nf"
+    process "DESEQ2_QC"
+
+    test("parse count data correctly") {
+
+        when {
+            process {
+                """
+                input[0] = file("${moduleTestDir}/data/countFile.tsv")
+                input[1] = file("${moduleTestDir}/data/deseq2_pca_header.txt")
+                input[2] = file("${moduleTestDir}/data/deseq2_clustering_header.txt")
+                """.stripIndent().trim()
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.dists_multiqc,
+                    process.out.dists_txt,
+                    process.out.log,
+                    process.out.pca_multiqc,
+                    process.out.pca_txt,
+                    process.out.rdata,
+                    process.out.size_factors
+                ).match() }
+            )
+        }
+
+    }
+
+}

modules/local/deseq2_qc/tests/main.nf.test.snap

@@ -0,0 +1,39 @@
+{
+    "parse count data correctly": {
+        "content": [
+            [
+
+            ],
+            [
+                "deseq2.sample.dists.txt:md5,1616ce40eb58ee75640efed219c6bbec"
+            ],
+            [
+                "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676"
+            ],
+            [
+
+            ],
+            [
+                "deseq2.pca.vals.txt:md5,4cda8e32ec39326c1350e77b4b607aad"
+            ],
+            [
+                "deseq2.dds.RData:md5,c7c1872e7566321d0c3f7ca56c463088"
+            ],
+            [
+                [
+                    "RAP1_IAA_30M_REP1.txt:md5,ce4ff0b74aeedc3dc12a764c3504c9df",
+                    "RAP1_UNINDUCED_REP1.txt:md5,51c9b23be5e82670aceb14f7e58dd867",
+                    "RAP1_UNINDUCED_REP2.txt:md5,2c56106abcd9d31980f672b6e2862ee8",
+                    "WT_REP1.txt:md5,5e3fe5f7e9b7f300be43649a8b496352",
+                    "WT_REP2.txt:md5,2ce093f2c2e92c1bde1cd3da91ac884c",
+                    "deseq2.size_factors.RData:md5,51c6643a0f8a9edabbff8df0165451f2"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-07T12:34:51.582179"
+    }
+}