add fq2bammeth config + test + snap, ci: nf-test job filter by tag cpu

nf-core · Dec 2, 2024 · 210199e · 210199e
1 parent 5ebc7e2
commit 210199e
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Showing 8 changed files with 31 additions and 46 deletions.
diff --git a/conf/modules/bwameth_align.config b/conf/modules/bwameth_align.config
@@ -1,6 +1,6 @@
 process {
     withName: BWAMETH_ALIGN {
-        cache = 'lenient'
+        cache = 'lenient' // This is set because in the module command the index files are touched so as to have bwameth not complain
         ext.args = ''
         publishDir = [
                 path: { "${params.outdir}/${params.aligner}/alignments" },

diff --git a/conf/modules/parabricks_fq2bammeth.config b/conf/modules/parabricks_fq2bammeth.config
@@ -0,0 +1,12 @@
+process {
+    withName: PARABRICKS_FQ2BAMMETH {
+        cache = 'lenient' // This is set because in the module command the index files are touched so as to have bwameth not complain
+        ext.args = '--low-memory'
+        publishDir = [
+                path: { "${params.outdir}/${params.aligner}/alignments" },
+                pattern: "*.bam",
+                mode: params.publish_dir_mode,
+                enabled: params.save_align_intermeds
+        ]
+    }
+}
diff --git a/conf/subworkflows/fastq_align_dedup_bwameth.config b/conf/subworkflows/fastq_align_dedup_bwameth.config
@@ -1,5 +1,6 @@
 
 includeConfig "../modules/bwameth_align.config"
+includeConfig "../modules/parabricks_fq2bammeth.config"
 includeConfig "../modules/samtools_sort.config"
 includeConfig "../modules/samtools_flagstat.config"
 includeConfig "../modules/samtools_stats.config"

diff --git a/tests/bismark_emseq_clip_r1.nf.test b/tests/bismark_emseq_clip_r1.nf.test
@@ -3,6 +3,7 @@ nextflow_pipeline {
     name "Test Workflow main.nf"
     script "../main.nf"
     config "./nextflow.config"
+    tag "cpu"
 
     test("Params: bismark | em_seq | clip_r1") {
         when {

diff --git a/tests/bwameth.nf.test b/tests/bwameth.nf.test
@@ -3,6 +3,7 @@ nextflow_pipeline {
     name "Test Workflow main.nf"
     script "../main.nf"
     config "./nextflow.config"
+    tag "cpu"
 
     test("Params: bwameth") {
         when {

diff --git a/tests/bwameth_use_gpu.nf.test b/tests/bwameth_use_gpu.nf.test
@@ -3,7 +3,6 @@ nextflow_pipeline {
     name "Test Workflow main.nf"
     script "../main.nf"
     config "./nextflow.config"
-
     tag "gpu"
 
     test("Params: bwameth | use_gpu") {
@@ -41,12 +40,12 @@ nextflow_pipeline {
         }
     }
 
-    test("Params: bwameth | use_gpu | with bwameth-index") {
+    test("Params: bwameth | use_gpu |with bwameth-index") {
         when {
             params {
-                aligner       = "bwameth"
+                aligner        = "bwameth"
                 bwameth_index = "https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz"
-                outdir        = "$outputDir"
+                outdir         = "$outputDir"
             }
         }
 

diff --git a/tests/bwameth_use_gpu.nf.test.snap b/tests/bwameth_use_gpu.nf.test.snap
@@ -1,4 +1,14 @@
 {
+    "Params: bwameth | use_gpu |with bwameth-index": {
+        "content": [
+            47
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-12-02T11:56:58.163433"
+    },
     "Params: bwameth | use_gpu": {
         "content": [
             36,
@@ -164,13 +174,6 @@
                 "multiqc/bwameth/multiqc_plots/svg/samtools_alignment_plot-cnt.svg",
                 "multiqc/bwameth/multiqc_plots/svg/samtools_alignment_plot-pct.svg",
                 "multiqc/bwameth/multiqc_report.html",
-                "parabricks",
-                "parabricks/SRR389222_sub1.bam",
-                "parabricks/SRR389222_sub1.bam.bai",
-                "parabricks/SRR389222_sub2.bam",
-                "parabricks/SRR389222_sub2.bam.bai",
-                "parabricks/SRR389222_sub3.bam",
-                "parabricks/SRR389222_sub3.bam.bai",
                 "pipeline_info",
                 "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
                 "trimgalore",
@@ -223,13 +226,7 @@
                 "samtools-flagstat-dp_Percentage_of_total.txt:md5,921b0c969e7c154c0cd18b331e2a6c1c",
                 "samtools-flagstat-dp_Read_counts.txt:md5,c0764320e38e62b48d59f608094804b8",
                 "samtools-stats-dp.txt:md5,99418ae30d5855a3d8cd9cfdf21dd14d",
-                "samtools_alignment_plot.txt:md5,34b8fa8a88b6f5ef00153b07aabc028d",
-                "SRR389222_sub1.bam:md5,a5d5600e09697b1d9a31b0547ab7edcf",
-                "SRR389222_sub1.bam.bai:md5,c95cb45c3f0a9a82bf78a7914b38ebaf",
-                "SRR389222_sub2.bam:md5,bb04f6c07f75892530c7d960997ac9a7",
-                "SRR389222_sub2.bam.bai:md5,fbe5ef44841a8b6028bdb7c14ae67e59",
-                "SRR389222_sub3.bam:md5,2c1cca453526e1672e87bb07e30af30a",
-                "SRR389222_sub3.bam.bai:md5,d7d62a85aac95328011ba48c37f3cf1c"
+                "samtools_alignment_plot.txt:md5,34b8fa8a88b6f5ef00153b07aabc028d"
             ],
             [
                 [
@@ -255,35 +252,13 @@
                 [
                     "SRR389222_sub3.markdup.sorted.bam",
                     "9eaa07df5ad58a78ab57ee55f948a044"
-                ],
-                [
-                    "SRR389222_sub1.bam",
-                    "97e6767c5ddea54cb2a6498192a09c68"
-                ],
-                [
-                    "SRR389222_sub2.bam",
-                    "313ae71af4023059a295ed8a132fd9ad"
-                ],
-                [
-                    "SRR389222_sub3.bam",
-                    "9eaa07df5ad58a78ab57ee55f948a044"
                 ]
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-12-02T08:58:09.474824"
-    },
-    "Params: bwameth | use_gpu | with bwameth-index": {
-        "content": [
-            47
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.0"
-        },
-        "timestamp": "2024-12-02T08:59:21.276625"
+        "timestamp": "2024-12-02T11:55:47.061799"
     }
 }
diff --git a/tests/nextflow.config b/tests/nextflow.config
@@ -28,10 +28,6 @@ process {
     withName: PRESEQ_LCEXTRAP {
         errorStrategy = 'ignore'
     }
-
-    withName: 'PARABRICKS_FQ2BAMMETH' {
-        ext.args = '--low-memory'
-    }
 }
 
 // Impose same minimum Nextflow version as the pipeline for testing