Merge pull request #183 from drpatelh/nf-test

Restructure local modules and main script names
nf-core · Aug 17, 2023 · 3f31ccc · 3f31ccc
2 parents 23d2f21 + de46456
commit 3f31ccc
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Showing 59 changed files with 680 additions and 586 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -44,15 +44,15 @@ jobs:
       matrix:
         NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
         test_tags:
-          - "sra"
-          - "sra_force_sratools_download"
-          - "sra_skip_fastq"
-          - "sra_with_atacseq"
-          - "sra_with_rnaseq"
-          - "sra_with_rnaseq_specific_ena"
-          - "sra_with_taxprofiler"
-          - "sra_with_viralrecon"
           - "modules_local"
+          - "sra_default_parameters"
+          - "sra_custom_ena_metadata_fields"
+          - "sra_force_sratools_download"
+          - "sra_nf_core_pipeline_atacseq"
+          - "sra_nf_core_pipeline_rnaseq"
+          - "sra_nf_core_pipeline_taxprofiler"
+          - "sra_nf_core_pipeline_viralrecon"
+          - "sra_skip_fastq_download"
         profile:
           - "docker"
 

diff --git a/main.nf b/main.nf
@@ -49,9 +49,9 @@ if (WorkflowMain.isSraId(ch_input)) {
 
 if (params.input_type == input_type) {
     if (params.input_type == 'sra') {
-        include { SRA } from './workflows/sra/main'
+        include { SRA } from './workflows/sra'
     } else if (params.input_type == 'synapse') {
-        include { SYNAPSE } from './workflows/synapse/main'
+        include { SYNAPSE } from './workflows/synapse'
     }
 } else {
     exit 1, "Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!"

diff --git a/modules.json b/modules.json
@@ -8,7 +8,8 @@
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff"
                     },
                     "custom/sratoolsncbisettings": {
                         "branch": "master",

diff --git a/...appings_config/multiqc_mappings_config.nf → ...les/local/multiqc_mappings_config/main.nf b/...appings_config/multiqc_mappings_config.nf → ...les/local/multiqc_mappings_config/main.nf
diff --git a/modules/local/multiqc_mappings_config/multiqc_mappings_config.nf.test.snap b/modules/local/multiqc_mappings_config/multiqc_mappings_config.nf.test.snap
diff --git a/...gs_config/multiqc_mappings_config.nf.test → ...ultiqc_mappings_config/tests/main.nf.test b/...gs_config/multiqc_mappings_config.nf.test → ...ultiqc_mappings_config/tests/main.nf.test
@@ -1,17 +1,19 @@
 nextflow_process {
 
-    name "Test Process MULTIQC_MAPPINGS_CONFIG"
-    script "modules/local/multiqc_mappings_config/multiqc_mappings_config.nf"
+    name "Test process: MULTIQC_MAPPINGS_CONFIG"
+    script "modules/local/multiqc_mappings_config/main.nf"
     process "MULTIQC_MAPPINGS_CONFIG"
-    tag "multiqc_mappings_config"
+    tag "modules"
     tag "modules_local"
+    tag "multiqc_mappings_config"
 
-    test("SRX9626017_SRR13191702") {
+    test("Should run without failures") {
 
         when {
             params {
-                outdir   = "$outputDir"
+                outdir = "$outputDir"
             }
+
             process {
                 """
                 input[0] = file(params.test_data['modules_local']['multiqc_mappings_config'], checkIfExists: true)
@@ -22,10 +24,8 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
+                { assert snapshot(process.out).match() }
             )
         }
-
     }
-
 }
diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap
@@ -0,0 +1,52 @@
+{
+    "SRX9626017_SRR13191702": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
+                        "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                ],
+                "versions": [
+                    "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                ],
+                "yml": [
+                    [
+                        "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
+                        "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2023-08-17T12:02:35+0000"
+    },
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
+                        "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                ],
+                "versions": [
+                    "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                ],
+                "yml": [
+                    [
+                        "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
+                        "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2023-08-17T12:02:35+0000"
+    }
+}
diff --git a/modules/local/sra_fastq_ftp/sra_fastq_ftp.nf → modules/local/sra_fastq_ftp/main.nf b/modules/local/sra_fastq_ftp/sra_fastq_ftp.nf → modules/local/sra_fastq_ftp/main.nf
diff --git a/modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test b/modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test
diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test
@@ -0,0 +1,34 @@
+nextflow_process {
+
+    name "Test process: SRA_FASTQ_FTP"
+    script "modules/local/sra_fastq_ftp/main.nf"
+    process "SRA_FASTQ_FTP"
+    tag "modules"
+    tag "modules_local"
+    tag "sra_fastq_ftp"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+
+            process {
+                """
+                input[0] = [
+                    [ id:'SRX9626017_SRR13191702', single_end:false, md5_1: '89c5be920021a035084d8aeb74f32df7', md5_2: '56271be38a80db78ef3bdfc5d9909b98' ], // meta map
+                    params.test_data['modules_local']['sra_fastq_ftp']
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/.../sra_fastq_ftp/sra_fastq_ftp.nf.test.snap → ...cal/sra_fastq_ftp/tests/main.nf.test.snap b/.../sra_fastq_ftp/sra_fastq_ftp.nf.test.snap → ...cal/sra_fastq_ftp/tests/main.nf.test.snap
diff --git a/.../sra_ids_to_runinfo/sra_ids_to_runinfo.nf → modules/local/sra_ids_to_runinfo/main.nf b/.../sra_ids_to_runinfo/sra_ids_to_runinfo.nf → modules/local/sra_ids_to_runinfo/main.nf
diff --git a/...ids_to_runinfo/sra_ids_to_runinfo.nf.test → ...cal/sra_ids_to_runinfo/tests/main.nf.test b/...ids_to_runinfo/sra_ids_to_runinfo.nf.test → ...cal/sra_ids_to_runinfo/tests/main.nf.test
@@ -1,17 +1,19 @@
 nextflow_process {
 
-    name "Test Process SRA_IDS_TO_RUNINFO"
-    script "modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf"
+    name "Test process: SRA_IDS_TO_RUNINFO"
+    script "modules/local/sra_ids_to_runinfo/main.nf"
     process "SRA_IDS_TO_RUNINFO"
-    tag "sra_ids_to_runinfo"
+    tag "modules"
     tag "modules_local"
+    tag "sra_ids_to_runinfo"
 
     test("Should run without failures") {
 
         when {
             params {
-                outdir   = "$outputDir"
+                outdir = "$outputDir"
             }
+
             process {
                 """
                 input[0] = 'SRR13191702'
@@ -23,10 +25,8 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
+                { assert snapshot(process.out).match() }
             )
         }
-
     }
-
 }
diff --git a/...o_runinfo/sra_ids_to_runinfo.nf.test.snap → ...ra_ids_to_runinfo/tests/main.nf.test.snap b/...o_runinfo/sra_ids_to_runinfo.nf.test.snap → ...ra_ids_to_runinfo/tests/main.nf.test.snap
diff --git a/...erge_samplesheet/sra_merge_samplesheet.nf → modules/local/sra_merge_samplesheet/main.nf b/...erge_samplesheet/sra_merge_samplesheet.nf → modules/local/sra_merge_samplesheet/main.nf
diff --git a/...samplesheet/sra_merge_samplesheet.nf.test → .../sra_merge_samplesheet/tests/main.nf.test b/...samplesheet/sra_merge_samplesheet.nf.test → .../sra_merge_samplesheet/tests/main.nf.test
@@ -1,17 +1,19 @@
 nextflow_process {
 
-    name "Test Process SRA_MERGE_SAMPLESHEET"
-    script "modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf"
+    name "Test process: SRA_MERGE_SAMPLESHEET"
+    script "modules/local/sra_merge_samplesheet/main.nf"
     process "SRA_MERGE_SAMPLESHEET"
-    tag "sra_merge_samplesheet"
+    tag "modules"
     tag "modules_local"
+    tag "sra_merge_samplesheet"
 
     test("Should run without failures") {
 
         when {
             params {
-                outdir   = "$outputDir"
+                outdir = "$outputDir"
             }
+
             process {
                 """
                 input[0] = params.test_data['modules_local']['sra_merge_samplesheet_samplesheets'].collect { file(it, checkIfExists: true) }
@@ -23,10 +25,8 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
+                { assert snapshot(process.out).match() }
             )
         }
-
     }
-
 }
diff --git a/...esheet/sra_merge_samplesheet.nf.test.snap → ...merge_samplesheet/tests/main.nf.test.snap b/...esheet/sra_merge_samplesheet.nf.test.snap → ...merge_samplesheet/tests/main.nf.test.snap
diff --git a/.../sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf → modules/local/sra_runinfo_to_ftp/main.nf b/.../sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf → modules/local/sra_runinfo_to_ftp/main.nf
diff --git a/...runinfo_to_ftp/sra_runinfo_to_ftp.nf.test → ...cal/sra_runinfo_to_ftp/tests/main.nf.test b/...runinfo_to_ftp/sra_runinfo_to_ftp.nf.test → ...cal/sra_runinfo_to_ftp/tests/main.nf.test
@@ -1,17 +1,19 @@
 nextflow_process {
 
-    name "Test Process SRA_RUNINFO_TO_FTP"
-    script "modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf"
+    name "Test process: SRA_RUNINFO_TO_FTP"
+    script "modules/local/sra_runinfo_to_ftp/main.nf"
     process "SRA_RUNINFO_TO_FTP"
-    tag "sra_runinfo_to_ftp"
+    tag "modules"
     tag "modules_local"
+    tag "sra_runinfo_to_ftp"
 
     test("Should run without failures") {
 
         when {
             params {
-                outdir   = "$outputDir"
+                outdir = "$outputDir"
             }
+
             process {
                 """
                 input[0] = file(params.test_data['modules_local']['sra_runinfo_to_ftp'], checkIfExists: true)
@@ -22,10 +24,8 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
+                { assert snapshot(process.out).match() }
             )
         }
-
     }
-
 }
diff --git a/...fo_to_ftp/sra_runinfo_to_ftp.nf.test.snap → ...ra_runinfo_to_ftp/tests/main.nf.test.snap b/...fo_to_ftp/sra_runinfo_to_ftp.nf.test.snap → ...ra_runinfo_to_ftp/tests/main.nf.test.snap
diff --git a/.../sra_to_samplesheet/sra_to_samplesheet.nf → modules/local/sra_to_samplesheet/main.nf b/.../sra_to_samplesheet/sra_to_samplesheet.nf → modules/local/sra_to_samplesheet/main.nf
diff --git a/modules/local/sra_to_samplesheet/sra_to_samplesheet.nf.test b/modules/local/sra_to_samplesheet/sra_to_samplesheet.nf.test