Merge pull request #425 from ggabernet/nf-test

Add nf-tests

Author: ggabernet

.nf-core.yml

@@ -1,7 +1,6 @@
 lint:
   files_exist:
     - conf/igenomes.config
-  included_configs: false
   multiqc_config:
     - report_comment
   nextflow_config:

CHANGELOG.md

@@ -11,8 +11,9 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - [#413](https://github.com/nf-core/airrflow/pull/413) Updated nf-core template to v3.3.2.
 - [#413](https://github.com/nf-core/airrflow/pull/413) Speeding up tests with smaller test data.
 - [#416](https://github.com/nf-core/airrflow/pull/416) Update Takara protocol names and docs. Add Takara SMART-seq protocol.
-- [#416](https://github.com/nf-core/airrflow/pull/416) Add nf-test tests.
+- [#416](https://github.com/nf-core/airrflow/pull/416) Add first nf-test.
 - [#422](https://github.com/nf-core/airrflow/pull/422) Template update to nf-core v3.4.1
+- [#425](https://github.com/nf-core/airrflow/pull/416) Add all nf-tests.
 
 ### `Fixed`
 
@@ -29,10 +30,9 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 | Dependency | Old version | New version |
 | ---------- | ----------- | ----------- |
-| enchantr   | 0.1.20      | 0.1.23      |
+| enchantr   | 0.1.20      | 0.1.24      |
 | presto     | 0.7.4       | 0.7.6       |
-| dowser     | 2.3         |             |
-| alakazam   | 1.3.1       |             |
+| dowser     | 2.3         | 2.4.0       |
 
 ## [4.3.1] - Revelio hotfix
 

assets/repertoire_comparison.Rmd

@@ -93,13 +93,7 @@ tryCatch( {
                   ggtitle("Number of sequences after each of the sequence assembly steps") +
                   theme(axis.text.x= element_text(angle = 45))
 
-    p <- ggplotly(seqs_plot) %>%
-      layout(shapes = list(list(type = "rect",
-              xref = "paper", yref = "paper",
-              x0 = -0.02, x1 = 1.02, y0 = -0.02, y1 = 1.02,
-              line = list(color = "black", width = 1.5),
-              fillcolor = 'rgba(0,0,0,0)',
-              layer = 'above')))
+    p <- ggplotly(seqs_plot)
   p
 
 
@@ -130,6 +124,8 @@ if (is.null(tab_seqs_assembled$sample_id)) {
 }
 
 dat <- tab_seqs_assembled %>%
+        filter( !grepl("-fail.tsv", output) ) %>%
+        filter( !grepl("productive-F.tsv", output) ) %>%
         tidyr::pivot_wider(id_cols=sample_id,
                             names_from=task,
                             values_from=output_size)
@@ -171,11 +167,7 @@ seqs_plot_assembled <- ggplot(data=tab_seqs_assembled,
               theme(axis.text.x = element_text(angle = 45)
               )
 
-p <- ggplotly(seqs_plot_assembled) |>
-  layout(
-    xaxis = list(showline = TRUE, linecolor = "black", linewidth = 0.66, mirror = TRUE),
-    yaxis = list(showline = TRUE, linecolor = "black", linewidth = 0.66, mirror = TRUE)
-  )
+p <- ggplotly(seqs_plot_assembled)
 p
 ```
 
@@ -218,11 +210,7 @@ g2 <- ggplot(family, aes(x=gene, y=seq_freq, fill=sample_id, group=sample_id)) +
     ylab("Frequency") +
     xlab("") +
     theme(legend.position = "right")
-p <- ggplotly(g2) |>
-  layout(
-    xaxis = list(showline = TRUE, linecolor = "black", linewidth = 0.66, mirror = TRUE),
-    yaxis = list(showline = TRUE, linecolor = "black", linewidth = 0.66, mirror = TRUE)
-  )
+p <- ggplotly(g2)
 p
 
 ggsave(filename = paste0(vfamily_dir, "/V_Family_distribution_patient.pdf"), plot = g2, width = 18, height = 15, units = "cm")
@@ -247,11 +235,7 @@ g2 <- ggplot(family, aes(x=gene, y=seq_freq, fill=sample_id, group=sample_id)) +
     theme(axis.text.x=element_text(angle=45, hjust=1, vjust=1)) +
     ylab("Frequency") +
     xlab("")
-p <- ggplotly(g2) |>
-  layout(
-    xaxis = list(showline = TRUE, linecolor = "black", linewidth = 0.66, mirror = TRUE),
-    yaxis = list(showline = TRUE, linecolor = "black", linewidth = 0.66, mirror = TRUE)
-  )
+p <- ggplotly(g2)
 p
 ggsave(filename = paste0(vfamily_dir, "/V_gene_distribution_by_sequence_patient.pdf"), plot = g2, width = 20, height = 40, units = "cm")
 ggsave(filename = paste0(vfamily_dir, "/V_gene_distribution_by_sequence_patient.png"), plot = g2, width = 20, height = 40, units = "cm")

conf/modules.config

@@ -495,7 +495,7 @@ process {
     // V(D)J annotation
     // -----------------
 
-    withName: 'FETCH_*' {
+    withName: 'FETCH_DATABASES' {
         publishDir = [
             path: { "${params.outdir}/databases" },
             mode: params.publish_dir_mode,

conf/test_fetchimgt.config

@@ -22,19 +22,9 @@ params {
     config_profile_description = 'Test pipeline when fetching the latest version of the IMGT references.'
 
     // Input data
-    input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_small_test_airr.tsv'
-    cprimers = pipelines_testdata_base_path + 'testdata-bcr/C_primers.fasta'
-    vprimers = pipelines_testdata_base_path + 'testdata-bcr/V_primers.fasta'
+    mode = 'assembled'
+    input = pipelines_testdata_base_path + 'testdata-reveal/test_assembled_metadata_hs.tsv'
     fetch_imgt = true
-
-    mode = 'fastq'
-
-    library_generation_method = 'specific_pcr_umi'
-    cprimer_position = 'R1'
-    umi_length = 8
-    umi_start = 6
-    umi_position = 'R1'
-    index_file = true
 }
 
 process{

conf/test_full.config

@@ -37,7 +37,7 @@ params {
     lineage_trees = true
     embeddings = 'antiberty,antiberta2,balmpaired,esm2'
     embedding_chain = "HL"
-    use_gpu = true
+    use_gpu = false // Megatest infrastructure not ready yet for GPU
 }
 
 process {

tests/.nftignore

@@ -24,8 +24,15 @@ pipeline_info/*.{html,json,txt,yml}
 **/*.fmt7
 **/*.RDS
 **/*.fastp.log
-presto/**/*
-vdj_annotation/01-assign-genes/**/*
-vdj_annotation/02-make-db/**/*
-vdj_annotation/04-select-productive/**/*
+**/*.bam
+**/*.bam.bai
+**/*.vloupe
+presto/**
+vdj_annotation/01-assign-genes/**
+vdj_annotation/02-make-db/**
+vdj_annotation/04-select-productive/**
+vdj_annotation/convert-db/**
+qc-filtering/bulk-qc-filtering/01-create-germlines/**
+vdj_annotation/select-locus/**/*
+databases/**
 **/reference-keys.txt

tests/default.nf.test

@@ -28,7 +28,10 @@ nextflow_pipeline {
                     // All stable path name, with a relative path
                     stable_name,
                     // All files with stable contents
-                    stable_path
+                    stable_path,
+                    // Additional files that are excluded in .nftignore but need to be checked
+                    "$outputDir/repertoire_comparison/Sequence_numbers_summary/Table_sequences_assembled.tsv",
+                    "$outputDir/repertoire_comparison/Sequence_numbers_summary/Table_sequences_assembly.tsv"
                 ).match() }
             )
         }

tests/default.nf.test.snap

@@ -28,16 +28,16 @@
                     "changeo": "1.3.0"
                 },
                 "CLONAL_ASSIGNMENT_COMPUTE": {
-                    "enchantr": "0.1.23"
+                    "enchantr": "0.1.24"
                 },
                 "CLONAL_ASSIGNMENT_REPORT": {
-                    "enchantr": "0.1.23"
+                    "enchantr": "0.1.24"
                 },
                 "COLLAPSE_DUPLICATES": {
-                    "enchantr": "0.1.23"
+                    "enchantr": "0.1.24"
                 },
                 "DOWSER_LINEAGES": {
-                    "enchantr": "0.1.23"
+                    "enchantr": "0.1.24"
                 },
                 "FASTP": {
                     "fastp": "0.23.4"
@@ -54,14 +54,14 @@
                 "FILTER_QUALITY": {
                     "alakazam": "1.3.1",
                     "optparse": "1.7.5",
-                    "stringi": "1.8.7",
+                    "stringi": "1.8.3",
                     "dplyr": "1.1.4",
                     "airr": "1.5.0",
                     "DT": "0.34.0",
                     "R": "4.5.1"
                 },
                 "FIND_CLONAL_THRESHOLD": {
-                    "enchantr": "0.1.23"
+                    "enchantr": "0.1.24"
                 },
                 "GUNZIP_UMI": {
                     "gunzip": 1.1
@@ -121,7 +121,7 @@
                     "presto": "0.7.6"
                 },
                 "REPORT_FILE_SIZE": {
-                    "enchantr": "0.1.23"
+                    "enchantr": "0.1.24"
                 },
                 "SAMPLESHEET_CHECK": {
                     "python": "3.9.1",
@@ -903,12 +903,14 @@
                 "Sample6_add-meta_command_log.txt:md5,70b00ba883c70c3070831895ccfa072c",
                 "Sample7_add-meta_command_log.txt:md5,7f45c2264149e92259b260eb940957f8",
                 "Sample8_add-meta_command_log.txt:md5,eaaaa70f2f95d61750d77605798a75b9"
-            ]
+            ],
+            "Table_sequences_assembled.tsv:md5,7330606135fab6f1bc7c33de4e455512",
+            "Table_sequences_assembly.tsv:md5,d6f5ac80a7781b76ec008c2ee4487cd6"
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.04.8"
         },
-        "timestamp": "2025-10-21T10:38:57.492281136"
+        "timestamp": "2025-11-04T13:26:21.925049633"
     }
 }

tests/test_10x_sc.nf.test

@@ -0,0 +1,38 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    tag "pipeline"
+    profile "test_10x_sc"
+
+    test("-profile test_10x_sc") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_airrflow_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path,
+                    // Additional files that are excluded in .nftignore but need to be checked
+                    "$outputDir/repertoire_comparison/Sequence_numbers_summary/Table_sequences_assembled.tsv"
+                ).match() }
+            )
+        }
+    }
+}