Add pipeline-level nf-test (BUILD_REFERENCES)

.github/workflows/ci.yml

@@ -39,6 +39,7 @@ jobs:
           - "latest-stable"
         test_profile:
           - "test_stub"
+          - "test_build"
         compute_profile:
           - "docker"
           - "singularity"

conf/test_build.config

@@ -5,9 +5,28 @@
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run nf-core/rnafusion -profile test_build,<docker/singularity> --outdir <OUTDIR> -stub
+        nextflow run nf-core/rnafusion -profile test_build,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
+Uses a minimal fasta and gtf for testing purposes.
+This test is designed to test the `build_references` subworkflow with the following processes on:
+- SAMTOOLS_FAIDX
+- HGNC_DOWNLOAD
+- GATK4_CREATESEQUENCEDICTIONARY
+- GET_RRNA_TRANSCRIPTS
+- GATK4_BEDTOINTERVALLIST
+- GTF_TO_REFFLAT
+- GFFREAD
+- STAR_GENOMEGENERATE
+- ARRIBA_DOWNLOAD
+- STARFUSION_BUILD
+- FUSIONREPORT_DOWNLOAD
+
+It does not test the following processes of the `build_references` subworkflow:
+- GENCODE_DOWNLOAD
+- FUSIONCATCHER_BUILD
+
+It does not test the main rnafusion subworkflows by setting references_only = true.
 */
 
 params {
@@ -18,7 +37,13 @@ params {
     references_only            = true
     input                      = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv'
     no_cosmic                  = true
-    all                        = true
+    all                        = false
+    arriba                     = true
+    fusioncatcher              = false
+    starfusion                 = true
+    fasta                      = 'https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/minigenome.fa'
+    gtf                        = 'https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/minigenome.gtf'
+    fusionreport               = true
 
     skip_salmon_index          = true
     starfusion_build           = true

tests/.nftignore

@@ -3,3 +3,30 @@ references/arriba/blacklist_hg38_GRCh38_v2.4.0.tsv.gz
 references/arriba/known_fusions_hg38_GRCh38_v2.4.0.tsv.gz
 references/ensembl/Homo_sapiens.GRCh38.102.dna.primary_assembly.fa
 references/hgnc/HGNC-DB-timestamp.txt
+references/fusion_report_db/DB-timestamp.txt
+references/salmon/salmon/ctable.bin
+references/salmon/salmon/pos.bin
+references/salmon/salmon/pre_indexing.log
+references/salmon/salmon/ref_indexing.log
+references/salmon/salmon/seq.bin
+references/star/Log.out
+starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/
+starfusion/ctat_genome_lib_build_dir/PFAM.domtblout.dat.gz
+starfusion/ctat_genome_lib_build_dir/blast_pairs.dat.gz
+starfusion/ctat_genome_lib_build_dir/blast_pairs.idx
+starfusion/ctat_genome_lib_build_dir/fusion_annot_lib.idx
+starfusion/ctat_genome_lib_build_dir/pfam_domains.dbm
+starfusion/ctat_genome_lib_build_dir/ref_annot.cdna.fa
+starfusion/ctat_genome_lib_build_dir/ref_annot.cdna.fa.idx
+starfusion/ctat_genome_lib_build_dir/ref_annot.cds
+starfusion/ctat_genome_lib_build_dir/ref_annot.cdsplus.fa
+starfusion/ctat_genome_lib_build_dir/ref_annot.cdsplus.fa.idx
+starfusion/ctat_genome_lib_build_dir/ref_annot.gtf.gene_spans
+starfusion/ctat_genome_lib_build_dir/ref_annot.pep
+starfusion/ctat_genome_lib_build_dir/ref_annot.prot_info.dbm
+starfusion/ctat_genome_lib_build_dir/ref_genome.fa.nin
+starfusion/ctat_genome_lib_build_dir/ref_genome.fa.njs
+starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/Log.out
+starfusion/ctat_genome_lib_build_dir/trans.blast.align_coords.align_coords.dbm
+references/star/genomeParameters.txt
+starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/genomeParameters.txt

tests/test_build.nf.test

@@ -0,0 +1,40 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    profile "test_build"
+    tag "pipeline"
+    tag "pipeline_rnafusion"
+    tag "test_build"
+
+    test("Test build references") {
+
+        when {
+            params {
+                outdir               = "$outputDir"
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            // Ignore files with timestamps in their names
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+
+}