Add nf-test for local subworkflow ARRIBA_WORKFLOW

CHANGELOG.md

@@ -19,7 +19,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add nf-test to local module: `FUSIONREPORT_DOWNLOAD` [#560](https://github.com/nf-core/rnafusion/pull/560)
 - Add nf-test to local subworkflow: `QC_WORKFLOW` [#568](https://github.com/nf-core/rnafusion/pull/568)
 - Add nf-test to local subworkflow: `TRIM_WORKFLOW` [#572](https://github.com/nf-core/rnafusion/pull/572)
-- Add nf-test to local module: `FUSIONREPORT_DETECT`. Improve `FUSIONREPORT_DOWNLOAD` module [#577](https://github.com/nf-core/rnafusion/pull/577)
+- Add nf-test to local module: `FUSIONREPORT_DETECT`. Improve `FUSIONREPORT_DOWNLOAD` module [#572](https://github.com/nf-core/rnafusion/pull/577)
+- Add nf-test to local subworkflow: `ARRIBA_WORKFLOW` [#578](https://github.com/nf-core/rnafusion/pull/578)
 
 ### Changed
 

subworkflows/local/arriba_workflow/main.nf

@@ -0,0 +1,97 @@
+include { ARRIBA_ARRIBA                               } from '../../../modules/nf-core/arriba/arriba/main'
+include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_FOR_ARRIBA } from '../../../modules/nf-core/samtools/index/main'
+include { SAMTOOLS_SORT as SAMTOOLS_SORT_FOR_ARRIBA   } from '../../../modules/nf-core/samtools/sort/main'
+include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_FOR_ARRIBA   } from '../../../modules/nf-core/samtools/view/main'
+include { STAR_ALIGN as STAR_FOR_ARRIBA               } from '../../../modules/nf-core/star/align/main'
+
+workflow ARRIBA_WORKFLOW {
+    take:
+        reads                           // channel [ meta, [ fastqs ]         ]
+        ch_gtf                          // channel [ meta, path_gtf           ]
+        ch_fasta                        // channel [ meta, path_fasta         ]
+        ch_starindex_ref                // channel [ meta, path_index         ]
+        ch_arriba_ref_blacklist         // channel [ meta, path_blacklist     ]
+        ch_arriba_ref_known_fusions     // channel [ meta, path_known_fusions ]
+        ch_arriba_ref_cytobands         // channel [ meta, path_cytobands     ]
+        ch_arriba_ref_protein_domains   // channel [ meta, path_proteins      ]
+        arriba                          // boolean
+        all                             // boolean
+        fusioninspector_only            // boolean
+        star_ignore_sjdbgtf             // boolean
+        seq_center                      // string
+        arriba_fusions                  // path
+        cram                            // array
+
+    main:
+        ch_versions   = Channel.empty()
+        ch_cram_index = Channel.empty()
+        ch_dummy_file = file("$baseDir/assets/dummy_file_arriba.txt", checkIfExists: true)
+
+        if (( arriba || all ) && !fusioninspector_only) {
+
+            STAR_FOR_ARRIBA(
+                reads,
+                ch_starindex_ref,
+                ch_gtf,
+                star_ignore_sjdbgtf,
+                '',
+                seq_center
+            )
+
+            ch_versions = ch_versions.mix(STAR_FOR_ARRIBA.out.versions)
+
+            if ( arriba_fusions ) {
+
+                ch_arriba_fusions = reads.combine( Channel.value( file( arriba_fusions, checkIfExists: true ) ) )
+                    .map { meta, reads, fusions -> [ meta, fusions ] }
+                ch_arriba_fusion_fail = ch_dummy_file
+
+            } else {
+
+                ARRIBA_ARRIBA (
+                    STAR_FOR_ARRIBA.out.bam,
+                    ch_fasta,
+                    ch_gtf,
+                    ch_arriba_ref_blacklist.map{ it[1] },
+                    ch_arriba_ref_known_fusions.map{ it[1] },
+                    ch_arriba_ref_cytobands.map{ it[1] },
+                    ch_arriba_ref_protein_domains.map{ it[1] }
+                )
+
+                ch_versions = ch_versions.mix(ARRIBA_ARRIBA.out.versions)
+
+                ch_arriba_fusions     = ARRIBA_ARRIBA.out.fusions
+                ch_arriba_fusion_fail = ARRIBA_ARRIBA.out.fusions_fail.map{ meta, file -> return file }
+            }
+
+            if ( cram.contains('arriba') ) {
+
+                SAMTOOLS_SORT_FOR_ARRIBA(STAR_FOR_ARRIBA.out.bam, ch_fasta)
+                ch_versions = ch_versions.mix(SAMTOOLS_SORT_FOR_ARRIBA.out.versions )
+
+                SAMTOOLS_VIEW_FOR_ARRIBA(SAMTOOLS_SORT_FOR_ARRIBA.out.bam.map { meta, bam -> [ meta, bam, [] ] }, ch_fasta, [])
+                ch_versions = ch_versions.mix(SAMTOOLS_VIEW_FOR_ARRIBA.out.versions )
+
+                SAMTOOLS_INDEX_FOR_ARRIBA(SAMTOOLS_VIEW_FOR_ARRIBA.out.cram)
+                ch_versions = ch_versions.mix(SAMTOOLS_INDEX_FOR_ARRIBA.out.versions )
+
+                // Join cram and index files
+                ch_cram_index = SAMTOOLS_VIEW_FOR_ARRIBA.out.cram.join(SAMTOOLS_INDEX_FOR_ARRIBA.out.crai)
+            }
+
+        } else {
+
+            ch_arriba_fusions = reads
+                .combine(Channel.value( file(ch_dummy_file, checkIfExists: true ) ) )
+                .map { meta, reads, fusions -> [ meta, fusions ] }
+
+            ch_arriba_fusion_fail = ch_dummy_file
+        }
+
+    emit:
+        fusions      = ch_arriba_fusions        // channel [ meta, path_fusions   ]
+        fusions_fail = ch_arriba_fusion_fail    // channel [ path, fusions_failed ]
+        cram_index   = ch_cram_index            // channel [ meta, cram, crai     ]
+        versions     = ch_versions              // channel [ versions             ]
+    }
+