portcullis/full: accommodate more outputs

modules/nf-core/portcullis/full/main.nf

@@ -13,10 +13,14 @@ process PORTCULLIS_FULL {
     tuple val(meta3), path(fasta)
 
     output:
-    tuple val(meta), path("*.log"), emit: log
-    tuple val(meta), path("*.bed"), emit: bed
-    tuple val(meta), path("*.tab"), emit: tab
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("*.pass.junctions.bed"), emit: pass_junctions_bed
+    tuple val(meta), path("*.pass.junctions.tab"), emit: pass_junctions_tab
+    tuple val(meta), path("*.portcullis.log")    , emit: log
+    tuple val(meta), path("*.intron.gff3")       , emit: intron_gff , optional: true
+    tuple val(meta), path("*.exon.gff3")         , emit: exon_gff   , optional: true
+    tuple val(meta), path("*.bam")               , emit: spliced_bam, optional: true
+    tuple val(meta), path("*.bai")               , emit: spliced_bai, optional: true
+    path "versions.yml"                          , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -34,8 +38,18 @@ process PORTCULLIS_FULL {
         $fasta \\
         $bam > ${prefix}.portcullis.log
 
-    cp ${prefix}/3-filt/*.bed .
-    cp ${prefix}/3-filt/*.tab .
+    cp ${prefix}/3-filt/*.pass.junctions.bed .
+    cp ${prefix}/3-filt/*.pass.junctions.tab .
+    if [ -f ${prefix}/3-filt/*.pass.junctions.intron.gff3 ] ; then
+        cp ${prefix}/3-filt/*.pass.junctions.intron.gff3 .
+    fi
+    if [ -f ${prefix}/3-filt/*.pass.junctions.exon.gff3 ] ; then
+        cp ${prefix}/3-filt/*.pass.junctions.exon.gff3 .
+    fi
+    if [ -f ${prefix}/2-junc/*.spliced.bam ] ; then
+        cp ${prefix}/2-junc/*.spliced.bam.bai .
+        cp ${prefix}/2-junc/*.spliced.bam .
+    fi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -48,8 +62,8 @@ process PORTCULLIS_FULL {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.portcullis.log
-    touch ${prefix}.portcullis.bed
-    touch ${prefix}.portcullis.tab
+    touch ${prefix}.pass.junctions.bed
+    touch ${prefix}.pass.junctions.tab
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/portcullis/full/meta.yml

@@ -9,8 +9,8 @@ tools:
   - "portcullis":
       description: "Portcullis is a tool that filters out invalid splice junctions from
         RNA-seq alignment data. It accepts BAM files from various RNA-seq mappers, analyzes
-        splice junctions and removes likely false positives, outputting filtered
-        results in multiple formats for downstream analysis."
+        splice junctions and removes likely false positives, outputting filtered results
+        in multiple formats for downstream analysis."
       homepage: "https://portcullis.readthedocs.io/en/latest/index.html"
       documentation: "https://portcullis.readthedocs.io/en/latest/using.html"
       doi: "10.1101/217620"
@@ -58,43 +58,92 @@ output:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-          pattern: "*.log"
-      - "*.log":
+            e.g. [ id:'sample1', single_end:false ]
+      - "*.portcullis.log":
           type: file
           description: Log file containing Portcullis execution details, processing steps,
             and filtering statistics
           pattern: "*.log"
           ontologies:
             - edam: "http://edamontology.org/format_2330"
-  - bed:
+  - pass_junctions_bed:
       - meta:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-          pattern: "*.bed"
-      - "*.bed":
+            e.g. [ id:'sample1', single_end:false ]
+      - "*.pass.junctions.bed":
           type: file
           description: |
             Filtered splice junction coordinates in BED format, containing genomic coordinates of valid splice junctions after filtering out false positives
-          pattern: "*.bed"
+          pattern: "*.pass.junctions.bed"
           ontologies:
             - edam: "http://edamontology.org/format_3003"
-  - tab:
+  - pass_junctions_tab:
       - meta:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-          pattern: "*.tab"
-      - "*.tab":
-          type: map
+            e.g. [ id:'sample1', single_end:false ]
+      - "*.pass.junctions.tab":
+          type: file
           description: |
             Tabular representation of filtered splice junctions with additional metrics including junction scores, read support, and filtering decision data
-          pattern: "*.tab"
+          pattern: "*.pass.junctions.tab"
           ontologies:
             - eadam: "http://edamontology.org/format_3475"
+  - intron_gff:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'sample1', single_end:false ]
+      - "*.intron.gff3":
+          type: file
+          description: |
+            Output intron-based junctions in GFF format.
+          pattern: "*.intron.gff3"
+          ontologies:
+            - edam: "http://edamontology.org/format_1975"
+  - exon_gff:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'sample1', single_end:false ]
+      - "*.exon.gff3":
+          type: file
+          description: |
+            Output exon-based junctions in GFF format.
+          pattern: "*.exon.gff3"
+          ontologies:
+            - edam: "http://edamontology.org/format_1975"
+  - spliced_bam:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'sample1', single_end:false ]
+      - "*.bam":
+          type: file
+          description: |
+            BAM file after filtering original BAM file by removing alignments associated with bad junctions
+          pattern: "*.bam"
+          ontologies:
+            - edam: "http://edamontology.org/format_2572"
+  - spliced_bai:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'sample1', single_end:false ]
+      - "*.bai":
+          type: file
+          description: |
+            Index of the output BAM file
+          pattern: "*.bai"
+          ontologies:
+            - edam: "http://edamontology.org/format_3327"
   - versions:
       - versions.yml:
           type: file
@@ -106,3 +155,4 @@ authors:
   - "@jblancoheredia"
 maintainer:
   - "@jblancoheredia"
+  - "@anoronh4"

modules/nf-core/portcullis/full/tests/main.nf.test

@@ -10,6 +10,7 @@ nextflow_process {
     tag "portcullis/full"
 
     test("portcullis_full_paired_end") {
+        config "./nextflow.config"
 
         when {
             process {
@@ -33,9 +34,13 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
+                { assert file(process.out.spliced_bam.get(0).get(1)).name == "portcullis_all.spliced.bam" },
+                { assert file(process.out.spliced_bai.get(0).get(1)).name == "portcullis_all.spliced.bam.bai" },
                 { assert snapshot(
-                    process.out.bed,
-                    process.out.tab,
+                    process.out.pass_junctions_bed,
+                    process.out.pass_junctions_tab,
+                    process.out.intron_gff,
+                    process.out.exon_gff,
                     process.out.versions
                     ).match()
                 }
@@ -70,8 +75,10 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.bed,
-                    process.out.tab,
+                    process.out.pass_junctions_bed,
+                    process.out.pass_junctions_tab,
+                    process.out.intron_gff,
+                    process.out.exon_gff,
                     process.out.versions
                     ).match()
                 }

modules/nf-core/portcullis/full/tests/main.nf.test.snap

@@ -7,10 +7,7 @@
                         "id": "test",
                         "single_end": false
                     },
-                    [
-                        "portcullis_filtered.pass.junctions.bed:md5,613288f6b446359fd0153a7e628e1489",
-                        "portcullis_filtered.rules_in.junctions.bed:md5,572427ab6ea0832a1810ed1e706d3920"
-                    ]
+                    "portcullis_filtered.pass.junctions.bed:md5,613288f6b446359fd0153a7e628e1489"
                 ]
             ],
             [
@@ -19,12 +16,25 @@
                         "id": "test",
                         "single_end": false
                     },
-                    [
-                        "portcullis_filtered.pass.junctions.tab:md5,6e2dd7e93f6b7a23d90d3c3c11e99085",
-                        "portcullis_filtered.rules_in.junctions.tab:md5,6e1aaeb5f73b94142cfa9794d7470a6c",
-                        "portcullis_filtered.rules_out.failed.junctions.tab:md5,be919d60ca646342f6edc2f530174353",
-                        "portcullis_filtered.rules_out.passed.junctions.tab:md5,725bc8ad2a2e8e8456123e25cbb5541b"
-                    ]
+                    "portcullis_filtered.pass.junctions.tab:md5,6e2dd7e93f6b7a23d90d3c3c11e99085"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "portcullis_filtered.pass.junctions.intron.gff3:md5,3ee2c3526bfb54f81bfd55a3ab679570"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "portcullis_filtered.pass.junctions.exon.gff3:md5,7a3c56aca8dcd39ee2dec40589511a81"
                 ]
             ],
             [
@@ -33,9 +43,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2025-03-07T08:45:09.959686"
+        "timestamp": "2025-04-01T11:06:43.691683"
     },
     "portcullis_full_paired_end_stub": {
         "content": [
@@ -45,7 +55,7 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.portcullis.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    "test.pass.junctions.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ]
             ],
             [
@@ -54,17 +64,23 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.portcullis.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    "test.pass.junctions.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ]
+            ],
+            [
+
+            ],
+            [
+
             ],
             [
                 "versions.yml:md5,b297b098450e5baaea436e822fe25b0e"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2025-03-07T08:45:14.189846"
+        "timestamp": "2025-04-01T11:06:52.265624"
     }
-}
+}

modules/nf-core/portcullis/full/tests/nextflow.config

@@ -0,0 +1,11 @@
+process {
+    withName: PORTCULLIS_FULL {
+        ext.args = {
+            [
+                "--intron_gff",
+                "--exon_gff",
+                "--separate"
+            ].join(" ").trim()
+        }
+    }
+}