Add nf-core mirtop

assets/multiqc_config.yml

@@ -31,3 +31,6 @@ module_order:
       info: "This section of the report shows FastQC results after UMI-based deduplication."
       path_filters:
         - "**/*.deduplicated_fastqc.zip"
+sp:
+  mirtop:
+    fn: mirtop_stats.log

conf/modules.config

@@ -337,6 +337,29 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
+
+    // Mirtop
+
+    withName: 'NFCORE_SMRNASEQ:MIRNA_QUANT:BAM_STATS_MIRNA_MIRTOP:.*' {
+        publishDir = [
+            path: { "${params.outdir}/mirna_quant/mirtop" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: 'MIRTOP_COUNTS' {
+        ext.args = '--add-extra'
+    }
+
+    withName: 'MIRTOP_GFF' {
+        publishDir = [
+            path: { "${params.outdir}/mirna_quant/mirtop/gff" },
+            mode: params.publish_dir_mode,
+        ]
+    }
+
+
     withName: 'NFCORE_SMRNASEQ:MIRNA_QUANT:TABLE_MERGE' {
         publishDir = [
             path: { "${params.outdir}/mirna_quant/mirtop" },
@@ -346,6 +369,7 @@ process {
     }
 
 
+
     //
     // GENOME_QUANT
     //

modules.json

@@ -35,6 +35,26 @@
                         "git_sha": "cf3ed075695639b0a0924eb0901146df1996dc08",
                         "installed_by": ["modules"]
                     },
+                    "mirtop/counts": {
+                        "branch": "master",
+                        "git_sha": "43b2b702abd8ab2cb1aa1365763f518413ad5721",
+                        "installed_by": ["bam_stats_mirna_mirtop"]
+                    },
+                    "mirtop/export": {
+                        "branch": "master",
+                        "git_sha": "43b2b702abd8ab2cb1aa1365763f518413ad5721",
+                        "installed_by": ["bam_stats_mirna_mirtop"]
+                    },
+                    "mirtop/gff": {
+                        "branch": "master",
+                        "git_sha": "43b2b702abd8ab2cb1aa1365763f518413ad5721",
+                        "installed_by": ["bam_stats_mirna_mirtop"]
+                    },
+                    "mirtop/stats": {
+                        "branch": "master",
+                        "git_sha": "43b2b702abd8ab2cb1aa1365763f518413ad5721",
+                        "installed_by": ["bam_stats_mirna_mirtop"]
+                    },
                     "mirtrace/qc": {
                         "branch": "master",
                         "git_sha": "6dd363c9b9b7cf30c4418597d20b6861848f0475",
@@ -105,6 +125,11 @@
                         "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["subworkflows"]
                     },
+                    "bam_stats_mirna_mirtop": {
+                        "branch": "master",
+                        "git_sha": "43b2b702abd8ab2cb1aa1365763f518413ad5721",
+                        "installed_by": ["subworkflows"]
+                    },
                     "bam_stats_samtools": {
                         "branch": "master",
                         "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",