Merge pull request #426 from atrigila/add_nf_core_mirtop

Add nf-core `mirtop`
nf-core · Sep 16, 2024 · 7e8c66e · 7e8c66e
2 parents 57c5bf9 + 708a9e1
commit 7e8c66e
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Showing 41 changed files with 1,412 additions and 39 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -29,6 +29,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#405]](https://github.com/nf-core/smrnaseq/pull/405) - Fix [Umicollapse algo wrong set](https://github.com/nf-core/smrnaseq/issues/404) - Fix potential bug in Umicollapse (not effective as we do not allow PE data in smrnaseq - but for consistency)
 - [[#420]](https://github.com/nf-core/smrnaseq/pull/420) - Fix [mirTrace produces an error in test nextflex](https://github.com/nf-core/smrnaseq/issues/419) - Allow config mode to be used in mirtrace/qc
 - [[#425]](https://github.com/nf-core/smrnaseq/pull/425) - Raise [minimum required NXF version for pipeline](https://github.com/nf-core/smrnaseq/issues/424) - usage of `arity` in some modules now requires this
+- [[#426]](https://github.com/nf-core/smrnaseq/pull/426) - Add [nf-core mirtop](https://github.com/nf-core/smrnaseq/issues/426) - replace local for nf-core `mirtop`
 
 ## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch
 

diff --git a/assets/multiqc_config.yml b/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
diff --git a/conf/modules.config b/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
     //

diff --git a/modules.json b/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",

diff --git a/modules/nf-core/mirtop/counts/environment.yml b/modules/nf-core/mirtop/counts/environment.yml
diff --git a/modules/nf-core/mirtop/counts/main.nf b/modules/nf-core/mirtop/counts/main.nf
diff --git a/modules/nf-core/mirtop/counts/meta.yml b/modules/nf-core/mirtop/counts/meta.yml
diff --git a/modules/nf-core/mirtop/counts/tests/main.nf.test b/modules/nf-core/mirtop/counts/tests/main.nf.test
diff --git a/modules/nf-core/mirtop/counts/tests/main.nf.test.snap b/modules/nf-core/mirtop/counts/tests/main.nf.test.snap
diff --git a/modules/nf-core/mirtop/counts/tests/nextflow.config b/modules/nf-core/mirtop/counts/tests/nextflow.config
diff --git a/modules/nf-core/mirtop/export/environment.yml b/modules/nf-core/mirtop/export/environment.yml