Merge pull request #444 from nschcolnicov/migrate_bowtie

Migrate bowtie

CHANGELOG.md

@@ -38,6 +38,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#438]](https://github.com/nf-core/smrnaseq/pull/438) - Update [Mirtop to latest version](https://github.com/nf-core/smrnaseq/issues/437) - Process samples separately and join results with `CSVTK_JOIN`.
 - [[#439]](https://github.com/nf-core/smrnaseq/pull/439) - Fix [Fix paired end samples processing](https://github.com/nf-core/smrnaseq/issues/415) - Fix paired end sample handling and add test profile.
 - [[#441]](https://github.com/nf-core/smrnaseq/pull/441) - Migrate [local contaminant bowtie to nf-core](https://github.com/nf-core/smrnaseq/issues/436) - Replace local processes with `BOWTIE2_ALIGN`.
+- [[#443]](https://github.com/nf-core/smrnaseq/pull/443) - Migrate [mirna and genome_quant bowtie to nf-core](https://github.com/nf-core/smrnaseq/issues/436) - Replace local processes with `BOWTIE_ALIGN`.
 
 ## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch
 

conf/modules.config

@@ -357,6 +357,14 @@ process {
         ]
     }
     withName: 'NFCORE_SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_MATURE' {
+        ext.args = [ "",
+            "-t",
+            "-k 50",
+            "--best",
+            "--strata",
+            "-e 99999",
+            "--chunkmbs 2048",
+        ].join(" ").trim()
         publishDir = [
             path: { "${params.outdir}/mirna_quant/bam/mature" },
             mode: params.publish_dir_mode,
@@ -374,6 +382,14 @@ process {
         ]
     }
     withName: 'NFCORE_SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_HAIRPIN' {
+        ext.args = [ "",
+            "-t",
+            "-k 50",
+            "--best",
+            "--strata",
+            "-e 99999",
+            "--chunkmbs 2048",
+        ].join(" ").trim()
         publishDir = [
             path: { "${params.outdir}/mirna_quant/bam/hairpin" },
             mode: params.publish_dir_mode,
@@ -408,6 +424,14 @@ process {
         ext.prefix  = {"${meta.id}_seqcluster"}
     }
     withName: 'NFCORE_SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_SEQCLUSTER' {
+        ext.args = [ "",
+            "-t",
+            "-k 50",
+            "--best",
+            "--strata",
+            "-e 99999",
+            "--chunkmbs 2048",
+        ].join(" ").trim()
         publishDir = [
             path: { "${params.outdir}/mirna_quant/bam/seqcluster" },
             mode: params.publish_dir_mode,
@@ -494,6 +518,14 @@ process {
         ]
     }
     withName: 'NFCORE_SMRNASEQ:GENOME_QUANT:BOWTIE_MAP_GENOME' {
+        ext.args = [ "",
+            "-t",
+            "-k 50",
+            "--best",
+            "--strata",
+            "-e 99999",
+            "--chunkmbs 2048",
+        ].join(" ").trim()
         publishDir = [
             path: { "${params.outdir}/genome_quant/bam" },
             mode: params.publish_dir_mode,

modules.json

@@ -16,6 +16,11 @@
                         "git_sha": "49852039cccef84bbf5a3c0e069fac81fa3f0202",
                         "installed_by": ["modules"]
                     },
+                    "bowtie/align": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "bowtie/build": {
                         "branch": "master",
                         "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",