Merge pull request #435 from atrigila/migrate_nf-core_bowtie

Migrate to nf-core `bowtie build`
nf-core · Sep 20, 2024 · 774742f · 774742f
2 parents 395f801 + 13930ea
commit 774742f
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -33,6 +33,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#430]](https://github.com/nf-core/smrnaseq/pull/430) - Emit a [warning if paired-end end data is used](https://github.com/nf-core/smrnaseq/issues/423) - pipeline handles SE data
 - [[#427]](https://github.com/nf-core/smrnaseq/pull/427) - Add [nf-core pigz uncompress](https://github.com/nf-core/smrnaseq/issues/422) - replace local `mirdeep_pigz`
 - [[#429]](https://github.com/nf-core/smrnaseq/pull/429) - Make [saving of intermediate files optional](https://github.com/nf-core/smrnaseq/issues/424) - Allows user to choose whether to save intermediate files or not. Replaces several params that referred to the same such as `params.save_aligned` and `params.save_aligned_mirna_quant`.
+- [[#433]](https://github.com/nf-core/smrnaseq/pull/433) - Replace local instances of bowtie for nf-core [`bowtie2`](https://github.com/nf-core/smrnaseq/issues/434) and [`bowtie1`](https://github.com/nf-core/smrnaseq/issues/433) - Additionally adds a `bioawk` module that cleans fasta files.
 - [[#432]](https://github.com/nf-core/smrnaseq/pull/432) - Update [MultiQC to latest version](https://github.com/nf-core/smrnaseq/issues/428) - Include UMIcollapse module in MultiQC.
 
 ## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch

diff --git a/conf/modules.config b/conf/modules.config
@@ -176,6 +176,17 @@ process {
         ]
     }
 
+    withName: 'CLEAN_FASTA' {
+        ext.args = "-c fastx '{gsub(/[^ATGCatgc]/, \"N\", \$seq); sub(/ .*/, \"\", \$name); print \">\"\$name\"\\n\"\$seq}'"
+        ext.prefix = {"${meta.id}_clean.fa"}
+        publishDir = [
+            path: { "${params.outdir}/bowtie_index/genome" },
+            mode: params.publish_dir_mode,
+            enabled: params.save_intermediates,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     //
     // UMI deduplication
     //

diff --git a/modules.json b/modules.json
@@ -5,11 +5,27 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
+                    "bioawk": {
+                        "branch": "master",
+                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/bioawk/bioawk.diff"
+                    },
                     "blat": {
                         "branch": "master",
                         "git_sha": "49852039cccef84bbf5a3c0e069fac81fa3f0202",
                         "installed_by": ["modules"]
                     },
+                    "bowtie/build": {
+                        "branch": "master",
+                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
+                        "installed_by": ["modules"]
+                    },
+                    "bowtie2/build": {
+                        "branch": "master",
+                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
+                        "installed_by": ["modules"]
+                    },
                     "cat/cat": {
                         "branch": "master",
                         "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",

diff --git a/modules/local/bowtie_contaminants.nf b/modules/local/bowtie_contaminants.nf
diff --git a/modules/local/bowtie_genome.nf b/modules/local/bowtie_genome.nf
diff --git a/modules/local/bowtie_mirna.nf b/modules/local/bowtie_mirna.nf
diff --git a/modules/nf-core/bioawk/bioawk.diff b/modules/nf-core/bioawk/bioawk.diff
diff --git a/modules/nf-core/bioawk/environment.yml b/modules/nf-core/bioawk/environment.yml
diff --git a/modules/nf-core/bioawk/main.nf b/modules/nf-core/bioawk/main.nf
diff --git a/modules/nf-core/bioawk/meta.yml b/modules/nf-core/bioawk/meta.yml
diff --git a/modules/nf-core/bioawk/tests/main.nf.test b/modules/nf-core/bioawk/tests/main.nf.test
diff --git a/modules/nf-core/bioawk/tests/main.nf.test.snap b/modules/nf-core/bioawk/tests/main.nf.test.snap
diff --git a/modules/nf-core/bioawk/tests/nextflow.config b/modules/nf-core/bioawk/tests/nextflow.config
diff --git a/modules/nf-core/bowtie/build/environment.yml b/modules/nf-core/bowtie/build/environment.yml