Add nanoq to the pipeline

nf-core · Jul 11, 2024 · bab16d7 · bab16d7
1 parent 2a679b6
commit bab16d7
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Showing 14 changed files with 647 additions and 24 deletions.
diff --git a/CITATIONS.md b/CITATIONS.md
@@ -42,6 +42,10 @@
 
   > Wick R (2021) Filtlong, URL: https://github.com/rrwick/Filtlong
 
+- [nanoq](https://github.com/esteinig/nanoq)
+
+  > Steinig, E., & Coin, L. (2022). Nanoq: ultra-fast quality control for nanopore reads. Journal of Open Source Software, 7(69). https://doi.org/10.21105/joss.02991
+
 - [BBTools](http://sourceforge.net/projects/bbmap/)
 
   > Bushnell B. (2022) BBMap, URL: http://sourceforge.net/projects/bbmap/

diff --git a/conf/modules.config b/conf/modules.config
@@ -294,6 +294,36 @@ process {
         ]
     }
 
+    withName: NANOQ {
+        ext.args = [
+            "-vv",
+            "--min-len ${params.longread_qc_qualityfilter_minlength}",
+            "--min-qual ${params.longread_qc_qualityfilter_minquality}"
+        ]
+        .join(' ').trim()
+        ext.prefix = { "${meta.id}_${meta.run_accession}_nanoq" }
+        publishDir = [
+            [
+                path: { "${params.outdir}/nanoq" },
+                mode: params.publish_dir_mode,
+                pattern: '*.fastq.gz',
+                enabled: params.save_preprocessed_reads
+            ],
+            [
+                path: { "${params.outdir}/nanoq" },
+                mode: params.publish_dir_mode,
+                pattern: '*.stats'
+            ],
+            [
+                path: { "${params.outdir}/analysis_ready_fastqs" },
+                mode: params.publish_dir_mode,
+                pattern: '*.fastq.gz',
+                enabled: params.save_analysis_ready_fastqs,
+                saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_longread_hostremoval && !params.longread_qc_skipqualityfilter && params.perform_longread_qc && params.save_analysis_ready_fastqs ? it : null }
+            ]
+        ]
+    }
+
     withName: BBMAP_BBDUK {
         ext.args =  [
                 "entropy=${params.shortread_complexityfilter_entropy}",

diff --git a/modules.json b/modules.json
@@ -195,6 +195,11 @@
                         "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
                         "installed_by": ["modules"]
                     },
+                    "nanoq": {
+                        "branch": "master",
+                        "git_sha": "c3b91db39082a74be952b2cc217dcb0129142b3f",
+                        "installed_by": ["modules"]
+                    },
                     "nonpareil/curve": {
                         "branch": "master",
                         "git_sha": "729335dda8ba226323edc54dec80ae959079207e",

diff --git a/modules/nf-core/nanoq/environment.yml b/modules/nf-core/nanoq/environment.yml
diff --git a/modules/nf-core/nanoq/main.nf b/modules/nf-core/nanoq/main.nf
diff --git a/modules/nf-core/nanoq/meta.yml b/modules/nf-core/nanoq/meta.yml
diff --git a/modules/nf-core/nanoq/tests/main.nf.test b/modules/nf-core/nanoq/tests/main.nf.test