v2.0.1

- Update versions (Dorado, MultiQC, Samtools). - Update Dorado default model - Some code cleanup
catg-umag · Jun 3, 2024 · 84af1e0 · 84af1e0
1 parent 67ff1c7
commit 84af1e0
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Showing 5 changed files with 8 additions and 45 deletions.
diff --git a/README.md b/README.md
@@ -30,7 +30,7 @@ nextflow run ont-basecalling-demultiplexing/ -profile apptainer -params-file my_
 | `output_dir`                             | False    | `demultiplex_results`                | Path to the folder where the results will be saved.                                                                     |
 | `fastq_output`                           | False    | `true`                               | If `true`, the pipeline will generate FASTQ files (if not, it would be UBAM files).                                     |
 | `qscore_filter`                          | False    | `10`                                 | Minimum QScore for the "pass" data, used for demultiplexing.                                                            |
-| `dorado_basecalling_model`               | False    | `dna_r10.4.1_e8.2_400bps_sup@v4.3.0` | Model used for basecalling.                                                                                             |
+| `dorado_basecalling_model`               | False    | `dna_r10.4.1_e8.2_400bps_sup@v5.0.0` | Model used for basecalling.                                                                                             |
 | `dorado_basecalling_extra_config`        | False    | -                                    | Extra configuration for Dorado basecalling.                                                                             |
 | `dorado_basecalling_gpus`                | False    | `1`                                  | Number of GPUs to use for basecalling.                                                                                  |
 | `skip_demultiplexingskip_demultiplexing` | False    | `false`                              | If `true`, the pipeline will not perform demultiplexing                                                                 |

diff --git a/conf/containers.config b/conf/containers.config
@@ -1,17 +1,17 @@
 // containers
 process {
-  withLabel: linux    { container = 'ubuntu:22.04' }
+  withLabel: linux    { container = 'ubuntu:24.04' }
   withLabel: fastqc   { container = 'quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0' }
   withLabel: nanoplot { container = 'quay.io/biocontainers/nanoplot:1.42.0--pyhdfd78af_0' }
-  withLabel: multiqc  { container = 'quay.io/biocontainers/multiqc:1.19--pyhdfd78af_0' }
+  withLabel: multiqc  { container = 'quay.io/biocontainers/multiqc:1.22.2--pyhdfd78af_0' }
   withLabel: pigz     { container = 'ghcr.io/dialvarezs/containers/utils:latest' }
   withLabel: pycoqc   { container = 'quay.io/biocontainers/pycoqc:2.5.2--py_0' }
-  withLabel: samtools { container = 'quay.io/biocontainers/samtools:1.19.2--h50ea8bc_0' }
+  withLabel: samtools { container = 'quay.io/biocontainers/samtools:1.20--h50ea8bc_0' }
 
   withLabel: dorado   {
 	container = params.use_dorado_container 
-  				? 'ghcr.io/dialvarezs/containers/dorado:0.5.3'
-				: null
+              ? 'ghcr.io/dialvarezs/containers/dorado:0.7.0'
+              : null
 	containerOptions = '--nv'
   }
 }
diff --git a/conf/params.config b/conf/params.config
@@ -5,7 +5,7 @@ params {
 	output_dir = 'demultiplex_results/'
 	fastq_output = true
 	qscore_filter = 10
-	dorado_basecalling_model = 'dna_r10.4.1_e8.2_400bps_sup@v4.3.0'
+	dorado_basecalling_model = 'dna_r10.4.1_e8.2_400bps_sup@v5.0.0'
 	dorado_basecalling_extra_config = ''
 	dorado_basecalling_gpus = 1
 	skip_demultiplexing = false

diff --git a/lib/groovy/utils.gvy b/lib/groovy/utils.gvy
@@ -1,32 +1,3 @@
-import org.yaml.snakeyaml.Yaml
-
-/*
- * Add default parameter values (a mapping) if they are not defined,
- * reading them from a YAML file
- */
-def addDefaultParamValues(params, defaultsFile) {
-  yaml = new Yaml()
-  defaultValues = yaml.load(file(defaultsFile))
-
-  defaultValues.each { name, value ->
-    params[name] = evaluateWorkflowVars(getParamValue(params, name, value))
-  }
-}
-
-/*
- * Evaluate workflow instrospection variables (workflow.*) inside a string
- */
-def evaluateWorkflowVars(value) {
-  matches = (value =~ /\$\{workflow\.[^}]*\}/).findAll()
-  evaluated = value
-  matches.each { m ->
-    name = (m =~ /(?<=\{workflow\.).*(?=\})/).findAll()[0]
-    evaluated = evaluated.replace(m, workflow[name].toString())
-  }
-
-  return evaluated
-}
-
 /*
  * Check if file exists of throw error
  */
@@ -43,14 +14,6 @@ def pathCheck(path, isDirectory = false) {
   return f
 }
 
-def isEmpty(params, name) {
-  return !params.containsKey(name) || params[name] == null
-}
-
-def getParamValue(params, name, defaultValue) {
-  return isEmpty(params, name) ? defaultValue : params[name]
-}
-
 def sanitizeFilename(filename) {
   return filename.toLowerCase().replaceAll(' ', '_').replaceAll('[^a-z0-9._-]', '')
 }

diff --git a/params.example.yml b/params.example.yml
@@ -4,7 +4,7 @@ sample_data: input/samples.csv
 output_dir: demultiplex_results/
 fastq_output: true
 qscore_filter: 10
-dorado_basecalling_model: dna_r10.4.1_e8.2_400bps_sup@v4.2.0
+dorado_basecalling_model: dna_r10.4.1_e8.2_400bps_sup@v5.0.0
 dorado_basecalling_extra_config: ''
 dorado_basecalling_gpus: 1
 skip_demultiplexing: false