chores: Remove deprecated version of the module

deprecated/gatk/dict/main.nf

@@ -1,19 +0,0 @@
-process gatk_dict {
-    tag {fasta}
-
-    container 'quay.io/biocontainers/gatk4-spark:4.1.4.1--1'
-
-    input:
-        path fasta
-
-    output:
-        path "${fasta.baseName}.dict"
-
-    script:
-    """
-    gatk --java-options "-Xmx${task.memory.giga}g" \
-        CreateSequenceDictionary \
-        --REFERENCE ${fasta} \
-        --OUTPUT ${fasta.baseName}.dict
-    """
-}

deprecated/gatk/dict/meta.yml

@@ -1,25 +0,0 @@
-name: gatk dict
-description: create a dictionary file from a fasta file
-keywords:
-    - dictionary
-tools:
-    - gatk:
-        description: |
-            The GATK toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping, developed in the Data Sciences Platform at the Broad Institute.
-        homepage: https://gatk.broadinstitute.org/hc/en-us
-        documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
-        doi: 10.1158/1538-7445.AM2017-3590
-input:
-    -
-        - input:
-            type: file
-            description: Input fasta file
-            pattern: "*.{fasta,fa}"
-output:
-    -
-        - dict:
-            type: file
-            description: gatk dictionary file
-            pattern: "*.{fasta,fa}.{dict}"
-authors:
-    - "@maxulysse"

deprecated/gatk/dict/test/main.nf

@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-nextflow.preview.dsl = 2
-include '../../../tests/functions/check_process_outputs.nf' params(params)
-include '../main.nf' params(params)
-
-// Define input channels
-input = '../../../test-datasets/tools/bwa/index/input/reference.fasta'
-
-// Run the workflow
-workflow {
-    gatk_dict(input)
-    // .check_output()
-}

deprecated/gatk/dict/test/nextflow.config

@@ -1,2 +0,0 @@
-docker.enabled = true
-params.outdir = './results'