refactor: Remove old unused nf-core functions (#182)

* refactor: Remove unused nf-core functions Signed-off-by: jvfe <[email protected]> * fix: Remove missing functions in RGI module Signed-off-by: jvfe <[email protected]> --------- Signed-off-by: jvfe <[email protected]>
beiko-lab · Jan 23, 2024 · 9fd06dd · 9fd06dd
1 parent 1639668
commit 9fd06dd
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Showing 7 changed files with 76 additions and 161 deletions.
diff --git a/modules.json b/modules.json
@@ -8,137 +8,183 @@
                     "bakta/bakta": {
                         "branch": "master",
                         "git_sha": "280c5c86b3da7dfcc92ebd5420584dd6ff26c4a8",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "bakta/baktadbdownload": {
                         "branch": "master",
                         "git_sha": "280c5c86b3da7dfcc92ebd5420584dd6ff26c4a8",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "blast/blastn": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/blast/blastn/blast-blastn.diff"
                     },
                     "blast/makeblastdb": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/blast/makeblastdb/blast-makeblastdb.diff"
                     },
                     "checkm/lineagewf": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/checkm/lineagewf/checkm-lineagewf.diff"
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff"
                     },
                     "diamond/blastp": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/diamond/blastp/diamond-blastp.diff"
                     },
                     "diamond/blastx": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/diamond/blastx/diamond-blastx.diff"
                     },
                     "diamond/makedb": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/diamond/makedb/diamond-makedb.diff"
                     },
                     "fastp": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/fastp/fastp.diff"
                     },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/fastqc/fastqc.diff"
                     },
                     "fasttree": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/fasttree/fasttree.diff"
                     },
                     "gubbins": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/gubbins/gubbins.diff"
                     },
                     "iqtree": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/iqtree/iqtree.diff"
                     },
                     "kraken2/kraken2": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/kraken2/kraken2/kraken2-kraken2.diff"
                     },
                     "mafft": {
                         "branch": "master",
                         "git_sha": "b265b4ff6a35b133b963b4eaddfca0ffb3395236",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/mafft/mafft.diff"
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/multiqc/multiqc.diff"
                     },
                     "panaroo/run": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/panaroo/run/panaroo-run.diff"
                     },
                     "phispy": {
                         "branch": "master",
                         "git_sha": "a60792caf1782dd570ad7a091b61806c592734d7",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/phispy/phispy.diff"
                     },
                     "prokka": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/prokka/prokka.diff"
                     },
                     "quast": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/quast/quast.diff"
                     },
                     "snpsites": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/snpsites/snpsites.diff"
                     },
                     "unicycler": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/unicycler/unicycler.diff"
                     }
                 }
@@ -148,4 +194,4 @@
             }
         }
     }
-}
+}
diff --git a/modules/local/functions.nf b/modules/local/functions.nf
diff --git a/modules/local/get_minikraken.nf b/modules/local/get_minikraken.nf
@@ -1,12 +1,4 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process KRAKEN2_DB {
-    //publishDir 'dbcache/', mode:'copy'
-    tag "minikraken"
     label 'process_medium'
     label 'error_retry_delay'
 
@@ -19,26 +11,4 @@ process KRAKEN2_DB {
     mkdir -p k2_standard_8gb_20201202
     tar xvf k2_standard_8gb_20201202.tar.gz -C k2_standard_8gb_20201202
     """
-    // stub:
-    /*
-    minikraken = file("./dbcache/k2_standard_8gb_20201202")
-    if (!minikraken.exists()){
-        println "FARRRRT"
-        """
-        curl https://genome-idx.s3.amazonaws.com/kraken/k2_standard_8gb_20201202.tar.gz --output k2_standard_8gb_20201202.tar.gz
-        mkdir -p k2_standard_8gb_20201202
-        tar xvf k2_standard_8gb_20201202.tar.gz -C k2_standard_8gb_20201202
-        """
-    }
-    else{
-        """
-        echo "database is cached"
-        """
-    }
-    */
-    // else{
-    //     """
-    //     ln -s ${minikraken} .
-    //     """
-    // }
 }
diff --git a/modules/local/get_software_versions.nf b/modules/local/get_software_versions.nf
@@ -1,13 +1,4 @@
-// Import generic module functions
-include { saveFiles } from './functions'
-
-params.options = [:]
-
 process GET_SOFTWARE_VERSIONS {
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', meta:[:], publish_by_meta:[]) }
-
     conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://depot.galaxyproject.org/singularity/python:3.8.3"

diff --git a/modules/local/mobsuite.nf b/modules/local/mobsuite.nf
@@ -1,4 +1,3 @@
-// Import generic module functions
 process MOB_RECON {
     tag "$meta.id"
     label 'process_low'
@@ -12,7 +11,6 @@ process MOB_RECON {
 
     input:
     tuple val(meta), path(fasta)
-    //path mob_db
 
     output:
     tuple val(meta), path("${meta.id}_mob_recon")                             , emit: mob_predictions
@@ -33,7 +31,7 @@ process MOB_RECON {
         mobsuite: \$(echo \$(mob_recon --version 2>&1) | sed 's/^.*mob_recon //; s/ .*\$//')
     END_VERSIONS
     """
-    //--database_directory $mob_db  \\
+
     stub:
     """
     mkdir ${meta.id}_mob_recon

diff --git a/modules/local/rgi.nf b/modules/local/rgi.nf
@@ -1,9 +1,3 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process UPDATE_RGI_DB {
     tag "CARD"
     label 'process_low'
@@ -36,9 +30,6 @@ process UPDATE_RGI_DB {
 process RGI {
     tag "$meta.id"
     label 'process_low'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
     conda (params.enable_conda ? "bioconda::rgi=6.0.2" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
@@ -57,8 +48,7 @@ process RGI {
     path "versions.yml", emit: version
 
     script:
-    def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def prefix   = task.ext.prefix ? "${meta.id}${options.suffix}" : "${meta.id}"
 
     """
     rgi load -i $card_db --local
@@ -70,8 +60,7 @@ process RGI {
     END_VERSIONS
     """
     stub:
-    def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def prefix   = task.ext.prefix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     touch ${prefix}_rgi.txt
     cat <<-END_VERSIONS > versions.yml