Fixes incorrectly quoted tags (#2113)

* Update main.nf

* Update meta.yml

* Re-add logos as not staged in a way that works with MultiQC config files

* Update main.nf

* Remove now unnecessary input channel

* Remove unused channel from tests

* Update hAMRonization to 1.1.1 and add hAMRonization farGene

* Fix hamronizatio ntests

* Prettier

* Fix fargene linting

* Correct file

* Fix fargene output

* Apply suggestions from code review

Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>

* Fix summarise tests

* Prettier

* Fix incorrect quotes in tags

Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>

modules/cellranger/mkref/main.nf

@@ -1,5 +1,5 @@
 process CELLRANGER_MKREF {
-    tag 'mkref'
+    tag "$fasta"
     label 'process_high'
 
     if (params.enable_conda) {

modules/eido/convert/main.nf

@@ -1,5 +1,5 @@
 process EIDO_CONVERT {
-    tag '$samplesheet'
+    tag "$samplesheet"
     label 'process_single'
 
     conda (params.enable_conda ? "conda-forge::eido=0.1.9" : null)

modules/eido/validate/main.nf

@@ -1,5 +1,5 @@
 process EIDO_VALIDATE {
-    tag '$samplesheet'
+    tag "$samplesheet"
     label 'process_single'
 
     conda (params.enable_conda ? "conda-forge::eido=0.1.9" : null)

modules/genmap/index/main.nf

@@ -1,5 +1,5 @@
 process GENMAP_INDEX {
-    tag '$fasta'
+    tag "$fasta"
     label 'process_high'
 
     conda (params.enable_conda ? "bioconda::genmap=1.3.0" : null)

modules/genmap/mappability/main.nf

@@ -1,5 +1,5 @@
 process GENMAP_MAPPABILITY {
-    tag '$index'
+    tag "$index"
     label 'process_high'
 
     conda (params.enable_conda ? "bioconda::genmap=1.3.0" : null)

modules/gunc/downloaddb/main.nf

@@ -1,5 +1,5 @@
 process GUNC_DOWNLOADDB {
-    tag '$db_name'
+    tag "$db_name"
     label 'process_single'
 
     conda (params.enable_conda ? "bioconda::gunc=1.0.5" : null)

modules/hmmcopy/generatemap/main.nf

@@ -1,5 +1,5 @@
 process HMMCOPY_GENERATEMAP {
-    tag '$bam'
+    tag "$bam"
     label 'process_long'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.

modules/hmmer/hmmbuild/main.nf

@@ -1,5 +1,5 @@
 process HMMER_HMMBUILD {
-    tag '$meta.id'
+    tag "$meta.id"
     label 'process_low'
 
     conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null)

modules/msisensor2/scan/main.nf

@@ -1,5 +1,5 @@
 process MSISENSOR2_SCAN {
-    tag '$fasta'
+    tag "$fasta"
     label 'process_medium'
 
     conda (params.enable_conda ? "bioconda::msisensor2=0.1" : null)

modules/multivcfanalyzer/main.nf

@@ -1,5 +1,5 @@
 process MULTIVCFANALYZER {
-    tag '$fasta'
+    tag "$fasta"
     label 'process_single'
 
     conda (params.enable_conda ? "bioconda::multivcfanalyzer=0.85.2" : null)

modules/seqtk/subseq/main.nf

@@ -1,5 +1,5 @@
 process SEQTK_SUBSEQ {
-    tag '$sequences'
+    tag "$sequences"
     label 'process_single'
 
     conda (params.enable_conda ? "bioconda::seqtk=1.3" : null)