From 2d1a2ec5ad7205aa235df50aee57f92970464796 Mon Sep 17 00:00:00 2001
From: jasmezz <jasmin.frangenberg@hki-jena.de>
Date: Wed, 30 Aug 2023 16:58:34 +0200
Subject: [PATCH 1/5] Update amrfinderplus, bakta, and multiqc

---
 modules.json                                  | 12 ++++++------
 modules/nf-core/amrfinderplus/run/main.nf     | 19 ++++++++++++-------
 modules/nf-core/amrfinderplus/update/main.nf  |  9 ++++-----
 modules/nf-core/bakta/bakta/main.nf           |  6 +++---
 modules/nf-core/bakta/baktadbdownload/main.nf |  6 +++---
 .../custom/dumpsoftwareversions/main.nf       |  6 +++---
 modules/nf-core/multiqc/main.nf               |  6 +++---
 7 files changed, 34 insertions(+), 30 deletions(-)

diff --git a/modules.json b/modules.json
index 2d47f5a7..aa7a4193 100644
--- a/modules.json
+++ b/modules.json
@@ -27,12 +27,12 @@
                     },
                     "amrfinderplus/run": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "868d4c3dc7a3db39d36184173e4fe3484499396e",
                         "installed_by": ["modules"]
                     },
                     "amrfinderplus/update": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "868d4c3dc7a3db39d36184173e4fe3484499396e",
                         "installed_by": ["modules"]
                     },
                     "antismash/antismashlite": {
@@ -47,12 +47,12 @@
                     },
                     "bakta/bakta": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "f05fa7c6753f92be861d606378860dcd5c828880",
                         "installed_by": ["modules"]
                     },
                     "bakta/baktadbdownload": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "f05fa7c6753f92be861d606378860dcd5c828880",
                         "installed_by": ["modules"]
                     },
                     "bioawk": {
@@ -63,7 +63,7 @@
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
                         "installed_by": ["modules"]
                     },
                     "deeparg/downloaddata": {
@@ -148,7 +148,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
                         "installed_by": ["modules"]
                     },
                     "prodigal": {
diff --git a/modules/nf-core/amrfinderplus/run/main.nf b/modules/nf-core/amrfinderplus/run/main.nf
index 8077bb48..40df8086 100644
--- a/modules/nf-core/amrfinderplus/run/main.nf
+++ b/modules/nf-core/amrfinderplus/run/main.nf
@@ -2,10 +2,10 @@ process AMRFINDERPLUS_RUN {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::ncbi-amrfinderplus=3.10.42"
+    conda "bioconda::ncbi-amrfinderplus=3.11.18"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.42--h6e70893_0':
-        'biocontainers/ncbi-amrfinderplus:3.10.42--h6e70893_0' }"
+        'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.11.18--h283d18e_0':
+        'biocontainers/ncbi-amrfinderplus:3.11.18--h283d18e_0' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -23,7 +23,8 @@ process AMRFINDERPLUS_RUN {
 
     script:
     def args = task.ext.args ?: ''
-    def is_compressed = fasta.getName().endsWith(".gz") ? true : false
+    def is_compressed_fasta = fasta.getName().endsWith(".gz") ? true : false
+    def is_compressed_db = fasta.getName().endsWith(".gz") ? true : false
     prefix = task.ext.prefix ?: "${meta.id}"
     organism_param = meta.containsKey("organism") ? "--organism ${meta.organism} --mutation_all ${prefix}-mutations.tsv" : ""
     fasta_name = fasta.getName().replace(".gz", "")
@@ -34,12 +35,16 @@ process AMRFINDERPLUS_RUN {
         }
     }
     """
-    if [ "$is_compressed" == "true" ]; then
+    if [ "$is_compressed_fasta" == "true" ]; then
         gzip -c -d $fasta > $fasta_name
     fi
 
-    mkdir amrfinderdb
-    tar xzvf $db -C amrfinderdb
+    if [ "$is_compressed_db" == "true" ]; then
+        mkdir amrfinderdb
+        tar xzvf $db -C amrfinderdb
+    else
+        mv $db amrfinderdb
+    fi
 
     amrfinder \\
         $fasta_param $fasta_name \\
diff --git a/modules/nf-core/amrfinderplus/update/main.nf b/modules/nf-core/amrfinderplus/update/main.nf
index a043a06a..bf3c5ef6 100644
--- a/modules/nf-core/amrfinderplus/update/main.nf
+++ b/modules/nf-core/amrfinderplus/update/main.nf
@@ -2,10 +2,10 @@ process AMRFINDERPLUS_UPDATE {
     tag "update"
     label 'process_single'
 
-    conda "bioconda::ncbi-amrfinderplus=3.10.42"
+    conda "bioconda::ncbi-amrfinderplus=3.11.18"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.42--h6e70893_0':
-        'biocontainers/ncbi-amrfinderplus:3.10.42--h6e70893_0' }"
+        'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.11.18--h283d18e_0':
+        'biocontainers/ncbi-amrfinderplus:3.11.18--h283d18e_0' }"
 
     output:
     path "amrfinderdb.tar.gz", emit: db
@@ -17,9 +17,8 @@ process AMRFINDERPLUS_UPDATE {
     script:
     def args = task.ext.args ?: ''
     """
-    mkdir amrfinderdb
     amrfinder_update -d amrfinderdb
-    tar czvf amrfinderdb.tar.gz -C \$(readlink amrfinderdb/latest) ./
+    tar czvf amrfinderdb.tar.gz -C amrfinderdb/\$(readlink amrfinderdb/latest) ./
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/bakta/bakta/main.nf b/modules/nf-core/bakta/bakta/main.nf
index 6399f5d0..fd0b76f2 100644
--- a/modules/nf-core/bakta/bakta/main.nf
+++ b/modules/nf-core/bakta/bakta/main.nf
@@ -2,10 +2,10 @@ process BAKTA_BAKTA {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::bakta=1.7.0"
+    conda "bioconda::bakta=1.8.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bakta:1.7.0--pyhdfd78af_1' :
-        'biocontainers/bakta:1.7.0--pyhdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/bakta:1.8.2--pyhdfd78af_0' :
+        'biocontainers/bakta:1.8.2--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/bakta/baktadbdownload/main.nf b/modules/nf-core/bakta/baktadbdownload/main.nf
index e62a2bed..de7e2199 100644
--- a/modules/nf-core/bakta/baktadbdownload/main.nf
+++ b/modules/nf-core/bakta/baktadbdownload/main.nf
@@ -1,10 +1,10 @@
 process BAKTA_BAKTADBDOWNLOAD {
     label 'process_single'
 
-    conda "bioconda::bakta=1.7.0"
+    conda "bioconda::bakta=1.8.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bakta:1.7.0--pyhdfd78af_1' :
-        'biocontainers/bakta:1.7.0--pyhdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/bakta:1.8.2--pyhdfd78af_0' :
+        'biocontainers/bakta:1.8.2--pyhdfd78af_0' }"
 
     output:
     path "db*"              , emit: db
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
index ebc87273..c9d014b1 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     label 'process_single'
 
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda "bioconda::multiqc=1.14"
+    conda "bioconda::multiqc=1.15"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.14--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.15--pyhdfd78af_0' }"
 
     input:
     path versions
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 1fc387be..65d7dd0d 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -1,10 +1,10 @@
 process MULTIQC {
     label 'process_single'
 
-    conda "bioconda::multiqc=1.14"
+    conda "bioconda::multiqc=1.15"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.14--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.15--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"

From d2307668eeb5edc9239e9548a6e9c178aa44e937 Mon Sep 17 00:00:00 2001
From: jasmezz <jasmin.frangenberg@hki-jena.de>
Date: Wed, 30 Aug 2023 17:16:29 +0200
Subject: [PATCH 2/5] Update changelog

---
 CHANGELOG.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e65ca457..f3491edf 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Dependencies`
 
+| Tool          | Previous version | New version |
+| ------------- | ---------------- | ----------- |
+| AMRFinderPlus | 3.10.42          | 3.11.18     |
+| Bakta         | 1.7.0            | 1.8.2       |
+| MultiQC       | 1.1.4            | 1.1.5       |
+
 ### `Deprecated`
 
 ## v1.1.3 - [2023-08-11]

From cd0f9147fe5a75c86331a89aa4c421af0af91f72 Mon Sep 17 00:00:00 2001
From: jasmezz <jasmin.frangenberg@hki-jena.de>
Date: Thu, 28 Sep 2023 16:17:15 +0200
Subject: [PATCH 3/5] Update amrfinderplus, fastqc

---
 modules.json                              | 4 ++--
 modules/nf-core/amrfinderplus/run/main.nf | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules.json b/modules.json
index aa7a4193..56b31119 100644
--- a/modules.json
+++ b/modules.json
@@ -27,7 +27,7 @@
                     },
                     "amrfinderplus/run": {
                         "branch": "master",
-                        "git_sha": "868d4c3dc7a3db39d36184173e4fe3484499396e",
+                        "git_sha": "016547e536216e0e839eb8ec678d13b25211c174",
                         "installed_by": ["modules"]
                     },
                     "amrfinderplus/update": {
@@ -93,7 +93,7 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117",
+                        "git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53",
                         "installed_by": ["modules"]
                     },
                     "gecco/run": {
diff --git a/modules/nf-core/amrfinderplus/run/main.nf b/modules/nf-core/amrfinderplus/run/main.nf
index 40df8086..f178b68f 100644
--- a/modules/nf-core/amrfinderplus/run/main.nf
+++ b/modules/nf-core/amrfinderplus/run/main.nf
@@ -24,7 +24,7 @@ process AMRFINDERPLUS_RUN {
     script:
     def args = task.ext.args ?: ''
     def is_compressed_fasta = fasta.getName().endsWith(".gz") ? true : false
-    def is_compressed_db = fasta.getName().endsWith(".gz") ? true : false
+    def is_compressed_db = db.getName().endsWith(".gz") ? true : false
     prefix = task.ext.prefix ?: "${meta.id}"
     organism_param = meta.containsKey("organism") ? "--organism ${meta.organism} --mutation_all ${prefix}-mutations.tsv" : ""
     fasta_name = fasta.getName().replace(".gz", "")

From e2801772514e488f8c5ff0c0ad6f91e1d3a8f94f Mon Sep 17 00:00:00 2001
From: jasmezz <jasmin.frangenberg@hki-jena.de>
Date: Thu, 28 Sep 2023 16:19:45 +0200
Subject: [PATCH 4/5] Comment out duplicate import line

---
 workflows/funcscan.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/funcscan.nf b/workflows/funcscan.nf
index e46c6c2b..f55933d1 100644
--- a/workflows/funcscan.nf
+++ b/workflows/funcscan.nf
@@ -5,7 +5,7 @@
 */
 include { validateParameters; paramsHelp; paramsSummaryLog; paramsSummaryMap; fromSamplesheet } from 'plugin/nf-validation'
 
-include { paramsSummaryLog; paramsSummaryMap; fromSamplesheet } from 'plugin/nf-validation'
+// include { paramsSummaryLog; paramsSummaryMap; fromSamplesheet } from 'plugin/nf-validation'
 
 def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
 def citation = '\n' + WorkflowMain.citation(workflow) + '\n'

From 7228cd9ca283af95dd553400b22b7ef36fc98581 Mon Sep 17 00:00:00 2001
From: jasmezz <jasmin.frangenberg@hki-jena.de>
Date: Thu, 28 Sep 2023 16:25:52 +0200
Subject: [PATCH 5/5] Remove fastqc

---
 modules.json                    |  5 ---
 modules/nf-core/fastqc/main.nf  | 55 ---------------------------------
 modules/nf-core/fastqc/meta.yml | 52 -------------------------------
 3 files changed, 112 deletions(-)
 delete mode 100644 modules/nf-core/fastqc/main.nf
 delete mode 100644 modules/nf-core/fastqc/meta.yml

diff --git a/modules.json b/modules.json
index 56b31119..584b643a 100644
--- a/modules.json
+++ b/modules.json
@@ -91,11 +91,6 @@
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
-                    "fastqc": {
-                        "branch": "master",
-                        "git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53",
-                        "installed_by": ["modules"]
-                    },
                     "gecco/run": {
                         "branch": "master",
                         "git_sha": "8c029dd8e67754d937fb6b6814e568f1decb2fea",
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
deleted file mode 100644
index 249f9064..00000000
--- a/modules/nf-core/fastqc/main.nf
+++ /dev/null
@@ -1,55 +0,0 @@
-process FASTQC {
-    tag "$meta.id"
-    label 'process_medium'
-
-    conda "bioconda::fastqc=0.11.9"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :
-        'biocontainers/fastqc:0.11.9--0' }"
-
-    input:
-    tuple val(meta), path(reads)
-
-    output:
-    tuple val(meta), path("*.html"), emit: html
-    tuple val(meta), path("*.zip") , emit: zip
-    path  "versions.yml"           , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    // Make list of old name and new name pairs to use for renaming in the bash while loop
-    def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
-    def rename_to = old_new_pairs*.join(' ').join(' ')
-    def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
-    """
-    printf "%s %s\\n" $rename_to | while read old_name new_name; do
-        [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
-    done
-
-    fastqc \\
-        $args \\
-        --threads $task.cpus \\
-        $renamed_files
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-    END_VERSIONS
-    """
-
-    stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    """
-    touch ${prefix}.html
-    touch ${prefix}.zip
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-    END_VERSIONS
-    """
-}
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
deleted file mode 100644
index 4da5bb5a..00000000
--- a/modules/nf-core/fastqc/meta.yml
+++ /dev/null
@@ -1,52 +0,0 @@
-name: fastqc
-description: Run FastQC on sequenced reads
-keywords:
-  - quality control
-  - qc
-  - adapters
-  - fastq
-tools:
-  - fastqc:
-      description: |
-        FastQC gives general quality metrics about your reads.
-        It provides information about the quality score distribution
-        across your reads, the per base sequence content (%A/C/G/T).
-        You get information about adapter contamination and other
-        overrepresented sequences.
-      homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
-      documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
-      licence: ["GPL-2.0-only"]
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: |
-        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-        respectively.
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - html:
-      type: file
-      description: FastQC report
-      pattern: "*_{fastqc.html}"
-  - zip:
-      type: file
-      description: FastQC report archive
-      pattern: "*_{fastqc.zip}"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-authors:
-  - "@drpatelh"
-  - "@grst"
-  - "@ewels"
-  - "@FelixKrueger"