From 10bb80743a738a9dd18326f4eae36fef686f6f48 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Fri, 29 Jan 2021 16:06:14 +0100
Subject: [PATCH 01/13] started adding quast modules

---
 software/quast/quast_noref/functions.nf | 59 ++++++++++++++++++++++++
 software/quast/quast_noref/main.nf      | 41 +++++++++++++++++
 software/quast/quast_noref/meta.yml     | 54 ++++++++++++++++++++++
 software/quast/quast_ref/functions.nf   | 59 ++++++++++++++++++++++++
 software/quast/quast_ref/main.nf        | 46 +++++++++++++++++++
 software/quast/quast_ref/meta.yml       | 61 +++++++++++++++++++++++++
 tests/software/quast/main.nf            | 20 ++++++++
 tests/software/quast/test.yml           |  0
 8 files changed, 340 insertions(+)
 create mode 100644 software/quast/quast_noref/functions.nf
 create mode 100644 software/quast/quast_noref/main.nf
 create mode 100644 software/quast/quast_noref/meta.yml
 create mode 100644 software/quast/quast_ref/functions.nf
 create mode 100644 software/quast/quast_ref/main.nf
 create mode 100644 software/quast/quast_ref/meta.yml
 create mode 100644 tests/software/quast/main.nf
 create mode 100644 tests/software/quast/test.yml

diff --git a/software/quast/quast_noref/functions.nf b/software/quast/quast_noref/functions.nf
new file mode 100644
index 00000000..d25eea86
--- /dev/null
+++ b/software/quast/quast_noref/functions.nf
@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/software/quast/quast_noref/main.nf b/software/quast/quast_noref/main.nf
new file mode 100644
index 00000000..2ad9ac79
--- /dev/null
+++ b/software/quast/quast_noref/main.nf
@@ -0,0 +1,41 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process QUAST {
+    tag "$fasta"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+
+    conda (params.enable_conda ? 'bioconda::quast=5.0.2' : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container 'https://depot.galaxyproject.org/singularity/quast:5.0.2--py37pl526hb5aa323_2'
+    } else {
+        container 'quay.io/biocontainers/quast:5.0.2--py37pl526hb5aa323_2'
+    }
+
+    input:
+    path consensus
+
+    output:
+    path "${prefix}"    , emit: results
+    path '*.tsv'        , emit: tsv
+    path '*.version.txt', emit: version
+
+    script:
+    def software         = getSoftwareName(task.process)
+    prefix               = options.suffix ?: software
+    """
+    quast.py \\
+        --output-dir $prefix \\
+        --threads $task.cpus \\
+        $options.args \\
+        $consensus
+    ln -s ${prefix}/report.tsv
+    echo \$(quast.py --version 2>&1) | sed 's/^.*QUAST v//; s/ .*\$//' > ${software}.version.txt
+    """
+}
diff --git a/software/quast/quast_noref/meta.yml b/software/quast/quast_noref/meta.yml
new file mode 100644
index 00000000..9b46bf42
--- /dev/null
+++ b/software/quast/quast_noref/meta.yml
@@ -0,0 +1,54 @@
+name: quast
+description: Quality Assessment Tool for Genome Assemblies
+keywords:
+  - quast
+  - assembly
+  - quality
+tools:
+  - star:
+      description: |
+        QUAST calculate quality metrics for genome assemblies
+      homepage: http://bioinf.spbau.ru/quast
+      doi:
+params:
+  - outdir:
+      type: string
+      description: |
+        The pipeline's output directory. By default, the module will
+        output files into `$params.outdir/<SOFTWARE>`
+  - publish_dir_mode:
+      type: string
+      description: |
+        Value for the Nextflow `publishDir` mode parameter.
+        Available: symlink, rellink, link, copy, copyNoFollow, move.
+  - enable_conda:
+      type: boolean
+      description: |
+        Run the module with Conda using the software specified
+        via the `conda` directive
+  - singularity_pull_docker_container:
+      type: boolean
+      description: |
+        Instead of directly downloading Singularity images for use with Singularity,
+        force the workflow to pull and convert Docker containers instead.
+
+input:
+  - consensus:
+      type: map
+      description: |
+        Groovy Map containing sample information
+
+output:
+  - report:
+      type: file
+      description: The lineage report
+      pattern: "{prefix}.lineage_report.csv"
+
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+
+authors:
+  - "@drpatelh"
+  - "@kevinmenden"
diff --git a/software/quast/quast_ref/functions.nf b/software/quast/quast_ref/functions.nf
new file mode 100644
index 00000000..d25eea86
--- /dev/null
+++ b/software/quast/quast_ref/functions.nf
@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/software/quast/quast_ref/main.nf b/software/quast/quast_ref/main.nf
new file mode 100644
index 00000000..0a811445
--- /dev/null
+++ b/software/quast/quast_ref/main.nf
@@ -0,0 +1,46 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process QUAST {
+    tag "$fasta"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+
+    conda (params.enable_conda ? 'bioconda::quast=5.0.2' : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container 'https://depot.galaxyproject.org/singularity/quast:5.0.2--py37pl526hb5aa323_2'
+    } else {
+        container 'quay.io/biocontainers/quast:5.0.2--py37pl526hb5aa323_2'
+    }
+
+    input:
+    path consensus
+    path fasta
+    path gff
+
+    output:
+    path "${prefix}"    , emit: results
+    path '*.tsv'        , emit: tsv
+    path '*.version.txt', emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    prefix       = options.suffix ?: software
+    def features = params.gff ? "--features $gff" : ''
+    """
+    quast.py \\
+        --output-dir $prefix \\
+        -r $fasta \\
+        $features \\
+        --threads $task.cpus \\
+        $options.args \\
+        ${consensus.join(' ')}
+    ln -s ${prefix}/report.tsv
+    echo \$(quast.py --version 2>&1) | sed 's/^.*QUAST v//; s/ .*\$//' > ${software}.version.txt
+    """
+}
diff --git a/software/quast/quast_ref/meta.yml b/software/quast/quast_ref/meta.yml
new file mode 100644
index 00000000..a1ca27b3
--- /dev/null
+++ b/software/quast/quast_ref/meta.yml
@@ -0,0 +1,61 @@
+name: quast
+description: Quality Assessment Tool for Genome Assemblies
+keywords:
+  - quast
+  - assembly
+  - quality
+tools:
+  - star:
+      description: |
+        QUAST calculate quality metrics for genome assemblies
+      homepage: http://bioinf.spbau.ru/quast
+      doi:
+params:
+  - outdir:
+      type: string
+      description: |
+        The pipeline's output directory. By default, the module will
+        output files into `$params.outdir/<SOFTWARE>`
+  - publish_dir_mode:
+      type: string
+      description: |
+        Value for the Nextflow `publishDir` mode parameter.
+        Available: symlink, rellink, link, copy, copyNoFollow, move.
+  - enable_conda:
+      type: boolean
+      description: |
+        Run the module with Conda using the software specified
+        via the `conda` directive
+  - singularity_pull_docker_container:
+      type: boolean
+      description: |
+        Instead of directly downloading Singularity images for use with Singularity,
+        force the workflow to pull and convert Docker containers instead.
+
+input:
+  - consensus:
+      type: map
+      description: |
+        Groovy Map containing sample information
+  - fasta:
+      type: file
+      description: |
+        The genome assembly to be evaluated
+  - gff:
+      type: file
+      description: The genome GFF file
+
+output:
+  - report:
+      type: file
+      description: The lineage report
+      pattern: "{prefix}.lineage_report.csv"
+
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+
+authors:
+  - "@drpatelh"
+  - "@kevinmenden"
diff --git a/tests/software/quast/main.nf b/tests/software/quast/main.nf
new file mode 100644
index 00000000..366b0c90
--- /dev/null
+++ b/tests/software/quast/main.nf
@@ -0,0 +1,20 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { QUAST as QUAST_NOREF } from '../../../software/quast/quast_noref/main.nf' addParams(options: [:])
+include { QUAST as QUAST_REF }   from '../../../software/quast/quast_ref/main.nf'   addParams(options: [:])
+
+workflow test_quast_noref {
+    consensus = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
+
+    QUAST_NOREF( consensus )
+}
+
+workflow test_quast_ref {
+    consensus = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
+    gff = file("${launchDir}/tests/data/gff/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true)
+    fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
+
+    QUAST_REF( consensus, fasta, gff )
+}
diff --git a/tests/software/quast/test.yml b/tests/software/quast/test.yml
new file mode 100644
index 00000000..e69de29b

From e8bd730164f01b9409a87968ed54c55ad40b7fd0 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Fri, 29 Jan 2021 16:14:33 +0100
Subject: [PATCH 02/13] added quast tests

---
 tests/software/quast/test.yml | 114 ++++++++++++++++++++++++++++++++++
 1 file changed, 114 insertions(+)

diff --git a/tests/software/quast/test.yml b/tests/software/quast/test.yml
index e69de29b..6d895298 100644
--- a/tests/software/quast/test.yml
+++ b/tests/software/quast/test.yml
@@ -0,0 +1,114 @@
+- name: quast_ref
+  command: nextflow run ./tests/software/quast -profile docker -entry test_quast_ref -c ./tests/config/nextflow.config
+  tags:
+    - quast
+    - quast_reference
+  files:
+    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tsv
+      md5sum: 4d24cc0da823a100a076aef36f9fd75e
+    - path: ./output/quast/quast/contigs_reports/GCA_011545545_1_ASM1154554v1_cds_from_genomic.mis_contigs.fa
+    - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.stdout
+    - path: ./output/quast/quast/aligned_stats/NGAx_plot.pdf
+    - path: ./output/quast/quast/report.pdf
+    - path: ./output/quast/quast/contigs_reports/misassemblies_report.tex
+      md5sum: ffe19cf4d5332952f0627e9cd82e3375
+    - path: ./output/quast/quast/aligned_stats/NAx_plot.pdf
+    - path: ./output/quast/quast/icarus.html
+    - path: ./output/quast/quast/report.tsv
+      md5sum: 503ebb57ffed0422fd7aff4025e21143
+    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tex
+      md5sum: 85614257e0bb62ac750f7872886b2fbf
+    - path: ./output/quast/quast/basic_stats/gc.icarus.txt
+      md5sum: b3a770802ff9b2dd4ee8e47bddb2df3e
+    - path: ./output/quast/quast/aligned_stats/cumulative_plot.pdf
+    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords.filtered
+      md5sum: ec9191d0acb5d5bce56b4842551a8598
+    - path: ./output/quast/quast/basic_stats/Nx_plot.pdf
+    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords
+      md5sum: dda3fc0addc41ecc0d5183dee6f95886
+    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords_tmp
+      md5sum: ce66eaeb99fdc11e4d50efadc1816e04
+    - path: ./output/quast/quast/contigs_reports/unaligned_report.tsv
+      md5sum: 769f2d9d7deb5e7a63e238d8ba0cfe13
+    - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
+    - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.mis_contigs.info
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.unaligned.info
+      md5sum: a8505cf206bf53ca369f7e3073fee587
+    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.sf
+    - path: ./output/quast/quast/transposed_report.txt
+      md5sum: 389e9fa2b29b967cb658c0770c941ce6
+    - path: ./output/quast/quast/genome_stats/GCA_011545545-1_ASM1154554v1_cds_from_genomic_gaps.txt
+      md5sum: c52381f09ea40b6141be5232494727b6
+    - path: ./output/quast/quast/quast.log
+    - path: ./output/quast/report.tsv
+      md5sum: 503ebb57ffed0422fd7aff4025e21143
+    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.txt
+      md5sum: 53c481fe8b3ef18280ea86cbded78b31
+    - path: ./output/quast/quast/contigs_reports/unaligned_report.txt
+      md5sum: c1c26797084ea743ec5a224ab97adb1f
+    - path: ./output/quast/quast/report.txt
+      md5sum: 41bf3c24e68afce5ef0ba91004e57f7d
+    - path: ./output/quast/quast/transposed_report.tex
+      md5sum: 2a69aada90cc1e788a4bc877c44d79c8
+    - path: ./output/quast/quast/basic_stats/GCA_011545545.1_ASM1154554v1_cds_from_genomic_GC_content_plot.pdf
+    - path: ./output/quast/quast/contigs_reports/misassemblies_report.tsv
+      md5sum: 33144f8d064782864e8400e3a08b2a3a
+    - path: ./output/quast/quast/contigs_reports/unaligned_report.tex
+      md5sum: 48562e30903fcf33946e13b602b0e324
+    - path: ./output/quast/quast/contigs_reports/misassemblies_plot.pdf
+    - path: ./output/quast/quast/transposed_report.tsv
+      md5sum: baab35c91e87432432113db1e4085f7b
+    - path: ./output/quast/quast/report.tex
+      md5sum: 8e72428ff7e7175bf47d58c10d8332e8
+    - path: ./output/quast/quast/contigs_reports/misassemblies_frcurve_plot.pdf
+    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.used_snps.gz
+      md5sum: 7b1db1b433cd95243a949bcb72e7e3a6
+    - path: ./output/quast/quast/contigs_reports/misassemblies_report.txt
+      md5sum: 0784e0d31e9f2a165730cc0029023427
+    - path: ./output/quast/quast/icarus_viewers/alignment_viewer.html
+      md5sum: bd63165a204a2ab424f8e81c647038d1
+    - path: ./output/quast/quast/contigs_reports/all_alignments_GCA_011545545-1_ASM1154554v1_cds_from_genomic.tsv
+      md5sum: c247152eb82b361106492642fd796e2c
+    - path: ./output/quast/quast/genome_stats/genome_info.txt
+      md5sum: 7c622ab66040d413a229419bf6b5181f
+    - path: ./output/quast/quast/basic_stats/NGx_plot.pdf
+    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.unaligned
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.stderr
+    - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html
+      md5sum: c42838b1553759fb0460a9854e39da36
+    - path: ./output/quast/quast/report.html
+    - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
+
+- name: quast_noref
+  command: nextflow run ./tests/software/quast -profile docker -entry test_quast_noref -c ./tests/config/nextflow.config
+  tags:
+    - quast
+    - quast_no_reference
+  files:
+    - path: ./output/quast/quast/report.pdf
+    - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
+    - path: ./output/quast/quast/transposed_report.tsv
+      md5sum: 1a82adfc057b6dc788034a6ce023cb56
+    - path: ./output/quast/quast/basic_stats/Nx_plot.pdf
+    - path: ./output/quast/quast/quast.log
+    - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
+    - path: ./output/quast/quast/transposed_report.tex
+      md5sum: a86aa094f9ab4bc1df35c5a7add2d0b0
+    - path: ./output/quast/quast/basic_stats/GCA_011545545.1_ASM1154554v1_genomic_GC_content_plot.pdf
+    - path: ./output/quast/quast/report.txt
+      md5sum: 7a2e442c18dd2730cfd38723f1c9c8f9
+    - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html
+      md5sum: dcf600c49ee86783475cb25215072630
+    - path: ./output/quast/quast/report.tsv
+      md5sum: 75882c0a5d811246395f5ea56146ce76
+    - path: ./output/quast/quast/report.tex
+      md5sum: 132edd2e916fc2a76a7b13973a0ffa4b
+    - path: ./output/quast/quast/icarus.html
+      md5sum: 9d7429362288c5078e6d6e7efcfc1ff7
+    - path: ./output/quast/quast/transposed_report.txt
+      md5sum: 154d88ec197c7b1bda5938232a79a00a
+    - path: ./output/quast/report.tsv
+      md5sum: 75882c0a5d811246395f5ea56146ce76
+    - path: ./output/quast/quast/report.html

From 34cfc32c29c7435f4463120714e708b60788ba81 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Fri, 29 Jan 2021 16:15:45 +0100
Subject: [PATCH 03/13] added quast workflow

---
 .github/workflows/quast.yml | 40 +++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 .github/workflows/quast.yml

diff --git a/.github/workflows/quast.yml b/.github/workflows/quast.yml
new file mode 100644
index 00000000..7030d638
--- /dev/null
+++ b/.github/workflows/quast.yml
@@ -0,0 +1,40 @@
+name: quast
+on:
+  push:
+    paths:
+      - software/quast/**
+      - .github/workflows/quast.yml
+      - tests
+  pull_request:
+    paths:
+      - software/pquast/**
+      - .github/workflows/quest.yml
+      - tests
+
+jobs:
+  ci_test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        nxf_version: [20.11.0-edge]
+    env:
+      NXF_ANSI_LOG: false
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          NXF_VER: ${{ matrix.nxf_version }}
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
+
+      # Test the module
+      - run: pytest --tag quest --symlink --wt 2

From 956bf22a58c00da45c6dbbd82a970c724a655ebf Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Mon, 1 Feb 2021 07:44:26 +0100
Subject: [PATCH 04/13] fixed bug; updated meta.yml

---
 .github/workflows/quast.yml         |  2 +-
 software/quast/quast_noref/meta.yml | 11 ++++++-----
 software/quast/quast_ref/meta.yml   | 17 +++++++++--------
 3 files changed, 16 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/quast.yml b/.github/workflows/quast.yml
index 7030d638..669d916b 100644
--- a/.github/workflows/quast.yml
+++ b/.github/workflows/quast.yml
@@ -37,4 +37,4 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag quest --symlink --wt 2
+      - run: pytest --tag quast --symlink --wt 2
diff --git a/software/quast/quast_noref/meta.yml b/software/quast/quast_noref/meta.yml
index 9b46bf42..8f758b10 100644
--- a/software/quast/quast_noref/meta.yml
+++ b/software/quast/quast_noref/meta.yml
@@ -5,9 +5,9 @@ keywords:
   - assembly
   - quality
 tools:
-  - star:
+  - quast:
       description: |
-        QUAST calculate quality metrics for genome assemblies
+        QUAST calculates quality metrics for genome assemblies
       homepage: http://bioinf.spbau.ru/quast
       doi:
 params:
@@ -34,15 +34,16 @@ params:
 
 input:
   - consensus:
-      type: map
+      type: file
       description: |
-        Groovy Map containing sample information
+        Fasta file containing the assembly of interest
 
 output:
-  - report:
+  - results:
       type: file
       description: The lineage report
       pattern: "{prefix}.lineage_report.csv"
+  - tsv:
 
   - version:
       type: file
diff --git a/software/quast/quast_ref/meta.yml b/software/quast/quast_ref/meta.yml
index a1ca27b3..03526be7 100644
--- a/software/quast/quast_ref/meta.yml
+++ b/software/quast/quast_ref/meta.yml
@@ -1,13 +1,13 @@
-name: quast
+name: quast_reference
 description: Quality Assessment Tool for Genome Assemblies
 keywords:
   - quast
   - assembly
   - quality
 tools:
-  - star:
+  - quast:
       description: |
-        QUAST calculate quality metrics for genome assemblies
+        QUAST calculates quality metrics for genome assemblies
       homepage: http://bioinf.spbau.ru/quast
       doi:
 params:
@@ -34,9 +34,9 @@ params:
 
 input:
   - consensus:
-      type: map
+      type: file
       description: |
-        Groovy Map containing sample information
+        Fasta file containing the assembly of interest
   - fasta:
       type: file
       description: |
@@ -46,10 +46,11 @@ input:
       description: The genome GFF file
 
 output:
-  - report:
-      type: file
-      description: The lineage report
+  - quast:
+      type: directory
+      description: Directory containing complete quast report
       pattern: "{prefix}.lineage_report.csv"
+  - report:
 
   - version:
       type: file

From b5298f94d80a40b609632f82761dfee41a9ae2c3 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Mon, 1 Feb 2021 13:13:21 +0100
Subject: [PATCH 05/13] refactored quast module

---
 software/quast/{quast_noref => }/functions.nf |  0
 software/quast/{quast_ref => }/main.nf        | 13 ++--
 software/quast/{quast_ref => }/meta.yml       | 12 +++-
 software/quast/quast_noref/main.nf            | 41 -------------
 software/quast/quast_noref/meta.yml           | 55 -----------------
 software/quast/quast_ref/functions.nf         | 59 -------------------
 tests/software/quast/main.nf                  | 23 +++++---
 7 files changed, 31 insertions(+), 172 deletions(-)
 rename software/quast/{quast_noref => }/functions.nf (100%)
 rename software/quast/{quast_ref => }/main.nf (82%)
 rename software/quast/{quast_ref => }/meta.yml (80%)
 delete mode 100644 software/quast/quast_noref/main.nf
 delete mode 100644 software/quast/quast_noref/meta.yml
 delete mode 100644 software/quast/quast_ref/functions.nf

diff --git a/software/quast/quast_noref/functions.nf b/software/quast/functions.nf
similarity index 100%
rename from software/quast/quast_noref/functions.nf
rename to software/quast/functions.nf
diff --git a/software/quast/quast_ref/main.nf b/software/quast/main.nf
similarity index 82%
rename from software/quast/quast_ref/main.nf
rename to software/quast/main.nf
index 0a811445..3690c08b 100644
--- a/software/quast/quast_ref/main.nf
+++ b/software/quast/main.nf
@@ -21,7 +21,9 @@ process QUAST {
     input:
     path consensus
     path fasta
+    val use_fasta
     path gff
+    val use_gff
 
     output:
     path "${prefix}"    , emit: results
@@ -29,14 +31,15 @@ process QUAST {
     path '*.version.txt', emit: version
 
     script:
-    def software = getSoftwareName(task.process)
-    prefix       = options.suffix ?: software
-    def features = params.gff ? "--features $gff" : ''
+    def software  = getSoftwareName(task.process)
+    prefix        = options.suffix ?: software
+    def features  = use_gff ? "--features $gff" : ''
+    def reference = use_fasta ? "-r $fasta" : ''
     """
     quast.py \\
         --output-dir $prefix \\
-        -r $fasta \\
-        $features \\
+        ${reference} \\
+        ${features} \\
         --threads $task.cpus \\
         $options.args \\
         ${consensus.join(' ')}
diff --git a/software/quast/quast_ref/meta.yml b/software/quast/meta.yml
similarity index 80%
rename from software/quast/quast_ref/meta.yml
rename to software/quast/meta.yml
index 03526be7..ae63de65 100644
--- a/software/quast/quast_ref/meta.yml
+++ b/software/quast/meta.yml
@@ -1,4 +1,4 @@
-name: quast_reference
+name: quast
 description: Quality Assessment Tool for Genome Assemblies
 keywords:
   - quast
@@ -40,10 +40,16 @@ input:
   - fasta:
       type: file
       description: |
-        The genome assembly to be evaluated
+        The genome assembly to be evaluated. Has to contain at least a non-empty string dummy value.
+  - use_fasta:
+      type: boolean
+      description: Whether to use a fasta reference
   - gff:
       type: file
-      description: The genome GFF file
+      description: The genome GFF file. Has to contain at least a non-empty string dummy value.
+  - use_gff:
+      type: boolean
+      description: Whether to use a gff reference
 
 output:
   - quast:
diff --git a/software/quast/quast_noref/main.nf b/software/quast/quast_noref/main.nf
deleted file mode 100644
index 2ad9ac79..00000000
--- a/software/quast/quast_noref/main.nf
+++ /dev/null
@@ -1,41 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-def options    = initOptions(params.options)
-
-process QUAST {
-    tag "$fasta"
-    label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
-
-    conda (params.enable_conda ? 'bioconda::quast=5.0.2' : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container 'https://depot.galaxyproject.org/singularity/quast:5.0.2--py37pl526hb5aa323_2'
-    } else {
-        container 'quay.io/biocontainers/quast:5.0.2--py37pl526hb5aa323_2'
-    }
-
-    input:
-    path consensus
-
-    output:
-    path "${prefix}"    , emit: results
-    path '*.tsv'        , emit: tsv
-    path '*.version.txt', emit: version
-
-    script:
-    def software         = getSoftwareName(task.process)
-    prefix               = options.suffix ?: software
-    """
-    quast.py \\
-        --output-dir $prefix \\
-        --threads $task.cpus \\
-        $options.args \\
-        $consensus
-    ln -s ${prefix}/report.tsv
-    echo \$(quast.py --version 2>&1) | sed 's/^.*QUAST v//; s/ .*\$//' > ${software}.version.txt
-    """
-}
diff --git a/software/quast/quast_noref/meta.yml b/software/quast/quast_noref/meta.yml
deleted file mode 100644
index 8f758b10..00000000
--- a/software/quast/quast_noref/meta.yml
+++ /dev/null
@@ -1,55 +0,0 @@
-name: quast
-description: Quality Assessment Tool for Genome Assemblies
-keywords:
-  - quast
-  - assembly
-  - quality
-tools:
-  - quast:
-      description: |
-        QUAST calculates quality metrics for genome assemblies
-      homepage: http://bioinf.spbau.ru/quast
-      doi:
-params:
-  - outdir:
-      type: string
-      description: |
-        The pipeline's output directory. By default, the module will
-        output files into `$params.outdir/<SOFTWARE>`
-  - publish_dir_mode:
-      type: string
-      description: |
-        Value for the Nextflow `publishDir` mode parameter.
-        Available: symlink, rellink, link, copy, copyNoFollow, move.
-  - enable_conda:
-      type: boolean
-      description: |
-        Run the module with Conda using the software specified
-        via the `conda` directive
-  - singularity_pull_docker_container:
-      type: boolean
-      description: |
-        Instead of directly downloading Singularity images for use with Singularity,
-        force the workflow to pull and convert Docker containers instead.
-
-input:
-  - consensus:
-      type: file
-      description: |
-        Fasta file containing the assembly of interest
-
-output:
-  - results:
-      type: file
-      description: The lineage report
-      pattern: "{prefix}.lineage_report.csv"
-  - tsv:
-
-  - version:
-      type: file
-      description: File containing software version
-      pattern: "*.{version.txt}"
-
-authors:
-  - "@drpatelh"
-  - "@kevinmenden"
diff --git a/software/quast/quast_ref/functions.nf b/software/quast/quast_ref/functions.nf
deleted file mode 100644
index d25eea86..00000000
--- a/software/quast/quast_ref/functions.nf
+++ /dev/null
@@ -1,59 +0,0 @@
-/*
- * -----------------------------------------------------
- *  Utility functions used in nf-core DSL2 module files
- * -----------------------------------------------------
- */
-
-/*
- * Extract name of software tool from process name using $task.process
- */
-def getSoftwareName(task_process) {
-    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-/*
- * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
- */
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args          = args.args ?: ''
-    options.args2         = args.args2 ?: ''
-    options.publish_by_id = args.publish_by_id ?: false
-    options.publish_dir   = args.publish_dir ?: ''
-    options.publish_files = args.publish_files
-    options.suffix        = args.suffix ?: ''
-    return options
-}
-
-/*
- * Tidy up and join elements of a list to return a path string
- */
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
-    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-/*
- * Function to save/publish module results
- */
-def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_id) {
-            path_list.add(args.publish_id)
-        }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
-            }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
-        }
-    }
-}
diff --git a/tests/software/quast/main.nf b/tests/software/quast/main.nf
index 366b0c90..7ef3d9ac 100644
--- a/tests/software/quast/main.nf
+++ b/tests/software/quast/main.nf
@@ -2,19 +2,24 @@
 
 nextflow.enable.dsl = 2
 
-include { QUAST as QUAST_NOREF } from '../../../software/quast/quast_noref/main.nf' addParams(options: [:])
-include { QUAST as QUAST_REF }   from '../../../software/quast/quast_ref/main.nf'   addParams(options: [:])
-
-workflow test_quast_noref {
-    consensus = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
-
-    QUAST_NOREF( consensus )
-}
+include { QUAST }   from '../../../software/quast/main.nf'   addParams(options: [:])
 
 workflow test_quast_ref {
     consensus = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
     gff = file("${launchDir}/tests/data/gff/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true)
     fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
+    def use_fasta = true
+    def use_gtf = true
 
-    QUAST_REF( consensus, fasta, gff )
+    QUAST( consensus, fasta, use_fasta, gff, use_gtf)
+}
+
+workflow test_quast_noref {
+    consensus = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
+    gff = file('gff_dummy')
+    fasta = file('fasta_dummy')
+    def use_fasta = false
+    def use_gtf = false
+
+    QUAST( consensus, fasta, use_fasta, gff, use_gtf)
 }

From a342296d7013301f3ad1769cfb492ddc3f14e8df Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Mon, 1 Feb 2021 13:36:25 +0100
Subject: [PATCH 06/13] fixed test md5s

---
 tests/software/quast/test.yml | 188 ++++++++++++++++++----------------
 1 file changed, 97 insertions(+), 91 deletions(-)

diff --git a/tests/software/quast/test.yml b/tests/software/quast/test.yml
index 6d895298..2ceccc54 100644
--- a/tests/software/quast/test.yml
+++ b/tests/software/quast/test.yml
@@ -4,82 +4,88 @@
     - quast
     - quast_reference
   files:
-    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tsv
-      md5sum: 4d24cc0da823a100a076aef36f9fd75e
-    - path: ./output/quast/quast/contigs_reports/GCA_011545545_1_ASM1154554v1_cds_from_genomic.mis_contigs.fa
-    - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.stdout
-    - path: ./output/quast/quast/aligned_stats/NGAx_plot.pdf
-    - path: ./output/quast/quast/report.pdf
-    - path: ./output/quast/quast/contigs_reports/misassemblies_report.tex
-      md5sum: ffe19cf4d5332952f0627e9cd82e3375
-    - path: ./output/quast/quast/aligned_stats/NAx_plot.pdf
-    - path: ./output/quast/quast/icarus.html
-    - path: ./output/quast/quast/report.tsv
-      md5sum: 503ebb57ffed0422fd7aff4025e21143
-    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tex
-      md5sum: 85614257e0bb62ac750f7872886b2fbf
-    - path: ./output/quast/quast/basic_stats/gc.icarus.txt
-      md5sum: b3a770802ff9b2dd4ee8e47bddb2df3e
-    - path: ./output/quast/quast/aligned_stats/cumulative_plot.pdf
+    - path: ./output/quast/quast/basic_stats/NGx_plot.pdf
     - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords.filtered
       md5sum: ec9191d0acb5d5bce56b4842551a8598
-    - path: ./output/quast/quast/basic_stats/Nx_plot.pdf
-    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords
-      md5sum: dda3fc0addc41ecc0d5183dee6f95886
-    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords_tmp
-      md5sum: ce66eaeb99fdc11e4d50efadc1816e04
-    - path: ./output/quast/quast/contigs_reports/unaligned_report.tsv
-      md5sum: 769f2d9d7deb5e7a63e238d8ba0cfe13
-    - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
-    - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.mis_contigs.info
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.unaligned.info
-      md5sum: a8505cf206bf53ca369f7e3073fee587
-    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.sf
-    - path: ./output/quast/quast/transposed_report.txt
-      md5sum: 389e9fa2b29b967cb658c0770c941ce6
-    - path: ./output/quast/quast/genome_stats/GCA_011545545-1_ASM1154554v1_cds_from_genomic_gaps.txt
-      md5sum: c52381f09ea40b6141be5232494727b6
-    - path: ./output/quast/quast/quast.log
-    - path: ./output/quast/report.tsv
-      md5sum: 503ebb57ffed0422fd7aff4025e21143
-    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.txt
-      md5sum: 53c481fe8b3ef18280ea86cbded78b31
-    - path: ./output/quast/quast/contigs_reports/unaligned_report.txt
-      md5sum: c1c26797084ea743ec5a224ab97adb1f
-    - path: ./output/quast/quast/report.txt
-      md5sum: 41bf3c24e68afce5ef0ba91004e57f7d
-    - path: ./output/quast/quast/transposed_report.tex
-      md5sum: 2a69aada90cc1e788a4bc877c44d79c8
-    - path: ./output/quast/quast/basic_stats/GCA_011545545.1_ASM1154554v1_cds_from_genomic_GC_content_plot.pdf
-    - path: ./output/quast/quast/contigs_reports/misassemblies_report.tsv
-      md5sum: 33144f8d064782864e8400e3a08b2a3a
-    - path: ./output/quast/quast/contigs_reports/unaligned_report.tex
-      md5sum: 48562e30903fcf33946e13b602b0e324
-    - path: ./output/quast/quast/contigs_reports/misassemblies_plot.pdf
-    - path: ./output/quast/quast/transposed_report.tsv
-      md5sum: baab35c91e87432432113db1e4085f7b
-    - path: ./output/quast/quast/report.tex
-      md5sum: 8e72428ff7e7175bf47d58c10d8332e8
-    - path: ./output/quast/quast/contigs_reports/misassemblies_frcurve_plot.pdf
-    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.used_snps.gz
-      md5sum: 7b1db1b433cd95243a949bcb72e7e3a6
-    - path: ./output/quast/quast/contigs_reports/misassemblies_report.txt
-      md5sum: 0784e0d31e9f2a165730cc0029023427
-    - path: ./output/quast/quast/icarus_viewers/alignment_viewer.html
-      md5sum: bd63165a204a2ab424f8e81c647038d1
-    - path: ./output/quast/quast/contigs_reports/all_alignments_GCA_011545545-1_ASM1154554v1_cds_from_genomic.tsv
-      md5sum: c247152eb82b361106492642fd796e2c
-    - path: ./output/quast/quast/genome_stats/genome_info.txt
-      md5sum: 7c622ab66040d413a229419bf6b5181f
-    - path: ./output/quast/quast/basic_stats/NGx_plot.pdf
-    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.unaligned
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.stderr
+    - path: ./output/quast/quast/aligned_stats/NGAx_plot.pdf
     - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html
       md5sum: c42838b1553759fb0460a9854e39da36
+    - path: ./output/quast/report.tsv
+      md5sum: b203a9d2c995bd66552eeb5cb0a98762
+    - path: ./output/quast/quast/report.tex
+      md5sum: 8168f197dfb2f781accdefaa0d90fc87
+    - path: ./output/quast/quast/contigs_reports/misassemblies_frcurve_plot.pdf
+    - path: ./output/quast/quast/transposed_report.tex
+      md5sum: 0b8fd00649a5758024c8093d5919f71c
+    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords
+      md5sum: dda3fc0addc41ecc0d5183dee6f95886
+    - path: ./output/quast/quast/transposed_report.txt
+      md5sum: 73216314e65ef91c24422d5bdd0795e4
     - path: ./output/quast/quast/report.html
+    - path: ./output/quast/quast/report.pdf
+    - path: ./output/quast/quast/contigs_reports/all_alignments_GCA_011545545-1_ASM1154554v1_cds_from_genomic.tsv
+      md5sum: c247152eb82b361106492642fd796e2c
+    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.used_snps.gz
+      md5sum: 7b1db1b433cd95243a949bcb72e7e3a6
+    - path: ./output/quast/quast/contigs_reports/unaligned_report.tex
+      md5sum: 48562e30903fcf33946e13b602b0e324
+    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.sf
+    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.txt
+      md5sum: 53c481fe8b3ef18280ea86cbded78b31
+    - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.mis_contigs.info
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: ./output/quast/quast/contigs_reports/unaligned_report.tsv
+      md5sum: 769f2d9d7deb5e7a63e238d8ba0cfe13
+    - path: ./output/quast/quast/basic_stats/GCA_011545545.1_ASM1154554v1_cds_from_genomic_GC_content_plot.pdf
+    - path: ./output/quast/quast/genome_stats/features_cumulative_plot.pdf
+    - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
+    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tex
+      md5sum: 85614257e0bb62ac750f7872886b2fbf
+    - path: ./output/quast/quast/quast.log
+    - path: ./output/quast/quast/contigs_reports/misassemblies_report.tsv
+      md5sum: 33144f8d064782864e8400e3a08b2a3a
+    - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.unaligned.info
+      md5sum: a8505cf206bf53ca369f7e3073fee587
+    - path: ./output/quast/quast/genome_stats/GCA_011545545-1_ASM1154554v1_cds_from_genomic_genomic_features_any.txt
+      md5sum: 307b3bb1f42fc2f11a60a2e9846021d7
+    - path: ./output/quast/quast/icarus.html
+      md5sum: 6e57f5f7d07528496fc2f35b449951fe
+    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tsv
+      md5sum: 4d24cc0da823a100a076aef36f9fd75e
+    - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.stderr
+    - path: ./output/quast/quast/aligned_stats/cumulative_plot.pdf
+    - path: ./output/quast/quast/genome_stats/genome_info.txt
+      md5sum: bc3df27ad7356c045c9a108f9d4bcfbe
+    - path: ./output/quast/quast/genome_stats/features_frcurve_plot.pdf
+    - path: ./output/quast/quast/contigs_reports/misassemblies_report.txt
+      md5sum: 0784e0d31e9f2a165730cc0029023427
+    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.unaligned
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.stdout
+    - path: ./output/quast/quast/contigs_reports/unaligned_report.txt
+      md5sum: c1c26797084ea743ec5a224ab97adb1f
+    - path: ./output/quast/quast/genome_stats/GCA_011545545-1_ASM1154554v1_cds_from_genomic_gaps.txt
+      md5sum: c52381f09ea40b6141be5232494727b6
+    - path: ./output/quast/quast/icarus_viewers/alignment_viewer.html
+      md5sum: ad5176f21d3c4809a9a8f9c27bb8d70a
+    - path: ./output/quast/quast/contigs_reports/misassemblies_report.tex
+      md5sum: ffe19cf4d5332952f0627e9cd82e3375
+    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords_tmp
+      md5sum: ce66eaeb99fdc11e4d50efadc1816e04
+    - path: ./output/quast/quast/basic_stats/gc.icarus.txt
+      md5sum: b3a770802ff9b2dd4ee8e47bddb2df3e
+    - path: ./output/quast/quast/basic_stats/Nx_plot.pdf
+    - path: ./output/quast/quast/transposed_report.tsv
+      md5sum: 1754bd6c6fa8a0172a342a48dd3ca505
     - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
+    - path: ./output/quast/quast/report.txt
+      md5sum: e334b3390a5028cbf88fe4ccab2b6499
+    - path: ./output/quast/quast/contigs_reports/misassemblies_plot.pdf
+    - path: ./output/quast/quast/report.tsv
+      md5sum: b203a9d2c995bd66552eeb5cb0a98762
+    - path: ./output/quast/quast/contigs_reports/GCA_011545545_1_ASM1154554v1_cds_from_genomic.mis_contigs.fa
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: ./output/quast/quast/aligned_stats/NAx_plot.pdf
 
 - name: quast_noref
   command: nextflow run ./tests/software/quast -profile docker -entry test_quast_noref -c ./tests/config/nextflow.config
@@ -87,28 +93,28 @@
     - quast
     - quast_no_reference
   files:
-    - path: ./output/quast/quast/report.pdf
-    - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
-    - path: ./output/quast/quast/transposed_report.tsv
-      md5sum: 1a82adfc057b6dc788034a6ce023cb56
-    - path: ./output/quast/quast/basic_stats/Nx_plot.pdf
-    - path: ./output/quast/quast/quast.log
-    - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
-    - path: ./output/quast/quast/transposed_report.tex
-      md5sum: a86aa094f9ab4bc1df35c5a7add2d0b0
-    - path: ./output/quast/quast/basic_stats/GCA_011545545.1_ASM1154554v1_genomic_GC_content_plot.pdf
-    - path: ./output/quast/quast/report.txt
-      md5sum: 7a2e442c18dd2730cfd38723f1c9c8f9
     - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html
-      md5sum: dcf600c49ee86783475cb25215072630
-    - path: ./output/quast/quast/report.tsv
-      md5sum: 75882c0a5d811246395f5ea56146ce76
-    - path: ./output/quast/quast/report.tex
-      md5sum: 132edd2e916fc2a76a7b13973a0ffa4b
-    - path: ./output/quast/quast/icarus.html
-      md5sum: 9d7429362288c5078e6d6e7efcfc1ff7
+      md5sum: d2680b8083139e62baf7af0f852d52b8
     - path: ./output/quast/quast/transposed_report.txt
-      md5sum: 154d88ec197c7b1bda5938232a79a00a
+      md5sum: b6b126e9dcfd8c8e7bd36dff9220caf0
     - path: ./output/quast/report.tsv
-      md5sum: 75882c0a5d811246395f5ea56146ce76
+      md5sum: 55d2938fcdb678e97d441cf32b9c740e
+    - path: ./output/quast/quast/icarus.html
+      md5sum: dcb11b4c7b6c21190c1344c46288d3f4
+    - path: ./output/quast/quast/report.txt
+      md5sum: c8e87f40e888a0395be04f78532d9deb
+    - path: ./output/quast/quast/transposed_report.tsv
+      md5sum: 27b6c755be5d70e3eed22e1bf3f68ce5
+    - path: ./output/quast/quast/quast.log
+    - path: ./output/quast/quast/report.tex
+      md5sum: 69c31172ae6257663b22bb192ba84682
+    - path: ./output/quast/quast/report.pdf
+    - path: ./output/quast/quast/basic_stats/GCA_011545545.1_ASM1154554v1_cds_from_genomic_GC_content_plot.pdf
+    - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
+    - path: ./output/quast/quast/report.tsv
+      md5sum: 55d2938fcdb678e97d441cf32b9c740e
+    - path: ./output/quast/quast/transposed_report.tex
+      md5sum: 213fb615afe21904e52d670e602c1f62
+    - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
+    - path: ./output/quast/quast/basic_stats/Nx_plot.pdf
     - path: ./output/quast/quast/report.html

From c43fe85a0c1e543ab9786348470492c7c22d9bc2 Mon Sep 17 00:00:00 2001
From: Kevin Menden <kevin.menden@t-online.de>
Date: Mon, 1 Feb 2021 14:02:57 +0100
Subject: [PATCH 07/13] Update software/quast/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 software/quast/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/software/quast/main.nf b/software/quast/main.nf
index 3690c08b..32a730fd 100644
--- a/software/quast/main.nf
+++ b/software/quast/main.nf
@@ -21,8 +21,8 @@ process QUAST {
     input:
     path consensus
     path fasta
-    val use_fasta
     path gff
+    val use_fasta
     val use_gff
 
     output:

From d88bf3bddae8359506692b3b92c75039ad945aaf Mon Sep 17 00:00:00 2001
From: Kevin Menden <kevin.menden@t-online.de>
Date: Mon, 1 Feb 2021 14:03:06 +0100
Subject: [PATCH 08/13] Update software/quast/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 software/quast/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/software/quast/main.nf b/software/quast/main.nf
index 32a730fd..2acdc270 100644
--- a/software/quast/main.nf
+++ b/software/quast/main.nf
@@ -38,8 +38,8 @@ process QUAST {
     """
     quast.py \\
         --output-dir $prefix \\
-        ${reference} \\
-        ${features} \\
+        $reference \\
+        $features \\
         --threads $task.cpus \\
         $options.args \\
         ${consensus.join(' ')}

From c807c6c438a04967b05b4c54a2f463d12d7c24fb Mon Sep 17 00:00:00 2001
From: Kevin Menden <kevin.menden@t-online.de>
Date: Mon, 1 Feb 2021 14:03:15 +0100
Subject: [PATCH 09/13] Update software/quast/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 software/quast/main.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/software/quast/main.nf b/software/quast/main.nf
index 2acdc270..4d5ed531 100644
--- a/software/quast/main.nf
+++ b/software/quast/main.nf
@@ -5,7 +5,6 @@ params.options = [:]
 def options    = initOptions(params.options)
 
 process QUAST {
-    tag "$fasta"
     label 'process_medium'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,

From 9885da628e6f170ca1375fbebdae27f9d8375d03 Mon Sep 17 00:00:00 2001
From: Kevin Menden <kevin.menden@t-online.de>
Date: Mon, 1 Feb 2021 14:03:22 +0100
Subject: [PATCH 10/13] Update software/quast/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 software/quast/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/software/quast/meta.yml b/software/quast/meta.yml
index ae63de65..004b1554 100644
--- a/software/quast/meta.yml
+++ b/software/quast/meta.yml
@@ -49,7 +49,7 @@ input:
       description: The genome GFF file. Has to contain at least a non-empty string dummy value.
   - use_gff:
       type: boolean
-      description: Whether to use a gff reference
+      description: Whether to use the provided gff reference annotation file
 
 output:
   - quast:

From f6c4e9d9c1d79e8846db04944734c7c93f1cad22 Mon Sep 17 00:00:00 2001
From: Kevin Menden <kevin.menden@t-online.de>
Date: Mon, 1 Feb 2021 14:03:36 +0100
Subject: [PATCH 11/13] Update software/quast/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 software/quast/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/software/quast/meta.yml b/software/quast/meta.yml
index 004b1554..dde96c97 100644
--- a/software/quast/meta.yml
+++ b/software/quast/meta.yml
@@ -43,7 +43,7 @@ input:
         The genome assembly to be evaluated. Has to contain at least a non-empty string dummy value.
   - use_fasta:
       type: boolean
-      description: Whether to use a fasta reference
+      description: Whether to use the provided fasta reference genome file
   - gff:
       type: file
       description: The genome GFF file. Has to contain at least a non-empty string dummy value.

From 05370b5e1609aa5bdaa7dca647e9cbcb2fdeaa54 Mon Sep 17 00:00:00 2001
From: Kevin Menden <kevin.menden@t-online.de>
Date: Mon, 1 Feb 2021 14:03:49 +0100
Subject: [PATCH 12/13] Update tests/software/quast/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 tests/software/quast/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/software/quast/main.nf b/tests/software/quast/main.nf
index 7ef3d9ac..ab9862da 100644
--- a/tests/software/quast/main.nf
+++ b/tests/software/quast/main.nf
@@ -11,7 +11,7 @@ workflow test_quast_ref {
     def use_fasta = true
     def use_gtf = true
 
-    QUAST( consensus, fasta, use_fasta, gff, use_gtf)
+    QUAST( consensus, fasta, gff, use_fasta, use_gtf )
 }
 
 workflow test_quast_noref {

From 0bd8506ea10d5373c17f97ad43602bd0b203b8a8 Mon Sep 17 00:00:00 2001
From: Kevin Menden <kevin.menden@t-online.de>
Date: Mon, 1 Feb 2021 14:04:08 +0100
Subject: [PATCH 13/13] Update tests/software/quast/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 tests/software/quast/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/software/quast/main.nf b/tests/software/quast/main.nf
index ab9862da..89a1637c 100644
--- a/tests/software/quast/main.nf
+++ b/tests/software/quast/main.nf
@@ -21,5 +21,5 @@ workflow test_quast_noref {
     def use_fasta = false
     def use_gtf = false
 
-    QUAST( consensus, fasta, use_fasta, gff, use_gtf)
+    QUAST( consensus, fasta, gff, use_fasta, use_gtf )
 }