From 38b450d0be865af4f60dd4674a4fc47ddbf1e6e1 Mon Sep 17 00:00:00 2001
From: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Date: Tue, 16 Mar 2021 09:54:29 +0000
Subject: [PATCH 01/12] hifiasm copied from fastqc

---
 software/hifiasm/functions.nf | 59 ++++++++++++++++++++++++++++
 software/hifiasm/main.nf      | 47 +++++++++++++++++++++++
 software/hifiasm/meta.yml     | 72 +++++++++++++++++++++++++++++++++++
 3 files changed, 178 insertions(+)
 create mode 100644 software/hifiasm/functions.nf
 create mode 100644 software/hifiasm/main.nf
 create mode 100644 software/hifiasm/meta.yml

diff --git a/software/hifiasm/functions.nf b/software/hifiasm/functions.nf
new file mode 100644
index 00000000..d25eea86
--- /dev/null
+++ b/software/hifiasm/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)}/$args.filename"
+        }
+    }
+}
diff --git a/software/hifiasm/main.nf b/software/hifiasm/main.nf
new file mode 100644
index 00000000..4e847876
--- /dev/null
+++ b/software/hifiasm/main.nf
@@ -0,0 +1,47 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process FASTQC {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0"
+    } else {
+        container "quay.io/biocontainers/fastqc:0.11.9--0"
+    }
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path("*.html"), emit: html
+    tuple val(meta), path("*.zip") , emit: zip
+    path  "*.version.txt"          , emit: version
+
+    script:
+    // Add soft-links to original FastQs for consistent naming in pipeline
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
+    if (meta.single_end) {
+        """
+        [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
+        fastqc $options.args --threads $task.cpus ${prefix}.fastq.gz
+        fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt
+        """
+    } else {
+        """
+        [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
+        [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
+        fastqc $options.args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
+        fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt
+        """
+    }
+}
diff --git a/software/hifiasm/meta.yml b/software/hifiasm/meta.yml
new file mode 100644
index 00000000..413aad8d
--- /dev/null
+++ b/software/hifiasm/meta.yml
@@ -0,0 +1,72 @@
+name: fastqc
+description: Run FastQC on sequenced reads
+keywords:
+    - quality control
+    - qc
+    - adapters
+    - fastq
+tools:
+    - fastqc:
+        description: |
+            FastQC gives general quality metrics about your reads.
+            It provides information about the quality score distribution
+            across your reads, the per base sequence content (%A/C/G/T).
+            You get information about adapter contamination and other
+            overrepresented sequences.
+        homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
+        documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$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:
+    - 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}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@drpatelh"
+    - "@grst"
+    - "@ewels"
+    - "@FelixKrueger"

From 2f675fbe7c60a67649dd4a02e72e2f1ee79f24d3 Mon Sep 17 00:00:00 2001
From: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Date: Tue, 16 Mar 2021 11:37:06 +0000
Subject: [PATCH 02/12] hifiasm tests init from fastqc

---
 tests/software/hifiasm/main.nf  | 28 ++++++++++++++++++++++++++++
 tests/software/hifiasm/test.yml | 19 +++++++++++++++++++
 2 files changed, 47 insertions(+)
 create mode 100644 tests/software/hifiasm/main.nf
 create mode 100644 tests/software/hifiasm/test.yml

diff --git a/tests/software/hifiasm/main.nf b/tests/software/hifiasm/main.nf
new file mode 100644
index 00000000..f10b2357
--- /dev/null
+++ b/tests/software/hifiasm/main.nf
@@ -0,0 +1,28 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FASTQC } from '../../../software/fastqc/main.nf' addParams( options: [:] )
+
+/*
+ * Test with single-end data
+ */
+workflow test_fastqc_single_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ] ]
+    FASTQC ( input )
+}
+
+/*
+ * Test with paired-end data
+ */
+workflow test_fastqc_paired_end {
+
+    def input = []
+    input = [[id: 'test', single_end: false], // meta map
+             [file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true),
+              file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true)]]
+    FASTQC (input)
+}
diff --git a/tests/software/hifiasm/test.yml b/tests/software/hifiasm/test.yml
new file mode 100644
index 00000000..0fe0ebe0
--- /dev/null
+++ b/tests/software/hifiasm/test.yml
@@ -0,0 +1,19 @@
+- name: fastqc single-end
+  command: nextflow run ./tests/software/fastqc/ -entry test_fastqc_single_end -c tests/config/nextflow.config
+  tags:
+    - fastqc
+    - fastqc_single_end
+  files:
+    - path: ./output/fastqc/test_fastqc.html
+    - path: ./output/fastqc/test_fastqc.zip
+
+- name: fastqc paired-end
+  command: nextflow run ./tests/software/fastqc/ -entry test_fastqc_paired_end -c tests/config/nextflow.config
+  tags:
+    - fastqc
+    - fastqc_paired_end
+  files:
+    - path: ./output/fastqc/test_1_fastqc.html
+    - path: ./output/fastqc/test_2_fastqc.html
+    - path: ./output/fastqc/test_2_fastqc.zip
+    - path: ./output/fastqc/test_1_fastqc.zip

From 390c835f9fc47574654aa0bfd55556bf376e98f2 Mon Sep 17 00:00:00 2001
From: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Date: Tue, 16 Mar 2021 11:54:42 +0000
Subject: [PATCH 03/12] meta.yml init; test.yml and main.nf for printing
 version

---
 software/hifiasm/meta.yml       | 23 ++++++++++-------------
 tests/software/hifiasm/main.nf  | 18 +++++++++---------
 tests/software/hifiasm/test.yml | 22 +++++-----------------
 3 files changed, 24 insertions(+), 39 deletions(-)

diff --git a/software/hifiasm/meta.yml b/software/hifiasm/meta.yml
index 413aad8d..9ef62628 100644
--- a/software/hifiasm/meta.yml
+++ b/software/hifiasm/meta.yml
@@ -1,20 +1,17 @@
-name: fastqc
-description: Run FastQC on sequenced reads
+name: hifiasm
+description: Run hifiasm on Pacbio HiFi reads
 keywords:
-    - quality control
-    - qc
-    - adapters
+    - genome assembly
+    - pacbaio
+    - hifi
+    - long reads
     - fastq
 tools:
-    - fastqc:
+    - hifiasm:
         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/
+            hifiasm generates a genome assembly from long Pacbio HiFi reads. ...Haplotype resolution ...Using short reads.
+        homepage: https://github.com/chhylp123/hifiasm
+        documentation: https://github.com/chhylp123/hifiasm
 params:
     - outdir:
         type: string
diff --git a/tests/software/hifiasm/main.nf b/tests/software/hifiasm/main.nf
index f10b2357..66824584 100644
--- a/tests/software/hifiasm/main.nf
+++ b/tests/software/hifiasm/main.nf
@@ -2,27 +2,27 @@
 
 nextflow.enable.dsl = 2
 
-include { FASTQC } from '../../../software/fastqc/main.nf' addParams( options: [:] )
+include { HIFIASM } from '../../../software/hifiasm/main.nf' addParams( options: [:] )
 
-/*
+/* 
  * Test with single-end data
  */
-workflow test_fastqc_single_end {
+/* workflow test_fastqc_single_end {
 
     def input = []
     input = [ [ id:'test', single_end:true ], // meta map
               [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ] ]
     FASTQC ( input )
-}
+} */
 
 /*
- * Test with paired-end data
+ * Test version printing
  */
-workflow test_fastqc_paired_end {
+workflow test_hifiasm_version {
 
-    def input = []
+/*     def input = []
     input = [[id: 'test', single_end: false], // meta map
              [file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true),
-              file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true)]]
-    FASTQC (input)
+              file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true)]] */
+    HIFIASM ()
 }
diff --git a/tests/software/hifiasm/test.yml b/tests/software/hifiasm/test.yml
index 0fe0ebe0..3825b238 100644
--- a/tests/software/hifiasm/test.yml
+++ b/tests/software/hifiasm/test.yml
@@ -1,19 +1,7 @@
-- name: fastqc single-end
-  command: nextflow run ./tests/software/fastqc/ -entry test_fastqc_single_end -c tests/config/nextflow.config
+- name: hifiasm 
+  command: nextflow run ./tests/software/hifiasm/ -entry test_hifiasm_version -c tests/config/nextflow.config
   tags:
-    - fastqc
-    - fastqc_single_end
+    - hifiasm
+    - hifiasm_version
   files:
-    - path: ./output/fastqc/test_fastqc.html
-    - path: ./output/fastqc/test_fastqc.zip
-
-- name: fastqc paired-end
-  command: nextflow run ./tests/software/fastqc/ -entry test_fastqc_paired_end -c tests/config/nextflow.config
-  tags:
-    - fastqc
-    - fastqc_paired_end
-  files:
-    - path: ./output/fastqc/test_1_fastqc.html
-    - path: ./output/fastqc/test_2_fastqc.html
-    - path: ./output/fastqc/test_2_fastqc.zip
-    - path: ./output/fastqc/test_1_fastqc.zip
+    - path: ./output/hifiasm/VERSION.txt

From b58233794b05b287d0887c6803c6c2f7abf10db4 Mon Sep 17 00:00:00 2001
From: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Date: Tue, 16 Mar 2021 13:14:43 +0000
Subject: [PATCH 04/12] Add hifiasm version printing

---
 software/hifiasm/main.nf        | 33 +++++++++++++++++++--------------
 tests/software/hifiasm/test.yml |  4 ++--
 2 files changed, 21 insertions(+), 16 deletions(-)

diff --git a/software/hifiasm/main.nf b/software/hifiasm/main.nf
index 4e847876..7a364be2 100644
--- a/software/hifiasm/main.nf
+++ b/software/hifiasm/main.nf
@@ -4,33 +4,34 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
 params.options = [:]
 options        = initOptions(params.options)
 
-process FASTQC {
-    tag "$meta.id"
-    label 'process_medium'
+process HIFIASM {
+    //tag "$meta.id"
+    label 'process_high'
     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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') } // publish_id:meta.id) }
 
-    conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
+    conda (params.enable_conda ? "bioconda::hifiasm=0.14" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0"
+        container "https://depot.galaxyproject.org/singularity/hifiasm:0.14--h8b12597_0"
     } else {
-        container "quay.io/biocontainers/fastqc:0.11.9--0"
+        container "quay.io/biocontainers/hifiasm:0.14--h8b12597_0"
     }
 
-    input:
-    tuple val(meta), path(reads)
+/*     input:
+    tuple val(meta), path(reads) */
 
     output:
-    tuple val(meta), path("*.html"), emit: html
-    tuple val(meta), path("*.zip") , emit: zip
+/*     tuple val(meta), path("*.html"), emit: html
+    tuple val(meta), path("*.zip") , emit: zip */
     path  "*.version.txt"          , emit: version
 
     script:
     // Add soft-links to original FastQs for consistent naming in pipeline
     def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
-    if (meta.single_end) {
+    //def prefix   = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
+  
+/*     if (meta.single_end) {
         """
         [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
         fastqc $options.args --threads $task.cpus ${prefix}.fastq.gz
@@ -43,5 +44,9 @@ process FASTQC {
         fastqc $options.args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
         fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt
         """
-    }
+    } */
+
+    """
+    hifiasm --version > ${software}.version.txt || exit 0
+    """
 }
diff --git a/tests/software/hifiasm/test.yml b/tests/software/hifiasm/test.yml
index 3825b238..e639f099 100644
--- a/tests/software/hifiasm/test.yml
+++ b/tests/software/hifiasm/test.yml
@@ -1,7 +1,7 @@
 - name: hifiasm 
-  command: nextflow run ./tests/software/hifiasm/ -entry test_hifiasm_version -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/hifiasm -entry test_hifiasm_version -c tests/config/nextflow.config
   tags:
     - hifiasm
     - hifiasm_version
   files:
-    - path: ./output/hifiasm/VERSION.txt
+    - path: ./output/hifiasm/hifiasm.version.txt

From 5a270c5ba7a0b382d2ca48ce42f7399a6003fa7d Mon Sep 17 00:00:00 2001
From: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Date: Tue, 16 Mar 2021 15:55:59 +0000
Subject: [PATCH 05/12] Removed spaced on an empty line

---
 software/hifiasm/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/software/hifiasm/main.nf b/software/hifiasm/main.nf
index 7a364be2..8686b6bc 100644
--- a/software/hifiasm/main.nf
+++ b/software/hifiasm/main.nf
@@ -30,7 +30,7 @@ process HIFIASM {
     // Add soft-links to original FastQs for consistent naming in pipeline
     def software = getSoftwareName(task.process)
     //def prefix   = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
-  
+
 /*     if (meta.single_end) {
         """
         [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz

From 7aaf0b72486a6948f8e93f5905e56339dbca9ee5 Mon Sep 17 00:00:00 2001
From: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Date: Sun, 2 May 2021 14:09:03 +0100
Subject: [PATCH 06/12] Reverted hifiasm from main

---
 software/hifiasm/functions.nf   | 59 ----------------------------
 software/hifiasm/main.nf        | 52 -------------------------
 software/hifiasm/meta.yml       | 69 ---------------------------------
 tests/software/hifiasm/main.nf  | 28 -------------
 tests/software/hifiasm/test.yml |  7 ----
 5 files changed, 215 deletions(-)
 delete mode 100644 software/hifiasm/functions.nf
 delete mode 100644 software/hifiasm/main.nf
 delete mode 100644 software/hifiasm/meta.yml
 delete mode 100644 tests/software/hifiasm/main.nf
 delete mode 100644 tests/software/hifiasm/test.yml

diff --git a/software/hifiasm/functions.nf b/software/hifiasm/functions.nf
deleted file mode 100644
index d25eea86..00000000
--- a/software/hifiasm/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)}/$args.filename"
-        }
-    }
-}
diff --git a/software/hifiasm/main.nf b/software/hifiasm/main.nf
deleted file mode 100644
index 8686b6bc..00000000
--- a/software/hifiasm/main.nf
+++ /dev/null
@@ -1,52 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
-process HIFIASM {
-    //tag "$meta.id"
-    label 'process_high'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') } // publish_id:meta.id) }
-
-    conda (params.enable_conda ? "bioconda::hifiasm=0.14" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/hifiasm:0.14--h8b12597_0"
-    } else {
-        container "quay.io/biocontainers/hifiasm:0.14--h8b12597_0"
-    }
-
-/*     input:
-    tuple val(meta), path(reads) */
-
-    output:
-/*     tuple val(meta), path("*.html"), emit: html
-    tuple val(meta), path("*.zip") , emit: zip */
-    path  "*.version.txt"          , emit: version
-
-    script:
-    // Add soft-links to original FastQs for consistent naming in pipeline
-    def software = getSoftwareName(task.process)
-    //def prefix   = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
-
-/*     if (meta.single_end) {
-        """
-        [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
-        fastqc $options.args --threads $task.cpus ${prefix}.fastq.gz
-        fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt
-        """
-    } else {
-        """
-        [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
-        [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
-        fastqc $options.args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
-        fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt
-        """
-    } */
-
-    """
-    hifiasm --version > ${software}.version.txt || exit 0
-    """
-}
diff --git a/software/hifiasm/meta.yml b/software/hifiasm/meta.yml
deleted file mode 100644
index 9ef62628..00000000
--- a/software/hifiasm/meta.yml
+++ /dev/null
@@ -1,69 +0,0 @@
-name: hifiasm
-description: Run hifiasm on Pacbio HiFi reads
-keywords:
-    - genome assembly
-    - pacbaio
-    - hifi
-    - long reads
-    - fastq
-tools:
-    - hifiasm:
-        description: |
-            hifiasm generates a genome assembly from long Pacbio HiFi reads. ...Haplotype resolution ...Using short reads.
-        homepage: https://github.com/chhylp123/hifiasm
-        documentation: https://github.com/chhylp123/hifiasm
-params:
-    - outdir:
-        type: string
-        description: |
-            The pipeline's output directory. By default, the module will
-            output files into `$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:
-    - 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}"
-    - version:
-        type: file
-        description: File containing software version
-        pattern: "*.{version.txt}"
-authors:
-    - "@drpatelh"
-    - "@grst"
-    - "@ewels"
-    - "@FelixKrueger"
diff --git a/tests/software/hifiasm/main.nf b/tests/software/hifiasm/main.nf
deleted file mode 100644
index 66824584..00000000
--- a/tests/software/hifiasm/main.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HIFIASM } from '../../../software/hifiasm/main.nf' addParams( options: [:] )
-
-/* 
- * Test with single-end data
- */
-/* workflow test_fastqc_single_end {
-
-    def input = []
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ] ]
-    FASTQC ( input )
-} */
-
-/*
- * Test version printing
- */
-workflow test_hifiasm_version {
-
-/*     def input = []
-    input = [[id: 'test', single_end: false], // meta map
-             [file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true),
-              file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true)]] */
-    HIFIASM ()
-}
diff --git a/tests/software/hifiasm/test.yml b/tests/software/hifiasm/test.yml
deleted file mode 100644
index e639f099..00000000
--- a/tests/software/hifiasm/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: hifiasm 
-  command: nextflow run ./tests/software/hifiasm -entry test_hifiasm_version -c tests/config/nextflow.config
-  tags:
-    - hifiasm
-    - hifiasm_version
-  files:
-    - path: ./output/hifiasm/hifiasm.version.txt

From 1abcc938379595db0840dc32d1681cdebc268f74 Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Fri, 28 Jan 2022 09:14:47 +0000
Subject: [PATCH 07/12] Ignores version file checking if testing for error

---
 tests/test_versions_yml.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/test_versions_yml.py b/tests/test_versions_yml.py
index 2f78ab2e..19ba1cf9 100644
--- a/tests/test_versions_yml.py
+++ b/tests/test_versions_yml.py
@@ -16,7 +16,8 @@ def _get_workflow_names():
         # test_config = yaml.safe_load(f.read_text())
         test_config = yaml.load(f.read_text(), Loader=yaml.BaseLoader)
         for workflow in test_config:
-            yield workflow["name"]
+            if 'exit_code' not in workflow:
+                yield workflow["name"]
 
 
 @pytest.mark.workflow(*_get_workflow_names())

From 70ea9ac9a863061e22e7b5a8dd3fe07a29ecf4c4 Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Fri, 28 Jan 2022 09:27:28 +0000
Subject: [PATCH 08/12] Added comment

---
 tests/test_versions_yml.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/tests/test_versions_yml.py b/tests/test_versions_yml.py
index 19ba1cf9..5d0bb39e 100644
--- a/tests/test_versions_yml.py
+++ b/tests/test_versions_yml.py
@@ -16,7 +16,9 @@ def _get_workflow_names():
         # test_config = yaml.safe_load(f.read_text())
         test_config = yaml.load(f.read_text(), Loader=yaml.BaseLoader)
         for workflow in test_config:
-            if 'exit_code' not in workflow:
+            # https://github.com/nf-core/modules/pull/1242 - added to cover tests 
+            # that expect an error and therefore will not generate a versions.yml
+            if 'exit_code' not in workflow: 
                 yield workflow["name"]
 
 

From 768073be6390c620e133230dea376466383832f5 Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Tue, 3 May 2022 11:46:19 +0100
Subject: [PATCH 09/12] bowtie2|Added support for large indexes

---
 modules/bowtie2/align/main.nf               |  4 ++
 tests/modules/bowtie2/align/main.nf         |  2 +-
 tests/modules/bowtie2/align/nextflow.config | 13 ++++++-
 tests/modules/bowtie2/align/test.yml        | 43 +++++++++++++++++++++
 4 files changed, 60 insertions(+), 2 deletions(-)

diff --git a/modules/bowtie2/align/main.nf b/modules/bowtie2/align/main.nf
index 20b08f72..e68dbf24 100644
--- a/modules/bowtie2/align/main.nf
+++ b/modules/bowtie2/align/main.nf
@@ -26,6 +26,8 @@ process BOWTIE2_ALIGN {
         def unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
         """
         INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
+        [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed 's/.rev.1.bt2l//'`
+        [ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1
         bowtie2 \\
             -x \$INDEX \\
             -U $reads \\
@@ -46,6 +48,8 @@ process BOWTIE2_ALIGN {
         def unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
         """
         INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
+        [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed 's/.rev.1.bt2l//'`
+        [ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1
         bowtie2 \\
             -x \$INDEX \\
             -1 ${reads[0]} \\
diff --git a/tests/modules/bowtie2/align/main.nf b/tests/modules/bowtie2/align/main.nf
index 2d3945e5..f91394ff 100644
--- a/tests/modules/bowtie2/align/main.nf
+++ b/tests/modules/bowtie2/align/main.nf
@@ -32,4 +32,4 @@ workflow test_bowtie2_align_paired_end {
 
     BOWTIE2_BUILD ( fasta )
     BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned )
-}
+}
\ No newline at end of file
diff --git a/tests/modules/bowtie2/align/nextflow.config b/tests/modules/bowtie2/align/nextflow.config
index 8730f1c4..b4640de7 100644
--- a/tests/modules/bowtie2/align/nextflow.config
+++ b/tests/modules/bowtie2/align/nextflow.config
@@ -1,5 +1,16 @@
+params {
+    force_large_index = false
+}
+
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
+}
+
+if (params.force_large_index) {
+    process {
+        withName: BOWTIE2_BUILD {
+            ext.args = '--large-index'
+        }
+    }
 }
diff --git a/tests/modules/bowtie2/align/test.yml b/tests/modules/bowtie2/align/test.yml
index 95d48b88..11e4c4e5 100644
--- a/tests/modules/bowtie2/align/test.yml
+++ b/tests/modules/bowtie2/align/test.yml
@@ -39,3 +39,46 @@
       md5sum: 52be6950579598a990570fbcf5372184
     - path: ./output/bowtie2/bowtie2/genome.rev.2.bt2
       md5sum: e3b4ef343dea4dd571642010a7d09597
+
+- name: bowtie2 align single-end large-index
+  command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config --force_large_index
+  tags:
+  tags:
+    - bowtie2
+    - bowtie2/align
+  files:
+    - path: ./output/bowtie2/test.bam
+    - path: ./output/bowtie2/test.bowtie2.log
+    - path: ./output/bowtie2/bowtie2/genome.3.bt2
+      md5sum: 8952b3e0b1ce9a7a5916f2e147180853
+    - path: ./output/bowtie2/bowtie2/genome.2.bt2
+      md5sum: 22c284084784a0720989595e0c9461fd
+    - path: ./output/bowtie2/bowtie2/genome.1.bt2
+      md5sum: 07d811cd4e350d56267183d2ac7023a5
+    - path: ./output/bowtie2/bowtie2/genome.4.bt2
+      md5sum: c25be5f8b0378abf7a58c8a880b87626
+    - path: ./output/bowtie2/bowtie2/genome.rev.1.bt2
+      md5sum: fda48e35925fb24d1c0785f021981e25
+    - path: ./output/bowtie2/bowtie2/genome.rev.2.bt2
+      md5sum: 802c26d32b970e1b105032b7ce7348b4
+
+- name: bowtie2 align paired-end large-index
+  command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config --force_large_index
+  tags:
+    - bowtie2
+    - bowtie2/align
+  files:
+    - path: ./output/bowtie2/test.bam
+    - path: ./output/bowtie2/test.bowtie2.log
+    - path: ./output/bowtie2/bowtie2/genome.3.bt2l
+      md5sum: 8952b3e0b1ce9a7a5916f2e147180853
+    - path: ./output/bowtie2/bowtie2/genome.2.bt2l
+      md5sum: 22c284084784a0720989595e0c9461fd
+    - path: ./output/bowtie2/bowtie2/genome.1.bt2l
+      md5sum: 07d811cd4e350d56267183d2ac7023a5
+    - path: ./output/bowtie2/bowtie2/genome.4.bt2l
+      md5sum: c25be5f8b0378abf7a58c8a880b87626
+    - path: ./output/bowtie2/bowtie2/genome.rev.1.bt2l
+      md5sum: fda48e35925fb24d1c0785f021981e25
+    - path: ./output/bowtie2/bowtie2/genome.rev.2.bt2l
+      md5sum: 802c26d32b970e1b105032b7ce7348b4

From 0f1ee7e50dccd1a8717cd448c518b67fb68c1d09 Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Tue, 3 May 2022 12:04:51 +0100
Subject: [PATCH 10/12] bowtie2|test fixes

---
 tests/modules/bowtie2/align/test.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/tests/modules/bowtie2/align/test.yml b/tests/modules/bowtie2/align/test.yml
index 11e4c4e5..961009b4 100644
--- a/tests/modules/bowtie2/align/test.yml
+++ b/tests/modules/bowtie2/align/test.yml
@@ -49,17 +49,17 @@
   files:
     - path: ./output/bowtie2/test.bam
     - path: ./output/bowtie2/test.bowtie2.log
-    - path: ./output/bowtie2/bowtie2/genome.3.bt2
+    - path: ./output/bowtie2/bowtie2/genome.3.bt2l
       md5sum: 8952b3e0b1ce9a7a5916f2e147180853
-    - path: ./output/bowtie2/bowtie2/genome.2.bt2
+    - path: ./output/bowtie2/bowtie2/genome.2.bt2l
       md5sum: 22c284084784a0720989595e0c9461fd
-    - path: ./output/bowtie2/bowtie2/genome.1.bt2
+    - path: ./output/bowtie2/bowtie2/genome.1.bt2l
       md5sum: 07d811cd4e350d56267183d2ac7023a5
-    - path: ./output/bowtie2/bowtie2/genome.4.bt2
+    - path: ./output/bowtie2/bowtie2/genome.4.bt2l
       md5sum: c25be5f8b0378abf7a58c8a880b87626
-    - path: ./output/bowtie2/bowtie2/genome.rev.1.bt2
+    - path: ./output/bowtie2/bowtie2/genome.rev.1.bt2l
       md5sum: fda48e35925fb24d1c0785f021981e25
-    - path: ./output/bowtie2/bowtie2/genome.rev.2.bt2
+    - path: ./output/bowtie2/bowtie2/genome.rev.2.bt2l
       md5sum: 802c26d32b970e1b105032b7ce7348b4
 
 - name: bowtie2 align paired-end large-index

From 40e6bd9dc16a7a4b63d399cf79f0bb1b7e3927c0 Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Tue, 3 May 2022 12:07:04 +0100
Subject: [PATCH 11/12] bowtie2|fix tags error

---
 tests/modules/bowtie2/align/test.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/modules/bowtie2/align/test.yml b/tests/modules/bowtie2/align/test.yml
index 961009b4..ea9aa72a 100644
--- a/tests/modules/bowtie2/align/test.yml
+++ b/tests/modules/bowtie2/align/test.yml
@@ -42,7 +42,6 @@
 
 - name: bowtie2 align single-end large-index
   command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config --force_large_index
-  tags:
   tags:
     - bowtie2
     - bowtie2/align

From 96d4a31cc15e3b20ee6a7df0ad39ca59feeb3a02 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 3 May 2022 15:31:05 +0200
Subject: [PATCH 12/12] Moved the BED file to the main tuple

---
 modules/vardictjava/main.nf       | 3 +--
 tests/modules/vardictjava/main.nf | 7 +++----
 2 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/modules/vardictjava/main.nf b/modules/vardictjava/main.nf
index 454b86a4..c99301bb 100644
--- a/modules/vardictjava/main.nf
+++ b/modules/vardictjava/main.nf
@@ -10,8 +10,7 @@ process VARDICTJAVA {
         'quay.io/biocontainers/vardict-java:1.8.3--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(bam), path(bai)
-    path(bed)
+    tuple val(meta), path(bam), path(bai), path(bed)
     tuple path(fasta), path(fasta_fai)
 
     output:
diff --git a/tests/modules/vardictjava/main.nf b/tests/modules/vardictjava/main.nf
index d392358a..e29490f3 100644
--- a/tests/modules/vardictjava/main.nf
+++ b/tests/modules/vardictjava/main.nf
@@ -9,15 +9,14 @@ workflow test_vardictjava {
     bam_input_ch = Channel.value([
         [ id:'test' ], // meta map
         file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
     ])
 
-    bed = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true))
-
     reference = Channel.value([
         file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
         file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
     ])
 
-    VARDICTJAVA ( bam_input_ch, bed, reference )
+    VARDICTJAVA ( bam_input_ch, reference )
 }