From 508761e05c04c47e7b3557c8b654032e69d212d3 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Tue, 8 Dec 2020 12:57:00 +0100
Subject: [PATCH 01/25] Added bowtie index and align modules

---
 software/bowtie/align/functions.nf | 59 ++++++++++++++++++++++++++++++
 software/bowtie/align/main.nf      | 40 ++++++++++++++++++++
 software/bowtie/align/meta.yml     |  0
 software/bowtie/index/functions.nf | 59 ++++++++++++++++++++++++++++++
 software/bowtie/index/main.nf      | 32 ++++++++++++++++
 software/bowtie/index/meta.yml     |  0
 6 files changed, 190 insertions(+)
 create mode 100644 software/bowtie/align/functions.nf
 create mode 100644 software/bowtie/align/main.nf
 create mode 100644 software/bowtie/align/meta.yml
 create mode 100644 software/bowtie/index/functions.nf
 create mode 100644 software/bowtie/index/main.nf
 create mode 100644 software/bowtie/index/meta.yml

diff --git a/software/bowtie/align/functions.nf b/software/bowtie/align/functions.nf
new file mode 100644
index 00000000..b3ac3801
--- /dev/null
+++ b/software/bowtie/align/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)}/$args.filename"
+        }
+    }
+}
diff --git a/software/bowtie/align/main.nf b/software/bowtie/align/main.nf
new file mode 100644
index 00000000..18ee4705
--- /dev/null
+++ b/software/bowtie/align/main.nf
@@ -0,0 +1,40 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process BOWTIE_ALIGN {
+    tag "$meta.id"
+    label 'process_high'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    conda     (params.enable_conda ? "bioconda::bowtie=1.3.0" : null)
+    container "quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1"
+
+    input:
+    tuple val(meta), path(reads)
+    path  index
+    path  gtf
+    
+    output:
+    tuple val(meta), path("*.sam")            , emit: sam
+    tuple val(meta), path("*.out")            , emit: log
+    path  "bowtie.version.txt"                , emit: version
+
+    script:
+    def software   = getSoftwareName(task.process)
+    def prefix     = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    index_array = index.collect()
+    index = index_array[0].baseName - ~/.\d$/
+    """
+    bowtie $options.args  \\
+    --threads $task.cpus \\
+    ${index}  \\
+    -q ${reads} \\
+    --un ${prefix}.unAl > ${prefix}.sam 2> ${prefix}.out
+    bowtie --version | head -n 1 | cut -d" " -f3 > ${software}.version.txt
+    """
+}
\ No newline at end of file
diff --git a/software/bowtie/align/meta.yml b/software/bowtie/align/meta.yml
new file mode 100644
index 00000000..e69de29b
diff --git a/software/bowtie/index/functions.nf b/software/bowtie/index/functions.nf
new file mode 100644
index 00000000..b3ac3801
--- /dev/null
+++ b/software/bowtie/index/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)}/$args.filename"
+        }
+    }
+}
diff --git a/software/bowtie/index/main.nf b/software/bowtie/index/main.nf
new file mode 100644
index 00000000..36f88451
--- /dev/null
+++ b/software/bowtie/index/main.nf
@@ -0,0 +1,32 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process BOWTIE_INDEX {
+    tag "$fasta"
+    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:'') }
+
+    conda     (params.enable_conda ? "bioconda::bowtie=1.3.0" : null)
+    container "quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1"
+    
+
+    input:
+    path fasta
+    path gtf
+
+    output:
+    path "*.index*"          , emit: index
+    path "*.version.txt"     , emit: version
+
+    script:
+    def software  = getSoftwareName(task.process)
+    """
+    bowtie-build --threads $task.cpus ${fasta} ${fasta.baseName}.index
+    bowtie --version | head -n 1 | cut -d" " -f3 > ${software}.version.txt
+    """
+}
\ No newline at end of file
diff --git a/software/bowtie/index/meta.yml b/software/bowtie/index/meta.yml
new file mode 100644
index 00000000..e69de29b

From 9d67da2b2ccbbc2fb44daa23421022e6a38ea45c Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Tue, 8 Dec 2020 13:40:32 +0100
Subject: [PATCH 02/25] added module yml files

---
 software/bowtie/align/main.nf  |  1 -
 software/bowtie/align/meta.yml | 57 ++++++++++++++++++++++++++++++++++
 software/bowtie/index/main.nf  |  1 -
 software/bowtie/index/meta.yml | 46 +++++++++++++++++++++++++++
 tests/software/bowtie/main.nf  | 26 ++++++++++++++++
 tests/software/bowtie/test.yml | 32 +++++++++++++++++++
 6 files changed, 161 insertions(+), 2 deletions(-)
 create mode 100644 tests/software/bowtie/main.nf
 create mode 100644 tests/software/bowtie/test.yml

diff --git a/software/bowtie/align/main.nf b/software/bowtie/align/main.nf
index 18ee4705..3885ecbe 100644
--- a/software/bowtie/align/main.nf
+++ b/software/bowtie/align/main.nf
@@ -17,7 +17,6 @@ process BOWTIE_ALIGN {
     input:
     tuple val(meta), path(reads)
     path  index
-    path  gtf
     
     output:
     tuple val(meta), path("*.sam")            , emit: sam
diff --git a/software/bowtie/align/meta.yml b/software/bowtie/align/meta.yml
index e69de29b..5b604289 100644
--- a/software/bowtie/align/meta.yml
+++ b/software/bowtie/align/meta.yml
@@ -0,0 +1,57 @@
+name: bowtie_align
+description: Align reads to a reference genome using bowtie
+keywords:
+    - align
+    - fasta
+    - genome
+    - reference
+tools:
+    - bowtie:
+        description: |
+            bowtie is a software package for mapping DNA sequences against
+            a large reference genome, such as the human genome.
+        homepage: http://bowtie-bio.sourceforge.net/index.shtml
+        documentation: http://bowtie-bio.sourceforge.net/manual.shtml
+        arxiv: arXiv:1303.3997
+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
+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.
+    - index:
+        type: file
+        description: Bowtie genome index files
+        pattern: "*.ebwt"
+output:
+    - index:
+        type: file
+        description: Bowtie genome index files
+        pattern: "*.ebwt"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@kevinmenden"
diff --git a/software/bowtie/index/main.nf b/software/bowtie/index/main.nf
index 36f88451..553651d5 100644
--- a/software/bowtie/index/main.nf
+++ b/software/bowtie/index/main.nf
@@ -17,7 +17,6 @@ process BOWTIE_INDEX {
 
     input:
     path fasta
-    path gtf
 
     output:
     path "*.index*"          , emit: index
diff --git a/software/bowtie/index/meta.yml b/software/bowtie/index/meta.yml
index e69de29b..0a8c23f7 100644
--- a/software/bowtie/index/meta.yml
+++ b/software/bowtie/index/meta.yml
@@ -0,0 +1,46 @@
+name: bowtie_index
+description: Create bowtie index for reference genome
+keywords:
+    - index
+    - fasta
+    - genome
+    - reference
+tools:
+    - bowtie:
+        description: |
+            bowtie is a software package for mapping DNA sequences against
+            a large reference genome, such as the human genome.
+        homepage: http://bowtie-bio.sourceforge.net/index.shtml
+        documentation: http://bowtie-bio.sourceforge.net/manual.shtml
+        arxiv: arXiv:1303.3997
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+            Value for the Nextflow `publishDir` mode parameter.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+        type: boolean
+        description: |
+            Run the module with Conda using the software specified
+            via the `conda` directive
+input:
+    - fasta:
+        type: file
+        description: Input genome fasta file
+output:
+    - index:
+        type: file
+        description: Bowtie genome index files
+        pattern: "*.ebwt"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@kevinmenden"
diff --git a/tests/software/bowtie/main.nf b/tests/software/bowtie/main.nf
new file mode 100644
index 00000000..1f6a54ff
--- /dev/null
+++ b/tests/software/bowtie/main.nf
@@ -0,0 +1,26 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BOWTIE_INDEX } from '../../../software/bowtie/index/main.nf' addParams( options: [:] )
+include { BOWTIE_ALIGN } from '../../../software/bowtie/align/main.nf'  addParams( options: [:] )
+
+
+
+workflow test_bowtie_index {
+    fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    BOWTIE_INDEX ( fasta ) 
+}
+
+workflow test_bowtie_alignment_single_end {
+
+    fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    BOWTIE_INDEX ( fasta ) 
+}
+
+    def input = []
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ]
+    BOWTIE_ALIGN ( input, BOWTIE_INDEX.index )
+}
+
diff --git a/tests/software/bowtie/test.yml b/tests/software/bowtie/test.yml
new file mode 100644
index 00000000..f1bd09fd
--- /dev/null
+++ b/tests/software/bowtie/test.yml
@@ -0,0 +1,32 @@
+- name: Run bowtie index
+  command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_index -c tests/config/nextflow.config
+  tags:
+    - bwa
+    - bwa_index
+  files:
+    - path: output/bwa/NC_010473.fa.amb
+      md5sum: 942a990ae872f1c0b8d72dda2db405d5
+    - path: output/bwa/NC_010473.fa.bwt
+      md5sum: 7301b52e2ecb893d429a49fa692447ae
+    - path: output/bwa/NC_010473.fa.pac
+      md5sum: 4d5e6fc45bbc968f7f859e9ca2cc89ad
+    - path: output/bwa/NC_010473.fa.sa
+      md5sum: a47dcc92e750e2f16fbd979b8ff9538e
+
+- name: Run bwa mem single-end
+  command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_mem_single_end -c tests/config/nextflow.config
+  tags:
+    - bwa
+    - bwa_mem
+  files:
+    - path: output/test_single_end/test.bam
+      md5sum: 3ee21210bac387e0335008146e4728bc
+
+- name: Run bwa mem paired-end
+  command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
+  tags:
+    - bwa
+    - bwa_mem
+  files:
+    - path: output/test_paired_end/test.bam
+      md5sum: 510d8acc6448c07cdacce8e64ec0904c

From 6660a597a3b19ee0f0e7fbe32540b4d77e60b034 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Tue, 8 Dec 2020 13:59:14 +0100
Subject: [PATCH 03/25] added tests for bowtie module

---
 tests/software/bowtie/main.nf  |  3 +-
 tests/software/bowtie/test.yml | 60 ++++++++++++++++++++--------------
 2 files changed, 36 insertions(+), 27 deletions(-)

diff --git a/tests/software/bowtie/main.nf b/tests/software/bowtie/main.nf
index 1f6a54ff..8a64cd34 100644
--- a/tests/software/bowtie/main.nf
+++ b/tests/software/bowtie/main.nf
@@ -16,11 +16,10 @@ workflow test_bowtie_alignment_single_end {
 
     fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
     BOWTIE_INDEX ( fasta ) 
-}
 
     def input = []
     input = [ [ id:'test', single_end:true ], // meta map
               [ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ]
-    BOWTIE_ALIGN ( input, BOWTIE_INDEX.index )
+    BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
 }
 
diff --git a/tests/software/bowtie/test.yml b/tests/software/bowtie/test.yml
index f1bd09fd..13b7b1fd 100644
--- a/tests/software/bowtie/test.yml
+++ b/tests/software/bowtie/test.yml
@@ -1,32 +1,42 @@
 - name: Run bowtie index
-  command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_index -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_index -c tests/config/nextflow.config
   tags:
-    - bwa
-    - bwa_index
+    - bowtie
+    - bowtie_index
   files:
-    - path: output/bwa/NC_010473.fa.amb
-      md5sum: 942a990ae872f1c0b8d72dda2db405d5
-    - path: output/bwa/NC_010473.fa.bwt
-      md5sum: 7301b52e2ecb893d429a49fa692447ae
-    - path: output/bwa/NC_010473.fa.pac
-      md5sum: 4d5e6fc45bbc968f7f859e9ca2cc89ad
-    - path: output/bwa/NC_010473.fa.sa
-      md5sum: a47dcc92e750e2f16fbd979b8ff9538e
+    - path: output/bowtie/NC_010473.index.1.ebwt
+      md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
+    - path: output/bowtie/NC_010473.index.2.ebwt
+      md5sum: bfd10c5319c6a0dbc540fd789254a5dd
+    - path: output/bowtie/NC_010473.index.3.ebwt
+      md5sum: cd201e81724f3099131aec16ef2cc53b
+    - path: output/bowtie/NC_010473.index.4.ebwt
+      md5sum: bbb9d6d21ad765d135f95290204e8433
+    - path: output/bowtie/NC_010473.index.rev.1.ebwt
+      md5sum: 44f719c2fe42e1f35d54e798775846d1
+    - path: output/bowtie/NC_010473.index.rev.2.ebwt
+      md5sum: f3c398bba5158f4039334a932d79c051
 
-- name: Run bwa mem single-end
-  command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_mem_single_end -c tests/config/nextflow.config
+- name: Run bowtie index and align signle-end
+  command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
   tags:
-    - bwa
-    - bwa_mem
+    - bowtie
+    - bwa_align
   files:
-    - path: output/test_single_end/test.bam
-      md5sum: 3ee21210bac387e0335008146e4728bc
+    - path: output/bowtie/NC_010473.index.1.ebwt
+      md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
+    - path: output/bowtie/NC_010473.index.2.ebwt
+      md5sum: bfd10c5319c6a0dbc540fd789254a5dd
+    - path: output/bowtie/NC_010473.index.3.ebwt
+      md5sum: cd201e81724f3099131aec16ef2cc53b
+    - path: output/bowtie/NC_010473.index.4.ebwt
+      md5sum: bbb9d6d21ad765d135f95290204e8433
+    - path: output/bowtie/NC_010473.index.rev.1.ebwt
+      md5sum: 44f719c2fe42e1f35d54e798775846d1
+    - path: output/bowtie/NC_010473.index.rev.2.ebwt
+      md5sum: f3c398bba5158f4039334a932d79c051
+    - path: output/bowtie/test.out
+      md5sum: 6edce9d0d8ad7f5ce837a5be7e0d7fbe
+    - path: output/bowtie/test.sam
+      md5sum: acdb36ea915ac2ac71b69a0b704d9d8a
 
-- name: Run bwa mem paired-end
-  command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
-  tags:
-    - bwa
-    - bwa_mem
-  files:
-    - path: output/test_paired_end/test.bam
-      md5sum: 510d8acc6448c07cdacce8e64ec0904c

From 73530e8df73af05d91b463bfb0863a4673e438be Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Tue, 8 Dec 2020 14:13:30 +0100
Subject: [PATCH 04/25] added bowtie index test github workflow

---
 .github/workflows/bowtie_index.yml | 36 ++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 .github/workflows/bowtie_index.yml

diff --git a/.github/workflows/bowtie_index.yml b/.github/workflows/bowtie_index.yml
new file mode 100644
index 00000000..80ff13c9
--- /dev/null
+++ b/.github/workflows/bowtie_index.yml
@@ -0,0 +1,36 @@
+name: bowtie_index
+on:
+    push:
+        paths:
+            - software/bowtie/index/**
+            - .github/workflows/bowtie_index.yml
+            - tests/software/bowtie/**
+    pull_request:
+        paths:
+            - software/bowtie/index/**
+            - .github/workflows/bowtie_index.yml
+            - tests/software/bowtie/**
+
+jobs:
+    ci_test:
+        runs-on: ubuntu-latest
+        env:
+            NXF_ANSI_LOG: false
+        steps:
+            - uses: actions/checkout@v2
+
+            - name: Install Nextflow
+              run: |
+                  export NXF_VER="20.07.1"
+                  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 bowtie_index --symlink --wt 2

From fee0707af1d3450780aa33f9d730f8f949fae10a Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Tue, 8 Dec 2020 14:19:34 +0100
Subject: [PATCH 05/25] added bowtie_align workflow test

---
 .github/workflows/bowtie_align.yml | 38 ++++++++++++++++++++++++++++++
 tests/software/bowtie/test.yml     |  2 +-
 2 files changed, 39 insertions(+), 1 deletion(-)
 create mode 100644 .github/workflows/bowtie_align.yml

diff --git a/.github/workflows/bowtie_align.yml b/.github/workflows/bowtie_align.yml
new file mode 100644
index 00000000..796b3389
--- /dev/null
+++ b/.github/workflows/bowtie_align.yml
@@ -0,0 +1,38 @@
+name: bowtie_align
+on:
+    push:
+        paths:
+            - software/bowtie/align/**
+            - software/bowtie/index/**
+            - .github/workflows/bowtie_align.yml
+            - tests/software/bowtie/**
+    pull_request:
+        paths:
+            - software/bowtie/align/**
+            - software/bowtie/index/**
+            - .github/workflows/bowtie_align.yml
+            - tests/software/bowtie/**
+
+jobs:
+    ci_test:
+        runs-on: ubuntu-latest
+        env:
+            NXF_ANSI_LOG: false
+        steps:
+            - uses: actions/checkout@v2
+
+            - name: Install Nextflow
+              run: |
+                  export NXF_VER="20.07.1"
+                  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 bowtie_align --symlink --wt 2
diff --git a/tests/software/bowtie/test.yml b/tests/software/bowtie/test.yml
index 13b7b1fd..fb58b089 100644
--- a/tests/software/bowtie/test.yml
+++ b/tests/software/bowtie/test.yml
@@ -21,7 +21,7 @@
   command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
   tags:
     - bowtie
-    - bwa_align
+    - bowtie_align
   files:
     - path: output/bowtie/NC_010473.index.1.ebwt
       md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c

From 560a6a578ba0b06521b05bcb8478a0b71f55c88b Mon Sep 17 00:00:00 2001
From: Kevin Menden <kevin.menden@t-online.de>
Date: Wed, 9 Dec 2020 15:45:05 +0100
Subject: [PATCH 06/25] Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 software/bowtie/align/main.nf | 27 +++++++++++++++------------
 1 file changed, 15 insertions(+), 12 deletions(-)

diff --git a/software/bowtie/align/main.nf b/software/bowtie/align/main.nf
index 3885ecbe..d2a00831 100644
--- a/software/bowtie/align/main.nf
+++ b/software/bowtie/align/main.nf
@@ -19,21 +19,24 @@ process BOWTIE_ALIGN {
     path  index
     
     output:
-    tuple val(meta), path("*.sam")            , emit: sam
-    tuple val(meta), path("*.out")            , emit: log
+    tuple val(meta), path("*.sam"), emit: sam
+    tuple val(meta), path("*.out"), emit: log
     path  "bowtie.version.txt"                , emit: version
 
     script:
-    def software   = getSoftwareName(task.process)
-    def prefix     = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    index_array = index.collect()
-    index = index_array[0].baseName - ~/.\d$/
+    def software  = getSoftwareName(task.process)
+    def prefix    = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def unaligned = params.save_unaligned ? "--un ${prefix}.unmapped" : ''
     """
-    bowtie $options.args  \\
-    --threads $task.cpus \\
-    ${index}  \\
-    -q ${reads} \\
-    --un ${prefix}.unAl > ${prefix}.sam 2> ${prefix}.out
+    INDEX=`find -L ./ -name "*.1.ebwt" | sed 's/.1.ebwt//'`
+    bowtie \\
+        --threads $task.cpus \\
+        $options.args \\
+        $INDEX \\
+        -q ${reads} \\
+	$unaligned \\
+	> ${prefix}.sam 2> ${prefix}.out
+
     bowtie --version | head -n 1 | cut -d" " -f3 > ${software}.version.txt
     """
-}
\ No newline at end of file
+}

From cc72028d3de786900f711a6749c6f21027314ffb Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Wed, 9 Dec 2020 15:58:56 +0100
Subject: [PATCH 07/25] output index as directory

---
 software/bowtie/align/main.nf  | 2 +-
 software/bowtie/align/meta.yml | 9 ++++++---
 software/bowtie/index/main.nf  | 7 ++++---
 3 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/software/bowtie/align/main.nf b/software/bowtie/align/main.nf
index d2a00831..30e5a55a 100644
--- a/software/bowtie/align/main.nf
+++ b/software/bowtie/align/main.nf
@@ -21,7 +21,7 @@ process BOWTIE_ALIGN {
     output:
     tuple val(meta), path("*.sam"), emit: sam
     tuple val(meta), path("*.out"), emit: log
-    path  "bowtie.version.txt"                , emit: version
+    path  "bowtie.version.txt", emit: version
 
     script:
     def software  = getSoftwareName(task.process)
diff --git a/software/bowtie/align/meta.yml b/software/bowtie/align/meta.yml
index 5b604289..fc18a2c9 100644
--- a/software/bowtie/align/meta.yml
+++ b/software/bowtie/align/meta.yml
@@ -29,6 +29,9 @@ params:
         description: |
             Run the module with Conda using the software specified
             via the `conda` directive
+    - save_unaligned:
+        type: boolean
+        description: Save unaligned reads
 input:
     - meta:
         type: map
@@ -45,10 +48,10 @@ input:
         description: Bowtie genome index files
         pattern: "*.ebwt"
 output:
-    - index:
+    - sam:
         type: file
-        description: Bowtie genome index files
-        pattern: "*.ebwt"
+        description: Output SAM file containing read alignments
+        pattern: "*.{sam}"
     - version:
         type: file
         description: File containing software version
diff --git a/software/bowtie/index/main.nf b/software/bowtie/index/main.nf
index 553651d5..5a0e18e5 100644
--- a/software/bowtie/index/main.nf
+++ b/software/bowtie/index/main.nf
@@ -19,13 +19,14 @@ process BOWTIE_INDEX {
     path fasta
 
     output:
-    path "*.index*"          , emit: index
-    path "*.version.txt"     , emit: version
+    path "bowtie", emit: index
+    path "*.version.txt", emit: version
 
     script:
     def software  = getSoftwareName(task.process)
     """
-    bowtie-build --threads $task.cpus ${fasta} ${fasta.baseName}.index
+    mkdir bowtie
+    bowtie-build --threads $task.cpus ${fasta} bowtie/${fasta.baseName}.index
     bowtie --version | head -n 1 | cut -d" " -f3 > ${software}.version.txt
     """
 }
\ No newline at end of file

From 42020ce5ac45c30603e926a33cd9d4ace725e842 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Wed, 9 Dec 2020 16:39:05 +0100
Subject: [PATCH 08/25] added tests for bowtie paired-end alignment; resolved
 index bug

---
 software/bowtie/align/main.nf |  6 +++---
 tests/software/bowtie/main.nf | 11 +++++++++++
 2 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/software/bowtie/align/main.nf b/software/bowtie/align/main.nf
index 30e5a55a..c35508d2 100644
--- a/software/bowtie/align/main.nf
+++ b/software/bowtie/align/main.nf
@@ -28,13 +28,13 @@ process BOWTIE_ALIGN {
     def prefix    = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     def unaligned = params.save_unaligned ? "--un ${prefix}.unmapped" : ''
     """
-    INDEX=`find -L ./ -name "*.1.ebwt" | sed 's/.1.ebwt//'`
+    INDEX=`find -L ./ -name "*.3.ebwt" | sed 's/.3.ebwt//'`
     bowtie \\
         --threads $task.cpus \\
         $options.args \\
-        $INDEX \\
+        \$INDEX \\
         -q ${reads} \\
-	$unaligned \\
+	    $unaligned \\
 	> ${prefix}.sam 2> ${prefix}.out
 
     bowtie --version | head -n 1 | cut -d" " -f3 > ${software}.version.txt
diff --git a/tests/software/bowtie/main.nf b/tests/software/bowtie/main.nf
index 8a64cd34..b5668bd1 100644
--- a/tests/software/bowtie/main.nf
+++ b/tests/software/bowtie/main.nf
@@ -23,3 +23,14 @@ workflow test_bowtie_alignment_single_end {
     BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
 }
 
+workflow test_bowtie_alignment_paired_end {
+    fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    BOWTIE_INDEX ( fasta ) 
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true),
+                file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz", checkIfExists: true) ] ]
+    BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
+}
+

From 0d7c8276b73fb07be1dde82ac115f5769687b7ca Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Wed, 9 Dec 2020 16:54:11 +0100
Subject: [PATCH 09/25] added test yml and md5s

---
 tests/software/bowtie/test.yml | 48 +++++++++++++++++++++++++---------
 1 file changed, 36 insertions(+), 12 deletions(-)

diff --git a/tests/software/bowtie/test.yml b/tests/software/bowtie/test.yml
index fb58b089..02ec5e50 100644
--- a/tests/software/bowtie/test.yml
+++ b/tests/software/bowtie/test.yml
@@ -4,17 +4,17 @@
     - bowtie
     - bowtie_index
   files:
-    - path: output/bowtie/NC_010473.index.1.ebwt
+    - path: output/bowtie/bowtie/NC_010473.index.1.ebwt
       md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
-    - path: output/bowtie/NC_010473.index.2.ebwt
+    - path: output/bowtie/bowtie/NC_010473.index.2.ebwt
       md5sum: bfd10c5319c6a0dbc540fd789254a5dd
-    - path: output/bowtie/NC_010473.index.3.ebwt
+    - path: output/bowtie/bowtie/NC_010473.index.3.ebwt
       md5sum: cd201e81724f3099131aec16ef2cc53b
-    - path: output/bowtie/NC_010473.index.4.ebwt
+    - path: output/bowtie/bowtie/NC_010473.index.4.ebwt
       md5sum: bbb9d6d21ad765d135f95290204e8433
-    - path: output/bowtie/NC_010473.index.rev.1.ebwt
+    - path: output/bowtie/bowtie/NC_010473.index.rev.1.ebwt
       md5sum: 44f719c2fe42e1f35d54e798775846d1
-    - path: output/bowtie/NC_010473.index.rev.2.ebwt
+    - path: output/bowtie/bowtie/NC_010473.index.rev.2.ebwt
       md5sum: f3c398bba5158f4039334a932d79c051
 
 - name: Run bowtie index and align signle-end
@@ -23,20 +23,44 @@
     - bowtie
     - bowtie_align
   files:
-    - path: output/bowtie/NC_010473.index.1.ebwt
+    - path: output/bowtie/bowtie/NC_010473.index.1.ebwt
       md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
-    - path: output/bowtie/NC_010473.index.2.ebwt
+    - path: output/bowtie/bowtie/NC_010473.index.2.ebwt
       md5sum: bfd10c5319c6a0dbc540fd789254a5dd
-    - path: output/bowtie/NC_010473.index.3.ebwt
+    - path: output/bowtie/bowtie/NC_010473.index.3.ebwt
       md5sum: cd201e81724f3099131aec16ef2cc53b
-    - path: output/bowtie/NC_010473.index.4.ebwt
+    - path: output/bowtie/bowtie/NC_010473.index.4.ebwt
       md5sum: bbb9d6d21ad765d135f95290204e8433
-    - path: output/bowtie/NC_010473.index.rev.1.ebwt
+    - path: output/bowtie/bowtie/NC_010473.index.rev.1.ebwt
       md5sum: 44f719c2fe42e1f35d54e798775846d1
-    - path: output/bowtie/NC_010473.index.rev.2.ebwt
+    - path: output/bowtie/bowtie/NC_010473.index.rev.2.ebwt
       md5sum: f3c398bba5158f4039334a932d79c051
     - path: output/bowtie/test.out
       md5sum: 6edce9d0d8ad7f5ce837a5be7e0d7fbe
     - path: output/bowtie/test.sam
       md5sum: acdb36ea915ac2ac71b69a0b704d9d8a
 
+
+- name: Run bowtie index and align paired_end
+  command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_paired_end -c tests/config/nextflow.config
+  tags:
+    - bowtie
+    - bowtie_align
+  files:
+    - path: output/bowtie/bowtie/NC_010473.index.1.ebwt
+      md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
+    - path: output/bowtie/bowtie/NC_010473.index.2.ebwt
+      md5sum: bfd10c5319c6a0dbc540fd789254a5dd
+    - path: output/bowtie/bowtie/NC_010473.index.3.ebwt
+      md5sum: cd201e81724f3099131aec16ef2cc53b
+    - path: output/bowtie/bowtie/NC_010473.index.4.ebwt
+      md5sum: bbb9d6d21ad765d135f95290204e8433
+    - path: output/bowtie/bowtie/NC_010473.index.rev.1.ebwt
+      md5sum: 44f719c2fe42e1f35d54e798775846d1
+    - path: output/bowtie/bowtie/NC_010473.index.rev.2.ebwt
+      md5sum: f3c398bba5158f4039334a932d79c051
+    - path: output/bowtie/test.out
+      md5sum: 6edce9d0d8ad7f5ce837a5be7e0d7fbe
+    - path: output/bowtie/test.sam
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+

From f35850bf14f312a14f1edc60d9cb861b09527b83 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Wed, 16 Dec 2020 11:02:58 +0100
Subject: [PATCH 10/25] bowtie bam output

---
 software/bowtie/align/main.nf  | 18 +++++++++++-------
 tests/software/bowtie/main.nf  |  8 +++-----
 tests/software/bowtie/test.yml | 12 ++++++------
 3 files changed, 20 insertions(+), 18 deletions(-)

diff --git a/software/bowtie/align/main.nf b/software/bowtie/align/main.nf
index c35508d2..6a7ea8d8 100644
--- a/software/bowtie/align/main.nf
+++ b/software/bowtie/align/main.nf
@@ -11,15 +11,15 @@ process BOWTIE_ALIGN {
         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::bowtie=1.3.0" : null)
-    container "quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1"
+    conda     (params.enable_conda ? "bioconda::bowtie=1.3.0 bioconda::samtools=1.10" : null)
+    container "quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0"
 
     input:
     tuple val(meta), path(reads)
     path  index
     
     output:
-    tuple val(meta), path("*.sam"), emit: sam
+    tuple val(meta), path("*.bam"), emit: bam
     tuple val(meta), path("*.out"), emit: log
     path  "bowtie.version.txt", emit: version
 
@@ -27,15 +27,19 @@ process BOWTIE_ALIGN {
     def software  = getSoftwareName(task.process)
     def prefix    = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     def unaligned = params.save_unaligned ? "--un ${prefix}.unmapped" : ''
+    def endedness = meta.single_end ? "$reads" : "-1 ${reads[0]} -2 ${reads[1]}"
     """
     INDEX=`find -L ./ -name "*.3.ebwt" | sed 's/.3.ebwt//'`
     bowtie \\
         --threads $task.cpus \\
-        $options.args \\
-        \$INDEX \\
-        -q ${reads} \\
+        --sam \\
+        -x \$INDEX \\
+        -q \\
 	    $unaligned \\
-	> ${prefix}.sam 2> ${prefix}.out
+        $options.args \\
+        $endedness \\
+	    2> ${prefix}.out \\
+        | samtools view $options.args2 -@ $task.cpus -bS -o ${prefix}.bam -
 
     bowtie --version | head -n 1 | cut -d" " -f3 > ${software}.version.txt
     """
diff --git a/tests/software/bowtie/main.nf b/tests/software/bowtie/main.nf
index b5668bd1..6b4e24e6 100644
--- a/tests/software/bowtie/main.nf
+++ b/tests/software/bowtie/main.nf
@@ -5,8 +5,6 @@ nextflow.enable.dsl = 2
 include { BOWTIE_INDEX } from '../../../software/bowtie/index/main.nf' addParams( options: [:] )
 include { BOWTIE_ALIGN } from '../../../software/bowtie/align/main.nf'  addParams( options: [:] )
 
-
-
 workflow test_bowtie_index {
     fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
     BOWTIE_INDEX ( fasta ) 
@@ -19,7 +17,7 @@ workflow test_bowtie_alignment_single_end {
 
     def input = []
     input = [ [ id:'test', single_end:true ], // meta map
-              [ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ]
+              [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ]
     BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
 }
 
@@ -29,8 +27,8 @@ workflow test_bowtie_alignment_paired_end {
 
     def input = []
     input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true),
-                file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz", checkIfExists: true) ] ]
+              [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
+                file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
     BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
 }
 
diff --git a/tests/software/bowtie/test.yml b/tests/software/bowtie/test.yml
index 02ec5e50..6a28578d 100644
--- a/tests/software/bowtie/test.yml
+++ b/tests/software/bowtie/test.yml
@@ -36,9 +36,9 @@
     - path: output/bowtie/bowtie/NC_010473.index.rev.2.ebwt
       md5sum: f3c398bba5158f4039334a932d79c051
     - path: output/bowtie/test.out
-      md5sum: 6edce9d0d8ad7f5ce837a5be7e0d7fbe
-    - path: output/bowtie/test.sam
-      md5sum: acdb36ea915ac2ac71b69a0b704d9d8a
+      md5sum: a81cb18024616415a6cec3108a36fccd
+    - path: output/bowtie/test.bam
+      md5sum: 8179c68a819accbc9137dc881736106f
 
 
 - name: Run bowtie index and align paired_end
@@ -60,7 +60,7 @@
     - path: output/bowtie/bowtie/NC_010473.index.rev.2.ebwt
       md5sum: f3c398bba5158f4039334a932d79c051
     - path: output/bowtie/test.out
-      md5sum: 6edce9d0d8ad7f5ce837a5be7e0d7fbe
-    - path: output/bowtie/test.sam
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
+      md5sum: a23e9a2a76e949aeb3693bcfae41a615
+    - path: output/bowtie/test.bam
+      md5sum: 9ce5aebf37128f4bb1d24e9548e22009
 

From d75cb751119dce05534ae7c8321e7eeec98f5e05 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Thu, 17 Dec 2020 07:33:44 +0100
Subject: [PATCH 11/25] added singularity; edge NXF version

---
 .github/workflows/bowtie_align.yml | 10 +++++++---
 .github/workflows/bowtie_index.yml | 11 ++++++++---
 software/bowtie/align/main.nf      |  8 ++++++--
 software/bowtie/align/meta.yml     |  5 +++++
 software/bowtie/index/main.nf      |  9 ++++++---
 software/bowtie/index/meta.yml     |  5 +++++
 6 files changed, 37 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/bowtie_align.yml b/.github/workflows/bowtie_align.yml
index 796b3389..e3b645c8 100644
--- a/.github/workflows/bowtie_align.yml
+++ b/.github/workflows/bowtie_align.yml
@@ -16,16 +16,20 @@ on:
 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: |
-                  export NXF_VER="20.07.1"
-                  wget -qO- get.nextflow.io | bash
-                  sudo mv nextflow /usr/local/bin/
+              wget -qO- get.nextflow.io | bash
+              sudo mv nextflow /usr/local/bin/
 
             - name: Set up Python
               uses: actions/setup-python@v2
diff --git a/.github/workflows/bowtie_index.yml b/.github/workflows/bowtie_index.yml
index 80ff13c9..9f5aa8ac 100644
--- a/.github/workflows/bowtie_index.yml
+++ b/.github/workflows/bowtie_index.yml
@@ -14,16 +14,21 @@ on:
 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: |
-                  export NXF_VER="20.07.1"
-                  wget -qO- get.nextflow.io | bash
-                  sudo mv nextflow /usr/local/bin/
+              wget -qO- get.nextflow.io | bash
+              sudo mv nextflow /usr/local/bin/
+
 
             - name: Set up Python
               uses: actions/setup-python@v2
diff --git a/software/bowtie/align/main.nf b/software/bowtie/align/main.nf
index 6a7ea8d8..58906d61 100644
--- a/software/bowtie/align/main.nf
+++ b/software/bowtie/align/main.nf
@@ -11,8 +11,12 @@ process BOWTIE_ALIGN {
         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::bowtie=1.3.0 bioconda::samtools=1.10" : null)
-    container "quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0"
+    conda (params.enable_conda ? "bioconda::bowtie=1.3.0 bioconda::samtools=1.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0"
+    } else {
+        container "quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0"
+    }
 
     input:
     tuple val(meta), path(reads)
diff --git a/software/bowtie/align/meta.yml b/software/bowtie/align/meta.yml
index fc18a2c9..633ef56a 100644
--- a/software/bowtie/align/meta.yml
+++ b/software/bowtie/align/meta.yml
@@ -29,6 +29,11 @@ params:
         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.
     - save_unaligned:
         type: boolean
         description: Save unaligned reads
diff --git a/software/bowtie/index/main.nf b/software/bowtie/index/main.nf
index 5a0e18e5..1a3801b6 100644
--- a/software/bowtie/index/main.nf
+++ b/software/bowtie/index/main.nf
@@ -11,9 +11,12 @@ process BOWTIE_INDEX {
         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::bowtie=1.3.0" : null)
-    container "quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1"
-    
+    conda (params.enable_conda ? "bioconda::bowtie=1.3.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bowtie:1.3.0--py38hed8969a_1"
+    } else {
+        container "quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1"
+    }
 
     input:
     path fasta
diff --git a/software/bowtie/index/meta.yml b/software/bowtie/index/meta.yml
index 0a8c23f7..db781a0a 100644
--- a/software/bowtie/index/meta.yml
+++ b/software/bowtie/index/meta.yml
@@ -29,6 +29,11 @@ params:
         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:
     - fasta:
         type: file

From 8d3fc30eb3d6d649f376f886c6f835186e06663e Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Thu, 17 Dec 2020 07:39:34 +0100
Subject: [PATCH 12/25] fixed yml formatting

---
 .github/workflows/bowtie_align.yml |  6 +--
 .github/workflows/bowtie_index.yml | 67 +++++++++++++++---------------
 2 files changed, 36 insertions(+), 37 deletions(-)

diff --git a/.github/workflows/bowtie_align.yml b/.github/workflows/bowtie_align.yml
index e3b645c8..8b9a19fe 100644
--- a/.github/workflows/bowtie_align.yml
+++ b/.github/workflows/bowtie_align.yml
@@ -26,10 +26,10 @@ jobs:
 
             - name: Install Nextflow
               env:
-                NXF_VER: ${{ matrix.nxf_version }}
+                  NXF_VER: ${{ matrix.nxf_version }}
               run: |
-              wget -qO- get.nextflow.io | bash
-              sudo mv nextflow /usr/local/bin/
+                  wget -qO- get.nextflow.io | bash
+                  sudo mv nextflow /usr/local/bin/
 
             - name: Set up Python
               uses: actions/setup-python@v2
diff --git a/.github/workflows/bowtie_index.yml b/.github/workflows/bowtie_index.yml
index 9f5aa8ac..291d04f5 100644
--- a/.github/workflows/bowtie_index.yml
+++ b/.github/workflows/bowtie_index.yml
@@ -1,41 +1,40 @@
 name: bowtie_index
 on:
-    push:
-        paths:
-            - software/bowtie/index/**
-            - .github/workflows/bowtie_index.yml
-            - tests/software/bowtie/**
-    pull_request:
-        paths:
-            - software/bowtie/index/**
-            - .github/workflows/bowtie_index.yml
-            - tests/software/bowtie/**
+  push:
+    paths:
+      - software/bowtie/index/**
+      - .github/workflows/bowtie_index.yml
+      - tests/software/bowtie/**
+  pull_request:
+    paths:
+      - software/bowtie/index/**
+      - .github/workflows/bowtie_index.yml
+      - tests/software/bowtie/**
 
 jobs:
-    ci_test:
-        runs-on: ubuntu-latest
-        strategy:
-            matrix:
-                nxf_version: [20.11.0-edge]
+  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_ANSI_LOG: false
-        steps:
-            - uses: actions/checkout@v2
+          NXF_VER: ${{ matrix.nxf_version }}
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
 
-            - 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
 
-
-            - 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 bowtie_index --symlink --wt 2
+      # Test the module
+      - run: pytest --tag bowtie_index --symlink --wt 2

From 57ab6dbcbf6e891c08133130c337cade188aefd8 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Thu, 17 Dec 2020 10:24:48 +0100
Subject: [PATCH 13/25] groovy formatting

---
 software/bowtie/align/main.nf | 18 +++++++++---------
 software/bowtie/index/main.nf | 12 ++++++------
 2 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/software/bowtie/align/main.nf b/software/bowtie/align/main.nf
index 58906d61..4271d33a 100644
--- a/software/bowtie/align/main.nf
+++ b/software/bowtie/align/main.nf
@@ -11,21 +11,21 @@ process BOWTIE_ALIGN {
         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::bowtie=1.3.0 bioconda::samtools=1.10" : null)
+    conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.10' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0"
+        container 'https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0'
     } else {
-        container "quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0"
+        container 'quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0'
     }
 
     input:
     tuple val(meta), path(reads)
     path  index
-    
+
     output:
-    tuple val(meta), path("*.bam"), emit: bam
-    tuple val(meta), path("*.out"), emit: log
-    path  "bowtie.version.txt", emit: version
+    tuple val(meta), path('*.bam'), emit: bam
+    tuple val(meta), path('*.out'), emit: log
+    path  'bowtie.version.txt', emit: version
 
     script:
     def software  = getSoftwareName(task.process)
@@ -39,10 +39,10 @@ process BOWTIE_ALIGN {
         --sam \\
         -x \$INDEX \\
         -q \\
-	    $unaligned \\
+        $unaligned \\
         $options.args \\
         $endedness \\
-	    2> ${prefix}.out \\
+        2> ${prefix}.out \\
         | samtools view $options.args2 -@ $task.cpus -bS -o ${prefix}.bam -
 
     bowtie --version | head -n 1 | cut -d" " -f3 > ${software}.version.txt
diff --git a/software/bowtie/index/main.nf b/software/bowtie/index/main.nf
index 1a3801b6..38f1c289 100644
--- a/software/bowtie/index/main.nf
+++ b/software/bowtie/index/main.nf
@@ -11,19 +11,19 @@ process BOWTIE_INDEX {
         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::bowtie=1.3.0" : null)
+    conda (params.enable_conda ? 'bioconda::bowtie=1.3.0' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/bowtie:1.3.0--py38hed8969a_1"
+        container 'https://depot.galaxyproject.org/singularity/bowtie:1.3.0--py38hed8969a_1'
     } else {
-        container "quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1"
+        container 'quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1'
     }
 
     input:
     path fasta
 
     output:
-    path "bowtie", emit: index
-    path "*.version.txt", emit: version
+    path 'bowtie', emit: index
+    path '*.version.txt', emit: version
 
     script:
     def software  = getSoftwareName(task.process)
@@ -32,4 +32,4 @@ process BOWTIE_INDEX {
     bowtie-build --threads $task.cpus ${fasta} bowtie/${fasta.baseName}.index
     bowtie --version | head -n 1 | cut -d" " -f3 > ${software}.version.txt
     """
-}
\ No newline at end of file
+}

From 41329b89820c92c63bdf1212e4df3935137aac05 Mon Sep 17 00:00:00 2001
From: Kevin Menden <kevin.menden@t-online.de>
Date: Fri, 18 Dec 2020 08:16:18 +0100
Subject: [PATCH 14/25] Apply suggestions from code review

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

diff --git a/software/bowtie/align/main.nf b/software/bowtie/align/main.nf
index 4271d33a..03bfd6e7 100644
--- a/software/bowtie/align/main.nf
+++ b/software/bowtie/align/main.nf
@@ -25,7 +25,7 @@ process BOWTIE_ALIGN {
     output:
     tuple val(meta), path('*.bam'), emit: bam
     tuple val(meta), path('*.out'), emit: log
-    path  'bowtie.version.txt', emit: version
+    path  '*.version.txt'         , emit: version
 
     script:
     def software  = getSoftwareName(task.process)
@@ -45,6 +45,6 @@ process BOWTIE_ALIGN {
         2> ${prefix}.out \\
         | samtools view $options.args2 -@ $task.cpus -bS -o ${prefix}.bam -
 
-    bowtie --version | head -n 1 | cut -d" " -f3 > ${software}.version.txt
+    echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//' > ${software}.version.txt
     """
 }
diff --git a/software/bowtie/index/main.nf b/software/bowtie/index/main.nf
index 38f1c289..8b982bcf 100644
--- a/software/bowtie/index/main.nf
+++ b/software/bowtie/index/main.nf
@@ -29,7 +29,7 @@ process BOWTIE_INDEX {
     def software  = getSoftwareName(task.process)
     """
     mkdir bowtie
-    bowtie-build --threads $task.cpus ${fasta} bowtie/${fasta.baseName}.index
-    bowtie --version | head -n 1 | cut -d" " -f3 > ${software}.version.txt
+    bowtie-build --threads $task.cpus $fasta bowtie/${fasta.baseName}
+    echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//' > ${software}.version.txt
     """
 }

From dc4108fd9b9d2982d84d24a7f765e5c5a0d3364d Mon Sep 17 00:00:00 2001
From: Kevin Menden <kevin.menden@t-online.de>
Date: Fri, 18 Dec 2020 09:13:35 +0100
Subject: [PATCH 15/25] Update software/bowtie/align/meta.yml

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

diff --git a/software/bowtie/align/meta.yml b/software/bowtie/align/meta.yml
index 633ef56a..50f5e8d0 100644
--- a/software/bowtie/align/meta.yml
+++ b/software/bowtie/align/meta.yml
@@ -53,7 +53,7 @@ input:
         description: Bowtie genome index files
         pattern: "*.ebwt"
 output:
-    - sam:
+    - bam:
         type: file
         description: Output SAM file containing read alignments
         pattern: "*.{sam}"

From a7f1ff29d7baf10417efc22dbc8de52dc8700ccc Mon Sep 17 00:00:00 2001
From: Kevin Menden <kevin.menden@t-online.de>
Date: Fri, 18 Dec 2020 09:13:42 +0100
Subject: [PATCH 16/25] Update software/bowtie/align/meta.yml

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

diff --git a/software/bowtie/align/meta.yml b/software/bowtie/align/meta.yml
index 50f5e8d0..b6909b61 100644
--- a/software/bowtie/align/meta.yml
+++ b/software/bowtie/align/meta.yml
@@ -56,7 +56,7 @@ output:
     - bam:
         type: file
         description: Output SAM file containing read alignments
-        pattern: "*.{sam}"
+        pattern: "*.{bam}"
     - version:
         type: file
         description: File containing software version

From 7805d25cc56190ac1ad88f0634fb32458cbc4379 Mon Sep 17 00:00:00 2001
From: Kevin Menden <kevin.menden@t-online.de>
Date: Fri, 18 Dec 2020 09:13:48 +0100
Subject: [PATCH 17/25] Update software/bowtie/align/meta.yml

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

diff --git a/software/bowtie/align/meta.yml b/software/bowtie/align/meta.yml
index b6909b61..72f7c0b5 100644
--- a/software/bowtie/align/meta.yml
+++ b/software/bowtie/align/meta.yml
@@ -55,7 +55,7 @@ input:
 output:
     - bam:
         type: file
-        description: Output SAM file containing read alignments
+        description: Output BAM file containing read alignments
         pattern: "*.{bam}"
     - version:
         type: file

From f840325eadf2c9853ca6b02f3c8a4d48cccc3ff4 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Fri, 18 Dec 2020 09:14:40 +0100
Subject: [PATCH 18/25] added unaligned output

---
 software/bowtie/align/main.nf  | 11 +++++
 software/bowtie/align/meta.yml | 88 ++++++++++++++++++----------------
 2 files changed, 57 insertions(+), 42 deletions(-)

diff --git a/software/bowtie/align/main.nf b/software/bowtie/align/main.nf
index 03bfd6e7..43425ca5 100644
--- a/software/bowtie/align/main.nf
+++ b/software/bowtie/align/main.nf
@@ -26,6 +26,8 @@ process BOWTIE_ALIGN {
     tuple val(meta), path('*.bam'), emit: bam
     tuple val(meta), path('*.out'), emit: log
     path  '*.version.txt'         , emit: version
+    tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq
+    path 'test.txt', emit: test
 
     script:
     def software  = getSoftwareName(task.process)
@@ -45,6 +47,15 @@ process BOWTIE_ALIGN {
         2> ${prefix}.out \\
         | samtools view $options.args2 -@ $task.cpus -bS -o ${prefix}.bam -
 
+    touch test.txt
+    if [ -f ${prefix}.unmapped.fastq ]; then
+        gzip ${prefix}.unmapped.fastq
+    fi
+    if [ -f ${prefix}.unmapped_1.fastq ]; then
+        gzip ${prefix}.unmapped_1.fastq
+        gzip ${prefix}.unmapped_2.fastq
+    fi
+
     echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//' > ${software}.version.txt
     """
 }
diff --git a/software/bowtie/align/meta.yml b/software/bowtie/align/meta.yml
index 633ef56a..b7dbdb83 100644
--- a/software/bowtie/align/meta.yml
+++ b/software/bowtie/align/meta.yml
@@ -7,59 +7,63 @@ keywords:
     - reference
 tools:
     - bowtie:
-        description: |
-            bowtie is a software package for mapping DNA sequences against
-            a large reference genome, such as the human genome.
-        homepage: http://bowtie-bio.sourceforge.net/index.shtml
-        documentation: http://bowtie-bio.sourceforge.net/manual.shtml
-        arxiv: arXiv:1303.3997
+          description: |
+              bowtie is a software package for mapping DNA sequences against
+              a large reference genome, such as the human genome.
+          homepage: http://bowtie-bio.sourceforge.net/index.shtml
+          documentation: http://bowtie-bio.sourceforge.net/manual.shtml
+          arxiv: arXiv:1303.3997
 params:
     - outdir:
-        type: string
-        description: |
-            The pipeline's output directory. By default, the module will
-            output files into `$params.outdir/<SOFTWARE>`
+          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.
+          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
+          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.
+          type: boolean
+          description: |
+              Instead of directly downloading Singularity images for use with Singularity,
+              force the workflow to pull and convert Docker containers instead.
     - save_unaligned:
-        type: boolean
-        description: Save unaligned reads
+          type: boolean
+          description: Save unaligned reads
 input:
     - meta:
-        type: map
-        description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+          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.
+          type: file
+          description: |
+              List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+              respectively.
     - index:
-        type: file
-        description: Bowtie genome index files
-        pattern: "*.ebwt"
+          type: file
+          description: Bowtie genome index files
+          pattern: "*.ebwt"
 output:
-    - sam:
-        type: file
-        description: Output SAM file containing read alignments
-        pattern: "*.{sam}"
+    - bam:
+          type: file
+          description: Output SAM file containing read alignments
+          pattern: "*.{bam}"
     - version:
-        type: file
-        description: File containing software version
-        pattern: "*.{version.txt}"
+          type: file
+          description: File containing software version
+          pattern: "*.{version.txt}"
+    - fastq:
+          type: file
+          description: Unaligned FastQ files
+          pattern: "*.fastq.gz"
 authors:
     - "@kevinmenden"

From 0eb20c14bf17d47419111dd5ebce7071dcf39569 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Fri, 18 Dec 2020 09:20:35 +0100
Subject: [PATCH 19/25] fixed unaligned output

---
 software/bowtie/align/main.nf | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/software/bowtie/align/main.nf b/software/bowtie/align/main.nf
index 43425ca5..de9e8b3d 100644
--- a/software/bowtie/align/main.nf
+++ b/software/bowtie/align/main.nf
@@ -27,12 +27,11 @@ process BOWTIE_ALIGN {
     tuple val(meta), path('*.out'), emit: log
     path  '*.version.txt'         , emit: version
     tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq
-    path 'test.txt', emit: test
 
     script:
     def software  = getSoftwareName(task.process)
     def prefix    = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def unaligned = params.save_unaligned ? "--un ${prefix}.unmapped" : ''
+    def unaligned = params.save_unaligned ? "--un ${prefix}.unmapped.fastq" : ''
     def endedness = meta.single_end ? "$reads" : "-1 ${reads[0]} -2 ${reads[1]}"
     """
     INDEX=`find -L ./ -name "*.3.ebwt" | sed 's/.3.ebwt//'`
@@ -47,7 +46,6 @@ process BOWTIE_ALIGN {
         2> ${prefix}.out \\
         | samtools view $options.args2 -@ $task.cpus -bS -o ${prefix}.bam -
 
-    touch test.txt
     if [ -f ${prefix}.unmapped.fastq ]; then
         gzip ${prefix}.unmapped.fastq
     fi

From 07f0a2476a4729166cc623cfef1e7b8d295c182e Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Fri, 18 Dec 2020 09:50:05 +0100
Subject: [PATCH 20/25] fixed linting errors

---
 software/bowtie/align/functions.nf |  3 +-
 software/bowtie/index/functions.nf |  3 +-
 software/bowtie/index/meta.yml     | 60 +++++++++++++++---------------
 tests/software/bowtie/test.yml     |  6 +--
 4 files changed, 36 insertions(+), 36 deletions(-)

diff --git a/software/bowtie/align/functions.nf b/software/bowtie/align/functions.nf
index b3ac3801..55d5271c 100644
--- a/software/bowtie/align/functions.nf
+++ b/software/bowtie/align/functions.nf
@@ -1,3 +1,4 @@
+
 /*
  * -----------------------------------------------------
  *  Utility functions used in nf-core DSL2 module files
@@ -56,4 +57,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}
\ No newline at end of file
diff --git a/software/bowtie/index/functions.nf b/software/bowtie/index/functions.nf
index b3ac3801..55d5271c 100644
--- a/software/bowtie/index/functions.nf
+++ b/software/bowtie/index/functions.nf
@@ -1,3 +1,4 @@
+
 /*
  * -----------------------------------------------------
  *  Utility functions used in nf-core DSL2 module files
@@ -56,4 +57,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}
\ No newline at end of file
diff --git a/software/bowtie/index/meta.yml b/software/bowtie/index/meta.yml
index db781a0a..e5296b05 100644
--- a/software/bowtie/index/meta.yml
+++ b/software/bowtie/index/meta.yml
@@ -7,45 +7,45 @@ keywords:
     - reference
 tools:
     - bowtie:
-        description: |
-            bowtie is a software package for mapping DNA sequences against
-            a large reference genome, such as the human genome.
-        homepage: http://bowtie-bio.sourceforge.net/index.shtml
-        documentation: http://bowtie-bio.sourceforge.net/manual.shtml
-        arxiv: arXiv:1303.3997
+          description: |
+              bowtie is a software package for mapping DNA sequences against
+              a large reference genome, such as the human genome.
+          homepage: http://bowtie-bio.sourceforge.net/index.shtml
+          documentation: http://bowtie-bio.sourceforge.net/manual.shtml
+          arxiv: arXiv:1303.3997
 params:
     - outdir:
-        type: string
-        description: |
-            The pipeline's output directory. By default, the module will
-            output files into `$params.outdir/<SOFTWARE>`
+          type: string
+          description: |
+              The pipeline's output directory. By default, the module will
+              output files into `$params.outdir/<SOFTWARE>`
     - publish_dir_mode:
-        type: string
-        description: |
-            Value for the Nextflow `publishDir` mode parameter.
-            Available: symlink, rellink, link, copy, copyNoFollow, move.
+          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
+          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.        
+          type: boolean
+          description: |
+              Instead of directly downloading Singularity images for use with Singularity,
+              force the workflow to pull and convert Docker containers instead.
 input:
     - fasta:
-        type: file
-        description: Input genome fasta file
+          type: file
+          description: Input genome fasta file
 output:
     - index:
-        type: file
-        description: Bowtie genome index files
-        pattern: "*.ebwt"
+          type: file
+          description: Bowtie genome index files
+          pattern: "*.ebwt"
     - version:
-        type: file
-        description: File containing software version
-        pattern: "*.{version.txt}"
+          type: file
+          description: File containing software version
+          pattern: "*.{version.txt}"
 authors:
     - "@kevinmenden"
diff --git a/tests/software/bowtie/test.yml b/tests/software/bowtie/test.yml
index 6a28578d..8d6404bc 100644
--- a/tests/software/bowtie/test.yml
+++ b/tests/software/bowtie/test.yml
@@ -17,7 +17,7 @@
     - path: output/bowtie/bowtie/NC_010473.index.rev.2.ebwt
       md5sum: f3c398bba5158f4039334a932d79c051
 
-- name: Run bowtie index and align signle-end
+- name: Run bowtie index and align single-end
   command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
   tags:
     - bowtie
@@ -40,8 +40,7 @@
     - path: output/bowtie/test.bam
       md5sum: 8179c68a819accbc9137dc881736106f
 
-
-- name: Run bowtie index and align paired_end
+- name: Run bowtie index and align paired-end
   command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_paired_end -c tests/config/nextflow.config
   tags:
     - bowtie
@@ -63,4 +62,3 @@
       md5sum: a23e9a2a76e949aeb3693bcfae41a615
     - path: output/bowtie/test.bam
       md5sum: 9ce5aebf37128f4bb1d24e9548e22009
-

From 0be13edc52acbc27131da6a24e76f139c776ecb6 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Fri, 18 Dec 2020 09:52:38 +0100
Subject: [PATCH 21/25] next try at editorconfig

---
 software/bowtie/align/functions.nf | 2 +-
 software/bowtie/index/functions.nf | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/software/bowtie/align/functions.nf b/software/bowtie/align/functions.nf
index 55d5271c..f237d7f0 100644
--- a/software/bowtie/align/functions.nf
+++ b/software/bowtie/align/functions.nf
@@ -57,4 +57,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
\ No newline at end of file
+}
diff --git a/software/bowtie/index/functions.nf b/software/bowtie/index/functions.nf
index 55d5271c..f237d7f0 100644
--- a/software/bowtie/index/functions.nf
+++ b/software/bowtie/index/functions.nf
@@ -57,4 +57,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
\ No newline at end of file
+}

From 299a3fa07e751da60680d1efad9f87f6d9e7fb88 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Fri, 18 Dec 2020 10:58:37 +0100
Subject: [PATCH 22/25] adding .index back

---
 software/bowtie/index/main.nf | 2 +-
 tests/software/bowtie/main.nf | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/software/bowtie/index/main.nf b/software/bowtie/index/main.nf
index 8b982bcf..b0156381 100644
--- a/software/bowtie/index/main.nf
+++ b/software/bowtie/index/main.nf
@@ -29,7 +29,7 @@ process BOWTIE_INDEX {
     def software  = getSoftwareName(task.process)
     """
     mkdir bowtie
-    bowtie-build --threads $task.cpus $fasta bowtie/${fasta.baseName}
+    bowtie-build --threads $task.cpus $fasta bowtie/${fasta.baseName}.index
     echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//' > ${software}.version.txt
     """
 }
diff --git a/tests/software/bowtie/main.nf b/tests/software/bowtie/main.nf
index 6b4e24e6..c496a619 100644
--- a/tests/software/bowtie/main.nf
+++ b/tests/software/bowtie/main.nf
@@ -31,4 +31,3 @@ workflow test_bowtie_alignment_paired_end {
                 file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
     BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
 }
-

From db0b631906d16561036434c00c775890f2d5a55d Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Fri, 18 Dec 2020 11:06:02 +0100
Subject: [PATCH 23/25] removed index from test output

---
 software/bowtie/index/main.nf  |  2 +-
 tests/software/bowtie/test.yml | 36 +++++++++++++++++-----------------
 2 files changed, 19 insertions(+), 19 deletions(-)

diff --git a/software/bowtie/index/main.nf b/software/bowtie/index/main.nf
index b0156381..8b982bcf 100644
--- a/software/bowtie/index/main.nf
+++ b/software/bowtie/index/main.nf
@@ -29,7 +29,7 @@ process BOWTIE_INDEX {
     def software  = getSoftwareName(task.process)
     """
     mkdir bowtie
-    bowtie-build --threads $task.cpus $fasta bowtie/${fasta.baseName}.index
+    bowtie-build --threads $task.cpus $fasta bowtie/${fasta.baseName}
     echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//' > ${software}.version.txt
     """
 }
diff --git a/tests/software/bowtie/test.yml b/tests/software/bowtie/test.yml
index 8d6404bc..188b8119 100644
--- a/tests/software/bowtie/test.yml
+++ b/tests/software/bowtie/test.yml
@@ -4,17 +4,17 @@
     - bowtie
     - bowtie_index
   files:
-    - path: output/bowtie/bowtie/NC_010473.index.1.ebwt
+    - path: output/bowtie/bowtie/NC_010473.1.ebwt
       md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
-    - path: output/bowtie/bowtie/NC_010473.index.2.ebwt
+    - path: output/bowtie/bowtie/NC_010473.2.ebwt
       md5sum: bfd10c5319c6a0dbc540fd789254a5dd
-    - path: output/bowtie/bowtie/NC_010473.index.3.ebwt
+    - path: output/bowtie/bowtie/NC_010473.3.ebwt
       md5sum: cd201e81724f3099131aec16ef2cc53b
-    - path: output/bowtie/bowtie/NC_010473.index.4.ebwt
+    - path: output/bowtie/bowtie/NC_010473.4.ebwt
       md5sum: bbb9d6d21ad765d135f95290204e8433
-    - path: output/bowtie/bowtie/NC_010473.index.rev.1.ebwt
+    - path: output/bowtie/bowtie/NC_010473.rev.1.ebwt
       md5sum: 44f719c2fe42e1f35d54e798775846d1
-    - path: output/bowtie/bowtie/NC_010473.index.rev.2.ebwt
+    - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
       md5sum: f3c398bba5158f4039334a932d79c051
 
 - name: Run bowtie index and align single-end
@@ -23,17 +23,17 @@
     - bowtie
     - bowtie_align
   files:
-    - path: output/bowtie/bowtie/NC_010473.index.1.ebwt
+    - path: output/bowtie/bowtie/NC_010473.1.ebwt
       md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
-    - path: output/bowtie/bowtie/NC_010473.index.2.ebwt
+    - path: output/bowtie/bowtie/NC_010473.2.ebwt
       md5sum: bfd10c5319c6a0dbc540fd789254a5dd
-    - path: output/bowtie/bowtie/NC_010473.index.3.ebwt
+    - path: output/bowtie/bowtie/NC_010473.3.ebwt
       md5sum: cd201e81724f3099131aec16ef2cc53b
-    - path: output/bowtie/bowtie/NC_010473.index.4.ebwt
+    - path: output/bowtie/bowtie/NC_010473.4.ebwt
       md5sum: bbb9d6d21ad765d135f95290204e8433
-    - path: output/bowtie/bowtie/NC_010473.index.rev.1.ebwt
+    - path: output/bowtie/bowtie/NC_010473.rev.1.ebwt
       md5sum: 44f719c2fe42e1f35d54e798775846d1
-    - path: output/bowtie/bowtie/NC_010473.index.rev.2.ebwt
+    - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
       md5sum: f3c398bba5158f4039334a932d79c051
     - path: output/bowtie/test.out
       md5sum: a81cb18024616415a6cec3108a36fccd
@@ -46,17 +46,17 @@
     - bowtie
     - bowtie_align
   files:
-    - path: output/bowtie/bowtie/NC_010473.index.1.ebwt
+    - path: output/bowtie/bowtie/NC_010473.1.ebwt
       md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
-    - path: output/bowtie/bowtie/NC_010473.index.2.ebwt
+    - path: output/bowtie/bowtie/NC_010473.2.ebwt
       md5sum: bfd10c5319c6a0dbc540fd789254a5dd
-    - path: output/bowtie/bowtie/NC_010473.index.3.ebwt
+    - path: output/bowtie/bowtie/NC_010473.3.ebwt
       md5sum: cd201e81724f3099131aec16ef2cc53b
-    - path: output/bowtie/bowtie/NC_010473.index.4.ebwt
+    - path: output/bowtie/bowtie/NC_010473.4.ebwt
       md5sum: bbb9d6d21ad765d135f95290204e8433
-    - path: output/bowtie/bowtie/NC_010473.index.rev.1.ebwt
+    - path: output/bowtie/bowtie/NC_010473.rev.1.ebwt
       md5sum: 44f719c2fe42e1f35d54e798775846d1
-    - path: output/bowtie/bowtie/NC_010473.index.rev.2.ebwt
+    - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
       md5sum: f3c398bba5158f4039334a932d79c051
     - path: output/bowtie/test.out
       md5sum: a23e9a2a76e949aeb3693bcfae41a615

From 32f6191ff31d40df5c565fe367b1c1f844d85da8 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Fri, 18 Dec 2020 11:11:19 +0100
Subject: [PATCH 24/25] editorconfig

---
 software/bowtie/align/functions.nf | 120 ++++++++++++++---------------
 software/bowtie/index/functions.nf | 120 ++++++++++++++---------------
 2 files changed, 120 insertions(+), 120 deletions(-)

diff --git a/software/bowtie/align/functions.nf b/software/bowtie/align/functions.nf
index f237d7f0..6f3b4b29 100644
--- a/software/bowtie/align/functions.nf
+++ b/software/bowtie/align/functions.nf
@@ -1,60 +1,60 @@
-
-/*
- * -----------------------------------------------------
- *  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"
-        }
-    }
-}
+
+/*
+ * -----------------------------------------------------
+ *  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/bowtie/index/functions.nf b/software/bowtie/index/functions.nf
index f237d7f0..6f3b4b29 100644
--- a/software/bowtie/index/functions.nf
+++ b/software/bowtie/index/functions.nf
@@ -1,60 +1,60 @@
-
-/*
- * -----------------------------------------------------
- *  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"
-        }
-    }
-}
+
+/*
+ * -----------------------------------------------------
+ *  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"
+        }
+    }
+}

From 8f75bac67e70b49c272c9436e0157098f71b139e Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Fri, 18 Dec 2020 11:16:58 +0100
Subject: [PATCH 25/25] update test.bam md5sums

---
 tests/software/bowtie/test.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/software/bowtie/test.yml b/tests/software/bowtie/test.yml
index 188b8119..229165ac 100644
--- a/tests/software/bowtie/test.yml
+++ b/tests/software/bowtie/test.yml
@@ -38,7 +38,7 @@
     - path: output/bowtie/test.out
       md5sum: a81cb18024616415a6cec3108a36fccd
     - path: output/bowtie/test.bam
-      md5sum: 8179c68a819accbc9137dc881736106f
+      md5sum: 9feed8a55d4b5e600dcc577768ef07fc
 
 - name: Run bowtie index and align paired-end
   command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_paired_end -c tests/config/nextflow.config
@@ -61,4 +61,4 @@
     - path: output/bowtie/test.out
       md5sum: a23e9a2a76e949aeb3693bcfae41a615
     - path: output/bowtie/test.bam
-      md5sum: 9ce5aebf37128f4bb1d24e9548e22009
+      md5sum: cf6a6381aa504e8342638ff3b509721e