From 89eee34df9a98a170af185cc4bd4f28b6816741a Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Wed, 16 Dec 2020 11:04:46 +0000
Subject: [PATCH 01/18] seacr | Added callpeak skeletonmain.nf

---
 software/seacr/callpeak/functions.nf | 59 ++++++++++++++++++++++++++++
 software/seacr/callpeak/main.nf      |  0
 software/seacr/callpeak/meta.yml     |  0
 3 files changed, 59 insertions(+)
 create mode 100644 software/seacr/callpeak/functions.nf
 create mode 100644 software/seacr/callpeak/main.nf
 create mode 100644 software/seacr/callpeak/meta.yml

diff --git a/software/seacr/callpeak/functions.nf b/software/seacr/callpeak/functions.nf
new file mode 100644
index 00000000..b3ac3801
--- /dev/null
+++ b/software/seacr/callpeak/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/seacr/callpeak/main.nf b/software/seacr/callpeak/main.nf
new file mode 100644
index 00000000..e69de29b
diff --git a/software/seacr/callpeak/meta.yml b/software/seacr/callpeak/meta.yml
new file mode 100644
index 00000000..e69de29b

From 3ff2b558e026840044ad7e446c30342a39ca9b7e Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Wed, 16 Dec 2020 11:04:46 +0000
Subject: [PATCH 02/18] seacr | Added callpeak skeleton

---
 software/seacr/callpeak/functions.nf | 59 ++++++++++++++++++++++++++++
 software/seacr/callpeak/main.nf      |  0
 software/seacr/callpeak/meta.yml     |  0
 3 files changed, 59 insertions(+)
 create mode 100644 software/seacr/callpeak/functions.nf
 create mode 100644 software/seacr/callpeak/main.nf
 create mode 100644 software/seacr/callpeak/meta.yml

diff --git a/software/seacr/callpeak/functions.nf b/software/seacr/callpeak/functions.nf
new file mode 100644
index 00000000..b3ac3801
--- /dev/null
+++ b/software/seacr/callpeak/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/seacr/callpeak/main.nf b/software/seacr/callpeak/main.nf
new file mode 100644
index 00000000..e69de29b
diff --git a/software/seacr/callpeak/meta.yml b/software/seacr/callpeak/meta.yml
new file mode 100644
index 00000000..e69de29b

From 74e7b5385f3fb1a5c37c65a3f2b6a9d45ea9f8f2 Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Thu, 17 Dec 2020 13:54:48 +0000
Subject: [PATCH 03/18] seacr | Added main process structure

---
 software/seacr/callpeak/main.nf | 41 +++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/software/seacr/callpeak/main.nf b/software/seacr/callpeak/main.nf
index e69de29b..3fcdf05d 100644
--- a/software/seacr/callpeak/main.nf
+++ b/software/seacr/callpeak/main.nf
@@ -0,0 +1,41 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process SEACR_CALLPEAK {
+    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::seacr=1.3" : null)
+
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0"
+    } else {
+        container 'quay.io/biocontainers/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0'
+    }
+    
+    input:
+    tuple val(meta), path(bedgraph), path(ctrlbedgraph)
+    
+    output:
+    tuple val(meta), path("*.bed"), emit: bed
+    path "*.version.txt"          , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+     SEACR_1.3.sh \\
+        $bedgraph \\
+        $ctrlbedgraph \\
+        $options.args \\
+        $prefix
+
+    echo 1.3' > ${software}.version.txt
+    """
+}

From a964d98d7fe2c9047bf6052ab9c683a5abd525f8 Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Thu, 17 Dec 2020 13:55:58 +0000
Subject: [PATCH 04/18] seacr | Added test data

---
 tests/data/bedgraph/IgG_1_to_chr20.bedgraph   | 10234 +++++++++
 tests/data/bedgraph/IgG_2_to_chr20.bedgraph   |  6879 ++++++
 .../data/bedgraph/K27me3_1_to_chr20.bedgraph  | 12451 ++++++++++
 .../data/bedgraph/K27me3_2_to_chr20.bedgraph  | 18871 ++++++++++++++++
 4 files changed, 48435 insertions(+)
 create mode 100644 tests/data/bedgraph/IgG_1_to_chr20.bedgraph
 create mode 100644 tests/data/bedgraph/IgG_2_to_chr20.bedgraph
 create mode 100644 tests/data/bedgraph/K27me3_1_to_chr20.bedgraph
 create mode 100644 tests/data/bedgraph/K27me3_2_to_chr20.bedgraph

diff --git a/tests/data/bedgraph/IgG_1_to_chr20.bedgraph b/tests/data/bedgraph/IgG_1_to_chr20.bedgraph
new file mode 100644
index 00000000..c218e58d
--- /dev/null
+++ b/tests/data/bedgraph/IgG_1_to_chr20.bedgraph
@@ -0,0 +1,10234 @@
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diff --git a/tests/data/bedgraph/IgG_2_to_chr20.bedgraph b/tests/data/bedgraph/IgG_2_to_chr20.bedgraph
new file mode 100644
index 00000000..d3ed1a15
--- /dev/null
+++ b/tests/data/bedgraph/IgG_2_to_chr20.bedgraph
@@ -0,0 +1,6879 @@
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diff --git a/tests/data/bedgraph/K27me3_1_to_chr20.bedgraph b/tests/data/bedgraph/K27me3_1_to_chr20.bedgraph
new file mode 100644
index 00000000..ce50d2fa
--- /dev/null
+++ b/tests/data/bedgraph/K27me3_1_to_chr20.bedgraph
@@ -0,0 +1,12451 @@
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diff --git a/tests/data/bedgraph/K27me3_2_to_chr20.bedgraph b/tests/data/bedgraph/K27me3_2_to_chr20.bedgraph
new file mode 100644
index 00000000..4fde093c
--- /dev/null
+++ b/tests/data/bedgraph/K27me3_2_to_chr20.bedgraph
@@ -0,0 +1,18871 @@
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From 4e55bdcf8432b36f67425d62d60c91bfaa6f80e4 Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Thu, 17 Dec 2020 14:20:02 +0000
Subject: [PATCH 05/18] seacr | removed test files

---
 tests/data/bedgraph/IgG_2_to_chr20.bedgraph   |  6879 ------
 .../data/bedgraph/K27me3_2_to_chr20.bedgraph  | 18871 ----------------
 2 files changed, 25750 deletions(-)
 delete mode 100644 tests/data/bedgraph/IgG_2_to_chr20.bedgraph
 delete mode 100644 tests/data/bedgraph/K27me3_2_to_chr20.bedgraph

diff --git a/tests/data/bedgraph/IgG_2_to_chr20.bedgraph b/tests/data/bedgraph/IgG_2_to_chr20.bedgraph
deleted file mode 100644
index d3ed1a15..00000000
--- a/tests/data/bedgraph/IgG_2_to_chr20.bedgraph
+++ /dev/null
@@ -1,6879 +0,0 @@
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diff --git a/tests/data/bedgraph/K27me3_2_to_chr20.bedgraph b/tests/data/bedgraph/K27me3_2_to_chr20.bedgraph
deleted file mode 100644
index 4fde093c..00000000
--- a/tests/data/bedgraph/K27me3_2_to_chr20.bedgraph
+++ /dev/null
@@ -1,18871 +0,0 @@
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From b24834dfce788212f29268651321215282545983 Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Thu, 17 Dec 2020 14:20:24 +0000
Subject: [PATCH 06/18] seacr | local testing implimented

---
 software/seacr/callpeak/main.nf |  2 +-
 tests/software/seacr/main.nf    | 20 +++++++++++++++
 tests/software/seacr/test.yml   | 44 +++++++++++++++++++++++++++++++++
 3 files changed, 65 insertions(+), 1 deletion(-)
 create mode 100644 tests/software/seacr/main.nf
 create mode 100644 tests/software/seacr/test.yml

diff --git a/software/seacr/callpeak/main.nf b/software/seacr/callpeak/main.nf
index 3fcdf05d..289b0151 100644
--- a/software/seacr/callpeak/main.nf
+++ b/software/seacr/callpeak/main.nf
@@ -36,6 +36,6 @@ process SEACR_CALLPEAK {
         $options.args \\
         $prefix
 
-    echo 1.3' > ${software}.version.txt
+    echo 1.3 > ${software}.version.txt
     """
 }
diff --git a/tests/software/seacr/main.nf b/tests/software/seacr/main.nf
new file mode 100644
index 00000000..7e3c4164
--- /dev/null
+++ b/tests/software/seacr/main.nf
@@ -0,0 +1,20 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEACR_CALLPEAK } from '../../../software/seacr/callpeak/main.nf' addParams( options: [ args:'norm stringent' ] )
+
+workflow test_seacr_callpeak {
+
+    def input = []
+    input = [[ id:'test_1'],
+              file("${launchDir}/tests/data/bedgraph/K27me3_1_to_chr20.bedgraph", checkIfExists: true),
+              file("${launchDir}/tests/data/bedgraph/IgG_1_to_chr20.bedgraph", checkIfExists: true) ]
+
+    SEACR_CALLPEAK ( input )
+}
+
+// For local testing
+workflow {
+    test_seacr_callpeak()
+}
\ No newline at end of file
diff --git a/tests/software/seacr/test.yml b/tests/software/seacr/test.yml
new file mode 100644
index 00000000..e9ec7ad7
--- /dev/null
+++ b/tests/software/seacr/test.yml
@@ -0,0 +1,44 @@
+- name: Run samtools call peak test workflow
+  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_flagstat -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_flagstat
+  files:
+    - path: output/samtools/test.paired_end.sorted.bam.flagstat
+      md5sum: 80590621c74f5ee43ada20d010a3837f
+
+- name: Run samtools idxstats test workflow
+  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_idxstats -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_idxstats
+  files:
+    - path: output/samtools/test.paired_end.sorted.bam.idxstats
+      md5sum: 3bee8b7d55e412da2b3816c5a18d60d5
+
+- name: Run samtools index test workflow
+  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_index -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_index
+  files:
+    - path: output/samtools/test.paired_end.sorted.bam.bai
+      md5sum: 67338c2995eae82c849830ca55aa7bd1
+
+- name: Run samtools sort test workflow
+  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_sort -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_sort
+  files:
+    - path: output/samtools/test.bam
+      md5sum: a41bfadacd2eeef1d31e05c135cc4f4e
+
+- name: Run samtools stats test workflow
+  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_stats -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_stats
+  files:
+    - path: output/samtools/test.paired_end.sorted.bam.stats
+      md5sum: 06c183864d6e47ab89b0650cae831a93

From 1aa7ed187a4a22ee92e3a0f42de2beccf748eab3 Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Thu, 17 Dec 2020 14:23:07 +0000
Subject: [PATCH 07/18] seacr | Updated gitignore to  ignore output folder

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 54d7a8c1..4e3815b1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,5 +2,6 @@
 work/
 results/
 test_output/
+output/
 .DS_Store
 *.code-workspace

From a57169a5dab1f84285962e1e04a9fb2108651d67 Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Thu, 17 Dec 2020 14:23:20 +0000
Subject: [PATCH 08/18] seacr | updated test script

---
 tests/software/seacr/test.yml | 48 +++++------------------------------
 1 file changed, 6 insertions(+), 42 deletions(-)

diff --git a/tests/software/seacr/test.yml b/tests/software/seacr/test.yml
index e9ec7ad7..88568d35 100644
--- a/tests/software/seacr/test.yml
+++ b/tests/software/seacr/test.yml
@@ -1,44 +1,8 @@
-- name: Run samtools call peak test workflow
-  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_flagstat -c tests/config/nextflow.config
+- name: Run seacr call peak test workflow
+  command: nextflow run ./tests/software/seacr/ -profile docker -entry test_seacr_callpeak -c tests/config/nextflow.config
   tags:
-    - samtools
-    - samtools_flagstat
+    - seacr
+    - seacr_callpeak
   files:
-    - path: output/samtools/test.paired_end.sorted.bam.flagstat
-      md5sum: 80590621c74f5ee43ada20d010a3837f
-
-- name: Run samtools idxstats test workflow
-  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_idxstats -c tests/config/nextflow.config
-  tags:
-    - samtools
-    - samtools_idxstats
-  files:
-    - path: output/samtools/test.paired_end.sorted.bam.idxstats
-      md5sum: 3bee8b7d55e412da2b3816c5a18d60d5
-
-- name: Run samtools index test workflow
-  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_index -c tests/config/nextflow.config
-  tags:
-    - samtools
-    - samtools_index
-  files:
-    - path: output/samtools/test.paired_end.sorted.bam.bai
-      md5sum: 67338c2995eae82c849830ca55aa7bd1
-
-- name: Run samtools sort test workflow
-  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_sort -c tests/config/nextflow.config
-  tags:
-    - samtools
-    - samtools_sort
-  files:
-    - path: output/samtools/test.bam
-      md5sum: a41bfadacd2eeef1d31e05c135cc4f4e
-
-- name: Run samtools stats test workflow
-  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_stats -c tests/config/nextflow.config
-  tags:
-    - samtools
-    - samtools_stats
-  files:
-    - path: output/samtools/test.paired_end.sorted.bam.stats
-      md5sum: 06c183864d6e47ab89b0650cae831a93
+    - path: output/seacr/test_1.stringent.bed
+      md5sum: 3ac70475669eb6a7b8ca89e19a08a28e
\ No newline at end of file

From 15e1b860f9a7cd436152a0faec2fb6626ea31839 Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Thu, 17 Dec 2020 14:25:42 +0000
Subject: [PATCH 09/18] seacr | added github action workflow

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

diff --git a/.github/workflows/seacr_callpeak.yml b/.github/workflows/seacr_callpeak.yml
new file mode 100644
index 00000000..8d342495
--- /dev/null
+++ b/.github/workflows/seacr_callpeak.yml
@@ -0,0 +1,40 @@
+name: seacr_callpeak
+on:
+  push:
+    paths:
+      - software/seacr/callpeak/**
+      - .github/workflows/seacr_callpeak.yml
+      - tests/software/seacr/**
+  pull_request:
+    paths:
+      - software/seacr/callpeak/**
+      - .github/workflows/seacr_callpeak.yml
+      - tests/software/seacr/**
+
+jobs:
+  ci_test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        nxf_version: [20.11.0-edge]
+    env:
+      NXF_ANSI_LOG: false
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          NXF_VER: ${{ matrix.nxf_version }}
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
+
+      # Test the module
+      - run: pytest --tag samtools_flagstat --symlink --wt 2

From 4436f59a1cb1ffe53e7d13d27d99c8feb388602f Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Thu, 17 Dec 2020 14:27:37 +0000
Subject: [PATCH 10/18] seacr | Syntax error

---
 .github/workflows/seacr_callpeak.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/seacr_callpeak.yml b/.github/workflows/seacr_callpeak.yml
index 8d342495..3d73a43e 100644
--- a/.github/workflows/seacr_callpeak.yml
+++ b/.github/workflows/seacr_callpeak.yml
@@ -37,4 +37,4 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag samtools_flagstat --symlink --wt 2
+      - run: pytest --tag seacr_callpeak --symlink --wt 2

From 9c00d1722c4ae6b8c658175f9511ce412a894053 Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Tue, 5 Jan 2021 09:50:47 +0000
Subject: [PATCH 11/18] seacr | PR review changes

---
 software/seacr/callpeak/main.nf | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/software/seacr/callpeak/main.nf b/software/seacr/callpeak/main.nf
index 289b0151..19523c7f 100644
--- a/software/seacr/callpeak/main.nf
+++ b/software/seacr/callpeak/main.nf
@@ -4,6 +4,8 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
 params.options = [:]
 def options    = initOptions(params.options)
 
+def VERSION = '1.3'
+
 process SEACR_CALLPEAK {
     tag "$meta.id"
     label 'process_medium'
@@ -11,8 +13,7 @@ process SEACR_CALLPEAK {
         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::seacr=1.3" : null)
-
+    conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.29.2" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0"
     } else {
@@ -30,12 +31,12 @@ process SEACR_CALLPEAK {
     def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
-     SEACR_1.3.sh \\
+    SEACR_1.3.sh \\
         $bedgraph \\
         $ctrlbedgraph \\
         $options.args \\
         $prefix
 
-    echo 1.3 > ${software}.version.txt
+    echo $VERSION > ${software}.version.txt
     """
 }

From 37840b3855ce8eccc640103b304700f39e0a8793 Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Tue, 5 Jan 2021 09:54:32 +0000
Subject: [PATCH 12/18] seacr | updated trailing whitespace

---
 software/seacr/callpeak/main.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/software/seacr/callpeak/main.nf b/software/seacr/callpeak/main.nf
index 19523c7f..7931e31a 100644
--- a/software/seacr/callpeak/main.nf
+++ b/software/seacr/callpeak/main.nf
@@ -19,10 +19,10 @@ process SEACR_CALLPEAK {
     } else {
         container 'quay.io/biocontainers/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0'
     }
-    
+
     input:
     tuple val(meta), path(bedgraph), path(ctrlbedgraph)
-    
+
     output:
     tuple val(meta), path("*.bed"), emit: bed
     path "*.version.txt"          , emit: version
@@ -39,4 +39,4 @@ process SEACR_CALLPEAK {
 
     echo $VERSION > ${software}.version.txt
     """
-}
+}
\ No newline at end of file

From c110088b5e72760345725b464f333f9a220cc172 Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Tue, 5 Jan 2021 09:56:15 +0000
Subject: [PATCH 13/18] Updated line endings

---
 software/seacr/callpeak/functions.nf | 118 +++++++++++++--------------
 1 file changed, 59 insertions(+), 59 deletions(-)

diff --git a/software/seacr/callpeak/functions.nf b/software/seacr/callpeak/functions.nf
index b3ac3801..d25eea86 100644
--- a/software/seacr/callpeak/functions.nf
+++ b/software/seacr/callpeak/functions.nf
@@ -1,59 +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"
-        }
-    }
-}
+/*
+ * -----------------------------------------------------
+ *  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 e25edbf7b8180043791ce6295ab669efbd0f0e64 Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Tue, 5 Jan 2021 10:18:00 +0000
Subject: [PATCH 14/18] seacr | Added meta file

---
 software/seacr/callpeak/meta.yml | 69 ++++++++++++++++++++++++++++++++
 1 file changed, 69 insertions(+)

diff --git a/software/seacr/callpeak/meta.yml b/software/seacr/callpeak/meta.yml
index e69de29b..3f7cbabc 100644
--- a/software/seacr/callpeak/meta.yml
+++ b/software/seacr/callpeak/meta.yml
@@ -0,0 +1,69 @@
+name: seacr_callpeak
+description: Call peaks using SEACR on sequenced reads in bedgraph format
+keywords:
+    - peak-caller
+    - peaks
+    - bedgraph
+    - cut&tag
+    - cut&run
+    - chromatin
+    - seacr
+tools:
+    - seacr:
+        description: |
+            SEACR is intended to call peaks and enriched regions from sparse CUT&RUN 
+            or chromatin profiling data in which background is dominated by "zeroes" 
+            (i.e. regions with no read coverage).
+        homepage: https://github.com/FredHutch/SEACR
+        documentation: https://github.com/FredHutch/SEACR
+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 ]
+    - bedgraph:
+        type: file
+        description: |
+            The target bedgraph file from which the peaks will be calculated.
+    - ctrlbedgraph:
+        type: file
+        description: |
+            Control (IgG) data bedgraph file to generate an empirical threshold for peak calling.
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bed:
+        type: file
+        description: Bed file containing the calculated peaks.
+        pattern: "*.bed"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@chris-cheshire"
\ No newline at end of file

From 6d34e6964fe4eed6a9a5eedb652c97de28f5839b Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Tue, 5 Jan 2021 10:20:13 +0000
Subject: [PATCH 15/18] seacr | added new line at end

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

diff --git a/software/seacr/callpeak/main.nf b/software/seacr/callpeak/main.nf
index 7931e31a..3d67a058 100644
--- a/software/seacr/callpeak/main.nf
+++ b/software/seacr/callpeak/main.nf
@@ -39,4 +39,4 @@ process SEACR_CALLPEAK {
 
     echo $VERSION > ${software}.version.txt
     """
-}
\ No newline at end of file
+}

From d9818cf3ab6149b6eb277ebea178ee73311bb8b9 Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Tue, 5 Jan 2021 10:21:32 +0000
Subject: [PATCH 16/18] seacr | updated whitespace

---
 software/seacr/callpeak/meta.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/software/seacr/callpeak/meta.yml b/software/seacr/callpeak/meta.yml
index 3f7cbabc..4efedd4f 100644
--- a/software/seacr/callpeak/meta.yml
+++ b/software/seacr/callpeak/meta.yml
@@ -11,9 +11,9 @@ keywords:
 tools:
     - seacr:
         description: |
-            SEACR is intended to call peaks and enriched regions from sparse CUT&RUN 
-            or chromatin profiling data in which background is dominated by "zeroes" 
-            (i.e. regions with no read coverage).
+            SEACR is intended to call peaks and enriched regions from sparse CUT&RUN
+             or chromatin profiling data in which background is dominated by "zeroes"
+             (i.e. regions with no read coverage).
         homepage: https://github.com/FredHutch/SEACR
         documentation: https://github.com/FredHutch/SEACR
 params:
@@ -66,4 +66,4 @@ output:
         description: File containing software version
         pattern: "*.{version.txt}"
 authors:
-    - "@chris-cheshire"
\ No newline at end of file
+    - "@chris-cheshire"

From f6432d3c9c64460f66d6e9ddd16e19e4e902ec91 Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Tue, 5 Jan 2021 10:22:37 +0000
Subject: [PATCH 17/18] seacr | updated whitespace

---
 software/seacr/callpeak/meta.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/software/seacr/callpeak/meta.yml b/software/seacr/callpeak/meta.yml
index 4efedd4f..f95725c9 100644
--- a/software/seacr/callpeak/meta.yml
+++ b/software/seacr/callpeak/meta.yml
@@ -12,8 +12,8 @@ tools:
     - seacr:
         description: |
             SEACR is intended to call peaks and enriched regions from sparse CUT&RUN
-             or chromatin profiling data in which background is dominated by "zeroes"
-             (i.e. regions with no read coverage).
+            or chromatin profiling data in which background is dominated by "zeroes"
+            (i.e. regions with no read coverage).
         homepage: https://github.com/FredHutch/SEACR
         documentation: https://github.com/FredHutch/SEACR
 params:

From 41233763ae55f160e431fabac8ca4873d345a3de Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Mon, 1 Feb 2021 09:46:24 +0000
Subject: [PATCH 18/18] Removed test-datasets submodule

---
 .gitmodules   | 3 ---
 test-datasets | 1 -
 2 files changed, 4 deletions(-)
 delete mode 100644 .gitmodules
 delete mode 160000 test-datasets

diff --git a/.gitmodules b/.gitmodules
deleted file mode 100644
index 44e06649..00000000
--- a/.gitmodules
+++ /dev/null
@@ -1,3 +0,0 @@
-[submodule "test-datasets"]
-    path = test-datasets
-    url = https://github.com/nf-core/test-datasets.git
diff --git a/test-datasets b/test-datasets
deleted file mode 160000
index aae85a5c..00000000
--- a/test-datasets
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit aae85a5c9c72238959108212481ce83bae569709