Merge pull request #21 from CCBR/cutadapt

Use cutadapt CCBR/nf-modules

.nf-core.yml

@@ -0,0 +1 @@
+repository_type: pipeline

MANIFEST.in

@@ -3,7 +3,7 @@ recursive-include bin
 recursive-include conf
 recursive-include assets
 recursive-include modules
-recursive-include submodules
+recursive-include subworkflows
 include CITATION.cff
 include LICENSE
 include VERSION

main.nf

@@ -17,10 +17,10 @@ input        : ${params.input}
 .stripIndent()
 
 // SUBMODULES
-include { INPUT_CHECK } from './submodules/local/input_check.nf'
-include { TRIM_COUNT  } from './submodules/local/trim_count.nf'
-include { MAGECK      } from './submodules/local/mageck.nf'
-include { BAGEL       } from './submodules/local/bagel.nf'
+include { INPUT_CHECK } from './subworkflows/local/input_check.nf'
+include { TRIM_COUNT  } from './subworkflows/local/trim_count.nf'
+include { MAGECK      } from './subworkflows/local/mageck.nf'
+include { BAGEL       } from './subworkflows/local/bagel.nf'
 
 // MODULES
 include { DRUGZ } from './modules/local/drugz.nf'

modules.json

@@ -0,0 +1,17 @@
+{
+    "name": "CCBR/CRUISE",
+    "homePage": "https://github.com/CCBR/CRUISE",
+    "repos": {
+        "https://github.com/CCBR/nf-modules": {
+            "modules": {
+                "CCBR": {
+                    "cutadapt": {
+                        "branch": "main",
+                        "git_sha": "a3525c765b76400269695235bbf164a948604c4a",
+                        "installed_by": ["modules"]
+                    }
+                }
+            }
+        }
+    }
+}

modules/CCBR/cutadapt/main.nf

@@ -0,0 +1,63 @@
+process CUTADAPT {
+    tag { meta.id }
+    label 'process_high'
+
+    container 'nciccbr/ncigb_cutadapt_v1.18:latest'
+
+    input:
+        tuple val(meta), path(reads)
+
+    output:
+        tuple val(meta), path('*.trim.fastq.gz'), emit: reads
+        tuple val(meta), path('*.log')          , emit: log
+        path "versions.yml"                     , emit: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def trimmed  = meta.single_end ? "-o ${prefix}.trim.fastq.gz" : "-o ${prefix}_1.trim.fastq.gz -p ${prefix}_2.trim.fastq.gz"
+    def args = task.ext.args ?: [
+            '--nextseq-trim=2',
+            '--trim-n -n 5 -O 5',
+            '-q 10,10',
+            '-b file:/opt2/TruSeq_and_nextera_adapters.consolidated.fa'
+        ]
+    if (meta.single_end) {
+        args += [
+            '-m 20'
+        ]
+    } else {
+        args += [
+            '-B file:/opt2/TruSeq_and_nextera_adapters.consolidated.fa',
+            '-m 20:20',
+        ]
+    }
+    args = args.join(' ').trim()
+    """
+    cutadapt \\
+        --cores ${task.cpus} \\
+        ${args} \\
+        ${trimmed} \\
+        ${reads} \\
+        > ${prefix}.cutadapt.log
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cutadapt: \$(cutadapt --version)
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix  = task.ext.prefix ?: "${meta.id}"
+    def trimmed = meta.single_end ? "${prefix}.trim.fastq.gz" : "${prefix}_1.trim.fastq.gz ${prefix}_2.trim.fastq.gz"
+    """
+    touch ${prefix}.cutadapt.log
+    touch ${trimmed}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cutadapt: \$(cutadapt --version)
+    END_VERSIONS
+    """
+}

modules/CCBR/cutadapt/meta.yml

@@ -0,0 +1,45 @@
+name: cutadapt
+description: Perform adapter/quality trimming on sequencing reads. Adapted from the nf-core cutadapt module.
+keywords:
+  - trimming
+  - adapter trimming
+  - adapters
+  - quality trimming
+tools:
+  - cuatadapt:
+      description: |
+        Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
+      documentation: https://cutadapt.readthedocs.io/en/stable/index.html
+      doi: 10.14806/ej.17.1.200
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: |
+        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+        respectively.
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: The trimmed/modified fastq reads
+      pattern: "*fastq.gz"
+  - log:
+      type: file
+      description: cuatadapt log file
+      pattern: "*cutadapt.log"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@kelly-sovacool"

pyproject.toml

@@ -61,7 +61,7 @@ Changelog = "https://github.com/CCBR/CRUISE/blob/main/docs/CHANGELOG.md"
 cruise = "."
 
 [tool.setuptools.package-data]
-"*" = ["CITATION.cff", "LICENSE", "VERSION", "main.nf", "nextflow.config", "assets/*", "bin/*", "conf/*", "modules/*/*", "submodules/*/*"]
+"*" = ["CITATION.cff", "LICENSE", "VERSION", "main.nf", "nextflow.config", "assets/*", "bin/*", "conf/*", "modules/*/*", "subworkflows/*/*"]
 
 [tool.setuptools.dynamic]
 version = {file = "VERSION"}

submodules/local/trim_count.nf → subworkflows/local/trim_count.nf

@@ -1,4 +1,4 @@
-include { TRIM_SE               } from '../../modules/local/trim.nf'
+include { CUTADAPT               } from '../../modules/CCBR/cutadapt'
 include { COUNT as MAGECK_COUNT } from "../../modules/local/mageck.nf"
 
 workflow TRIM_COUNT {
@@ -7,8 +7,8 @@ workflow TRIM_COUNT {
         library
 
     main:
-        TRIM_SE(raw_reads)
-        TRIM_SE.out.reads
+        CUTADAPT(raw_reads)
+        CUTADAPT.out.reads
         .multiMap { meta, fastq ->
             id: meta.id
             fastq: fastq
@@ -22,5 +22,5 @@ workflow TRIM_COUNT {
 
     emit:
         count = MAGECK_COUNT.out.count
-        trimmed_reads = TRIM_SE.out.reads
+        trimmed_reads = CUTADAPT.out.reads
 }