Run nextflow lint -format

main.nf

@@ -10,10 +10,10 @@
  * given `params.foo` specify on the run command line `--foo some_value`.
  */
 
-params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
-params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
+params.reads = "${baseDir}/data/ggal/ggal_gut_{1,2}.fq"
+params.transcriptome = "${baseDir}/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
 params.outdir = "results"
-params.multiqc = "$baseDir/multiqc"
+params.multiqc = "${baseDir}/multiqc"
 
 
 // import modules
@@ -25,15 +25,17 @@ include { MULTIQC } from './modules/multiqc'
  */
 workflow {
 
-log.info """\
+    log.info(
+        """\
   R N A S E Q - N F   P I P E L I N E
   ===================================
   transcriptome: ${params.transcriptome}
   reads        : ${params.reads}
   outdir       : ${params.outdir}
   """
+    )
 
-  read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true ) 
-  RNASEQ( params.transcriptome, read_pairs_ch )
-  MULTIQC( RNASEQ.out, params.multiqc )
+    read_pairs_ch = channel.fromFilePairs(params.reads, checkIfExists: true)
+    RNASEQ(params.transcriptome, read_pairs_ch)
+    MULTIQC(RNASEQ.out, params.multiqc)
 }

modules/fastqc/main.nf

@@ -1,9 +1,9 @@
 params.outdir = 'results'
 
 process FASTQC {
-    tag "FASTQC on $sample_id"
+    tag "FASTQC on ${sample_id}"
     conda 'bioconda::fastqc=0.12.1'
-    publishDir params.outdir, mode:'copy'
+    publishDir params.outdir, mode: 'copy'
 
     input:
     tuple val(sample_id), path(reads)
@@ -13,6 +13,6 @@ process FASTQC {
 
     script:
     """
-    fastqc.sh "$sample_id" "$reads"
+    fastqc.sh "${sample_id}" "${reads}"
     """
 }

modules/index/main.nf

@@ -1,16 +1,15 @@
-
 process INDEX {
-    tag "$transcriptome.simpleName"
+    tag "${transcriptome.simpleName}"
     conda 'bioconda::salmon=1.10.3'
-    
+
     input:
-    path transcriptome 
+    path transcriptome
 
     output:
-    path 'index' 
+    path 'index'
 
     script:
     """
-    salmon index --threads $task.cpus -t $transcriptome -i index
+    salmon index --threads ${task.cpus} -t ${transcriptome} -i index
     """
 }

modules/multiqc/main.nf

@@ -2,7 +2,7 @@ params.outdir = 'results'
 
 process MULTIQC {
     conda 'bioconda::multiqc=1.27.1'
-    publishDir params.outdir, mode:'copy'
+    publishDir params.outdir, mode: 'copy'
 
     input:
     path '*'
@@ -13,7 +13,7 @@ process MULTIQC {
 
     script:
     """
-    cp $config/* .
+    cp ${config}/* .
     echo "custom_logo: \$PWD/nextflow_logo.png" >> multiqc_config.yaml
     multiqc -n multiqc_report.html .
     """

modules/quant/main.nf

@@ -1,17 +1,16 @@
-
 process QUANT {
-    tag "$pair_id"
+    tag "${pair_id}"
     conda 'bioconda::salmon=1.10.3'
 
     input:
-    path index 
-    tuple val(pair_id), path(reads) 
+    path index
+    tuple val(pair_id), path(reads)
 
     output:
-    path pair_id 
+    path pair_id
 
     script:
     """
-    salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
+    salmon quant --threads ${task.cpus} --libType=U -i ${index} -1 ${reads[0]} -2 ${reads[1]} -o ${pair_id}
     """
 }

modules/rnaseq.nf

@@ -5,15 +5,15 @@ include { QUANT } from './quant'
 include { FASTQC } from './fastqc'
 
 workflow RNASEQ {
-  take:
+    take:
     transcriptome
     read_pairs_ch
- 
-  main: 
+
+    main:
     INDEX(transcriptome)
     FASTQC(read_pairs_ch)
     QUANT(INDEX.out, read_pairs_ch)
 
-  emit: 
-     QUANT.out | concat(FASTQC.out) | collect
-}
+    emit:
+    QUANT.out | concat(FASTQC.out) | collect
+}

nextflow.config

@@ -11,9 +11,9 @@
  */
 
 manifest {
-  description = 'Proof of concept of a RNA-seq pipeline implemented with Nextflow'
-  author = 'Paolo Di Tommaso'
-  nextflowVersion = '>=23.10.0'
+    description = 'Proof of concept of a RNA-seq pipeline implemented with Nextflow'
+    author = 'Paolo Di Tommaso'
+    nextflowVersion = '>=23.10.0'
 }
 
 /*
@@ -30,119 +30,119 @@ params.multiqc = "${projectDir}/multiqc"
  */
 
 profiles {
-  standard {
-    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
-  }
-
-  'all-reads' {
-    params.reads = "${projectDir}/data/ggal/ggal_*_{1,2}.fq"
-  }
-
-  'arm64' {
-    process.arch = 'arm64'
-  }
-
-  'wave' {
-    wave.enabled = true
-    wave.strategy = 'conda'
-    wave.freeze = true
-  }
-
-  'wave-mirror' {
-    wave.enabled = true
-    wave.strategy = 'container'
-    wave.mirror = true
-    wave.build.repository = 'quay.io'
-  }
-
-  'docker' {
-    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
-    docker.enabled = true
-  }
-
-  'singularity' {
-    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
-    singularity.enabled = true
-    singularity.autoMounts = true
-  }
-
-  'conda' {
-    conda.enabled = true
-    conda.channels = 'conda-forge,bioconda'
-  }
-
-  'mamba' {
-    conda.enabled = true
-    conda.useMicromamba = true
-    conda.channels = 'conda-forge,bioconda'
-  }
-
-  'slurm' {
-    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
-    process.executor = 'slurm'
-    singularity.enabled = true
-  }
-
-  'batch' {
-    params.reads = 's3://rnaseq-nf/data/ggal/lung_{1,2}.fq'
-    params.transcriptome = 's3://rnaseq-nf/data/ggal/transcript.fa'
-    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
-    process.executor = 'awsbatch'
-    process.queue = 'nextflow-ci'
-    workDir = 's3://nextflow-ci/work'
-    aws.region = 'eu-west-1'
-    aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
-  }
-
-  's3-data' {
-    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
-    params.reads = 's3://rnaseq-nf/data/ggal/lung_{1,2}.fq'
-    params.transcriptome = 's3://rnaseq-nf/data/ggal/transcript.fa'
-  }
-
-  'google-batch' {
-      params.transcriptome = 'gs://rnaseq-nf/data/ggal/transcript.fa'
-      params.reads = 'gs://rnaseq-nf/data/ggal/gut_{1,2}.fq'
-      params.multiqc = 'gs://rnaseq-nf/multiqc'
-      process.executor = 'google-batch'
-      process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
-      /*
-       * replace with your own bucket!
-       */
-      workDir = 'gs://rnaseq-nf/scratch'
-      google.region  = 'europe-west2'
-  }
-
-  'gs-data' {
-      process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
-      params.transcriptome = 'gs://rnaseq-nf/data/ggal/transcript.fa'
-      params.reads = 'gs://rnaseq-nf/data/ggal/gut_{1,2}.fq'
-  }
-
-  'azure-batch' {
-    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
-    workDir = 'az://nf-scratch/work'
-    process.executor = 'azurebatch'
-    /*
-     *place with your own Azure pool name!
-     */
-    process.queue = 'nextflow-ci'
-
-    /*
-     * make sure the following variables are defined in your environment
-     * - AZURE_BATCH_ACCOUNT_NAME
-     * - AZURE_BATCH_ACCOUNT_KEY
-     * - AZURE_STORAGE_ACCOUNT_NAME
-     * - AZURE_STORAGE_ACCOUNT_KEY
-     * see https://www.nextflow.io/docs/latest/azure.html#azure-batch
-     */
-
-    azure {
-      batch {
-        location = 'westeurope'
-        autoPoolMode = true
-        deletePoolsOnCompletion = true
-      }
+    standard {
+        process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
+    }
+
+    'all-reads' {
+        params.reads = "${projectDir}/data/ggal/ggal_*_{1,2}.fq"
+    }
+
+    arm64 {
+        process.arch = 'arm64'
+    }
+
+    wave {
+        wave.enabled = true
+        wave.strategy = 'conda'
+        wave.freeze = true
+    }
+
+    'wave-mirror' {
+        wave.enabled = true
+        wave.strategy = 'container'
+        wave.mirror = true
+        wave.build.repository = 'quay.io'
+    }
+
+    docker {
+        process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
+        docker.enabled = true
+    }
+
+    singularity {
+        process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
+        singularity.enabled = true
+        singularity.autoMounts = true
+    }
+
+    conda {
+        conda.enabled = true
+        conda.channels = 'conda-forge,bioconda'
+    }
+
+    mamba {
+        conda.enabled = true
+        conda.useMicromamba = true
+        conda.channels = 'conda-forge,bioconda'
+    }
+
+    slurm {
+        process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
+        process.executor = 'slurm'
+        singularity.enabled = true
+    }
+
+    batch {
+        params.reads = 's3://rnaseq-nf/data/ggal/lung_{1,2}.fq'
+        params.transcriptome = 's3://rnaseq-nf/data/ggal/transcript.fa'
+        process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
+        process.executor = 'awsbatch'
+        process.queue = 'nextflow-ci'
+        workDir = 's3://nextflow-ci/work'
+        aws.region = 'eu-west-1'
+        aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
+    }
+
+    's3-data' {
+        process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
+        params.reads = 's3://rnaseq-nf/data/ggal/lung_{1,2}.fq'
+        params.transcriptome = 's3://rnaseq-nf/data/ggal/transcript.fa'
+    }
+
+    'google-batch' {
+        params.transcriptome = 'gs://rnaseq-nf/data/ggal/transcript.fa'
+        params.reads = 'gs://rnaseq-nf/data/ggal/gut_{1,2}.fq'
+        params.multiqc = 'gs://rnaseq-nf/multiqc'
+        process.executor = 'google-batch'
+        process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
+        /*
+         * replace with your own bucket!
+         */
+        workDir = 'gs://rnaseq-nf/scratch'
+        google.region = 'europe-west2'
+    }
+
+    'gs-data' {
+        process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
+        params.transcriptome = 'gs://rnaseq-nf/data/ggal/transcript.fa'
+        params.reads = 'gs://rnaseq-nf/data/ggal/gut_{1,2}.fq'
+    }
+
+    'azure-batch' {
+        process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
+        workDir = 'az://nf-scratch/work'
+        process.executor = 'azurebatch'
+        /*
+         *place with your own Azure pool name!
+         */
+        process.queue = 'nextflow-ci'
+
+        /*
+         * make sure the following variables are defined in your environment
+         * - AZURE_BATCH_ACCOUNT_NAME
+         * - AZURE_BATCH_ACCOUNT_KEY
+         * - AZURE_STORAGE_ACCOUNT_NAME
+         * - AZURE_STORAGE_ACCOUNT_KEY
+         * see https://www.nextflow.io/docs/latest/azure.html#azure-batch
+         */
+
+        azure {
+            batch {
+                location = 'westeurope'
+                autoPoolMode = true
+                deletePoolsOnCompletion = true
+            }
+        }
     }
-  }
 }