General refactor and format

conf/base.config

@@ -11,13 +11,13 @@
 process {
 
     // TODO nf-core: Check the defaults for all processes
-    cpus   = { 1      * task.attempt }
-    memory = { 6.GB   * task.attempt }
-    time   = { 4.h    * task.attempt }
+    cpus = { 1 * task.attempt }
+    memory = { 6.GB * task.attempt }
+    time = { 4.h * task.attempt }
 
     errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
-    maxRetries    = 1
-    maxErrors     = '-1'
+    maxRetries = 1
+    maxErrors = '-1'
 
     // Process-specific resource requirements
     // NOTE - Please try and reuse the labels below as much as possible.
@@ -26,40 +26,40 @@ process {
     //        adding in your local modules too.
     // TODO nf-core: Customise requirements for specific processes.
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
-    withLabel:process_single {
-        cpus   = { 1                   }
+    withLabel: process_single {
+        cpus = { 1 }
         memory = { 6.GB * task.attempt }
-        time   = { 4.h  * task.attempt }
+        time = { 4.h * task.attempt }
     }
-    withLabel:process_low {
-        cpus   = { 2     * task.attempt }
+    withLabel: process_low {
+        cpus = { 2 * task.attempt }
         memory = { 12.GB * task.attempt }
-        time   = { 4.h   * task.attempt }
+        time = { 4.h * task.attempt }
     }
-    withLabel:process_medium {
-        cpus   = { 6     * task.attempt }
+    withLabel: process_medium {
+        cpus = { 6 * task.attempt }
         memory = { 36.GB * task.attempt }
-        time   = { 8.h   * task.attempt }
+        time = { 8.h * task.attempt }
     }
-    withLabel:process_high {
-        cpus   = { 12    * task.attempt }
+    withLabel: process_high {
+        cpus = { 12 * task.attempt }
         memory = { 72.GB * task.attempt }
-        time   = { 16.h  * task.attempt }
+        time = { 16.h * task.attempt }
     }
-    withLabel:process_long {
-        time   = { 20.h  * task.attempt }
+    withLabel: process_long {
+        time = { 20.h * task.attempt }
     }
-    withLabel:process_high_memory {
+    withLabel: process_high_memory {
         memory = { 200.GB * task.attempt }
     }
-    withLabel:error_ignore {
+    withLabel: error_ignore {
         errorStrategy = 'ignore'
     }
-    withLabel:error_retry {
+    withLabel: error_retry {
         errorStrategy = 'retry'
-        maxRetries    = 2
+        maxRetries = 2
     }
-    withName:CUSTOM_DUMPSOFTWAREVERSIONS {
+    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
         cache = false
     }
 }

conf/modules.config

@@ -78,7 +78,7 @@ process {
     // SALMON SA
     // -----------------------------
 
-    if (params.run_salmon_SA) {
+    if (params.salmon_sa) {
 
         withName: 'NFCORE_DUALRNASEQ:DUALRNASEQ:SALMON_SELECTIVE_ALIGNMENT:SALMON_INDEX' {
             publishDir = [
@@ -128,12 +128,13 @@ process {
     // SALMON AB
     // -----------------------------
 
-    if (params.run_salmon_AB) {
+    if (params.salmon_ab) {
 
         withName: 'NFCORE_DUALRNASEQ:DUALRNASEQ:SALMON_ALIGNMENT_BASED:STAR_GENOMEGENERATE' {
             ext.args = '--sjdbGTFfeatureExon quant --sjdbGTFtagExonParentTranscript parent'
             publishDir = [
                 path: { "${params.outdir}/salmon_AB/star/" },
+
                 mode: params.publish_dir_mode
             ]
         }
@@ -196,7 +197,7 @@ process {
     // STAR GENOME
     // -----------------------------
 
-    if (params.run_star) {
+    if (params.star) {
 
         withName: 'NFCORE_DUALRNASEQ:DUALRNASEQ:STAR_ALIGNMENT:STAR_GENOMEGENERATE' {
             ext.args = '--sjdbGTFfeatureExon quant --sjdbGTFtagExonParentTranscript parent'
@@ -230,7 +231,7 @@ process {
     // HTSEQ
     // -----------------------------
 
-    if (params.run_htseq) {
+    if (params.htseq) {
 
         withName: 'NFCORE_DUALRNASEQ:DUALRNASEQ:PREPARE_REFERENCE_FILES:COMBINE_PATHOGEN_HOST_GFF_FILES_HTSEQ' {
             publishDir = [
@@ -281,7 +282,7 @@ process {
             ${fastqc_args_value} \
             --quiet
             """.trim()
-        ext.when         = { !(params.skip_tools && params.skip_tools.split(',').contains('fastqc')) }
+        ext.when         = { params.fastqc }
         publishDir       = [
             [
                 path: { "${params.outdir}/fastqc/${meta.id}" },
@@ -297,7 +298,7 @@ process {
             ${fastqc_args_value} \
             --quiet
             """.trim()
-        ext.when         = { !(params.skip_tools && (params.skip_tools.split(',').contains('fastqc') || params.skip_tools.split(',').contains('cutadapt'))) }
+        ext.when         = { params.fastqc && (params.cutadapt) }
         publishDir       = [
             [
                 path: { "${params.outdir}/fastqc_after_trimming/${meta.id}" },
@@ -317,7 +318,7 @@ process {
             ${cutadapt_args_value} \
             --quiet
             """.trim()
-        ext.when         = { !(params.skip_tools && params.skip_tools.split(',').contains('cutadapt')) }
+        ext.when         = { params.cutadapt }
         publishDir       = [
             [
                 path: { "${params.outdir}/cutadapt/${meta.id}" },

conf/test.config

@@ -14,12 +14,12 @@ process {
     resourceLimits = [
         cpus: 2,
         memory: '6.GB',
-        time: '1.h'
+        time: '1.h',
     ]
 }
 
 params {
-    config_profile_name        = 'Test profile'
+    config_profile_name = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Limit resources so that this can run on GitHub Actions
@@ -37,13 +37,13 @@ params {
 
     // Genome references
     //genome = 'R64-1-1'
-    host_fasta_genome  = "data/GRCh38.p13_sub.fasta"
+    host_fasta_genome = "data/GRCh38.p13_sub.fasta"
     host_gff = "data/Human_gencode.v33_sub.gff3"
 
     pathogen_fasta_transcripts = "data/SL1344_sub_transcriptome.fasta"
     host_fasta_transcripts = "data/Human_gencode.v33_sub_transcriptome.fasta"
     libtype = ""
 
-    pathogen_fasta_genome  = "data/SL1344_sub.fasta"
+    pathogen_fasta_genome = "data/SL1344_sub.fasta"
     pathogen_gff = "data/SL1344_sub.gff3"
 }

conf/test_2_fasta_pathogen.config

@@ -5,25 +5,25 @@
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run nf-core/dualrnaseq -profile test_hackathon,<docker/singularity> --outdir <OUTDIR>
+        nextflow run nf-core/dualrnaseq -profile test_2_fasta_pathogen,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
 
 params {
-    config_profile_name        = 'Test profile'
+    config_profile_name = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
+    max_cpus = 2
     max_memory = '6.GB'
-    max_time   = '6.h'
+    max_time = '6.h'
 
-    input  = "https://raw.githubusercontent.com/nf-core/test-datasets/dualrnaseq/spreadsheet/spreadsheet.csv"
+    input = "https://raw.githubusercontent.com/nf-core/test-datasets/dualrnaseq/spreadsheet/spreadsheet.csv"
 
     // Genome references
 
-    fasta_host  = "https://github.com/nf-core/test-datasets/raw/dualrnaseq/references/GRCh38.p13_sub.fasta"
+    fasta_host = "https://github.com/nf-core/test-datasets/raw/dualrnaseq/references/GRCh38.p13_sub.fasta"
     gff_host = "https://github.com/nf-core/test-datasets/raw/dualrnaseq/references/Human_gencode.v33_sub.gff3"
     gff_host_tRNA = "data/human.tRNAs.gff.gz"
     transcript_fasta_pathogen = "data/SL1344_sub_transcriptome.fasta"

conf/test_full.config

@@ -11,7 +11,7 @@
 */
 
 params {
-    config_profile_name        = 'Full test profile'
+    config_profile_name = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test

conf/test_local.config

@@ -5,13 +5,13 @@
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run nf-core/dualrnaseq -profile test_hackathon,<docker/singularity> --outdir <OUTDIR>
+        nextflow run nf-core/dualrnaseq -profile test_local,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
 
 params {
-    config_profile_name        = 'Test profile with small files'
+    config_profile_name = 'Test profile with small files'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Ignore igenomes
@@ -26,7 +26,7 @@ params {
     // Genome references
 
     // fasta_host  = "https://github.com/nf-core/test-datasets/raw/dualrnaseq/references/GRCh38.p13_sub.fasta"
-    host_fasta_genome  = "data/GRCh38.p13_sub.fasta"
+    host_fasta_genome = "data/GRCh38.p13_sub.fasta"
     host_gff = "data/Human_gencode.v33_sub.gff3"
     // gff_host = "https://github.com/nf-core/test-datasets/raw/dualrnaseq/references/Human_gencode.v33_sub.gff3"
     // gff_host_tRNA = 'data/human.tRNAs.gff'
@@ -36,40 +36,39 @@ params {
 
     // fasta_pathogen  = "https://github.com/nf-core/test-datasets/raw/dualrnaseq/references/SL1344_sub.fasta"
     // gff_pathogen = "https://github.com/nf-core/test-datasets/raw/dualrnaseq/references/SL1344_sub.gff3"
-    pathogen_fasta_genome  = "data/SL1344_sub.fasta"
+    pathogen_fasta_genome = "data/SL1344_sub.fasta"
     pathogen_gff = "data/SL1344_sub.gff3"
-
 }
 
 process {
-// Override the label definitions so can run locally
-    withLabel:process_single {
-    cpus = 1
-    memory = 2.GB
-    time = '5m'
+    // Override the label definitions so can run locally
+    withLabel: process_single {
+        cpus = 1
+        memory = 2.GB
+        time = '5m'
     }
 
-    withLabel:process_low {
-    cpus = 1
-    memory = 4.GB
-    time = '5m'
+    withLabel: process_low {
+        cpus = 1
+        memory = 4.GB
+        time = '5m'
     }
 
-    withLabel:process_medium {
-    cpus = 2
-    memory = 6.GB
-    time = '5m'
+    withLabel: process_medium {
+        cpus = 2
+        memory = 6.GB
+        time = '5m'
     }
 
-    withLabel:process_high {
-    cpus = 2
-    memory = 6.GB
-    time = '5m'
+    withLabel: process_high {
+        cpus = 2
+        memory = 6.GB
+        time = '5m'
     }
 
-    withLabel:process_high_memory {
-    cpus = 2
-    memory = 6.GB
-    time = '5m'
+    withLabel: process_high_memory {
+        cpus = 2
+        memory = 6.GB
+        time = '5m'
     }
 }

main.nf

@@ -16,9 +16,9 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { DUALRNASEQ  } from './workflows/dualrnaseq'
+include { DUALRNASEQ } from './workflows/dualrnaseq'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_dualrnaseq_pipeline'
-include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_dualrnaseq_pipeline'
+include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_dualrnaseq_pipeline'
 // include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_dualrnaseq_pipeline'
 
 
@@ -53,7 +53,7 @@ workflow NFCORE_DUALRNASEQ {
     //
     // WORKFLOW: Run pipeline
     //
-    DUALRNASEQ (samplesheet)
+    DUALRNASEQ(samplesheet)
 
     emit:
     multiqc_report = DUALRNASEQ.out.multiqc_report // channel: /path/to/multiqc_report.html
@@ -68,42 +68,34 @@ workflow NFCORE_DUALRNASEQ {
 */
 
 workflow {
-
-    main:
     //
     // SUBWORKFLOW: Run initialisation tasks
     //
-    PIPELINE_INITIALISATION (
+    PIPELINE_INITIALISATION(
         params.version,
         params.validate_params,
         params.monochrome_logs,
         args,
         params.outdir,
-        params.input
+        params.input,
     )
 
     //
     // WORKFLOW: Run main workflow
     //
-    NFCORE_DUALRNASEQ (
+    NFCORE_DUALRNASEQ(
         PIPELINE_INITIALISATION.out.samplesheet
     )
     //
     // SUBWORKFLOW: Run completion tasks
     //
-    PIPELINE_COMPLETION (
+    PIPELINE_COMPLETION(
         params.email,
         params.email_on_fail,
         params.plaintext_email,
         params.outdir,
         params.monochrome_logs,
         params.hook_url,
-        NFCORE_DUALRNASEQ.out.multiqc_report
+        NFCORE_DUALRNASEQ.out.multiqc_report,
     )
 }
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    THE END
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/