nf-core · lmReef · Jun 24, 2025 · Apr 17, 2025 · Apr 22, 2025 · Apr 22, 2025
diff --git a/conf/base.config b/conf/base.config
@@ -11,9 +11,9 @@
 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
@@ -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
     }
-    withName:CUSTOM_DUMPSOFTWAREVERSIONS {
+    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
         cache = false
     }
 }
diff --git a/conf/igenomes.config b/conf/igenomes.config
diff --git a/conf/modules.config b/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}" },

diff --git a/conf/test.config b/conf/test.config
@@ -14,7 +14,7 @@ process {
     resourceLimits = [
         cpus: 2,
         memory: '6.GB',
-        time: '1.h'
+        time: '1.h',
     ]
 }
 
@@ -31,19 +31,19 @@ params {
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
     //input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
-    igenomes_ignore = true
+    igenomes_ignore            = true
 
-    input = "data/samplesheet_test_local.csv"
+    input                      = "data/samplesheet_test_local.csv"
 
     // Genome references
     //genome = 'R64-1-1'
-    host_fasta_genome  = "data/GRCh38.p13_sub.fasta"
-    host_gff = "data/Human_gencode.v33_sub.gff3"
+    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 = ""
+    host_fasta_transcripts     = "data/Human_gencode.v33_sub_transcriptome.fasta"
+    libtype                    = ""
 
-    pathogen_fasta_genome  = "data/SL1344_sub.fasta"
-    pathogen_gff = "data/SL1344_sub.gff3"
+    pathogen_fasta_genome      = "data/SL1344_sub.fasta"
+    pathogen_gff               = "data/SL1344_sub.gff3"
 }
diff --git a/conf/test_2_fasta_pathogen.config b/conf/test_2_fasta_pathogen.config
@@ -5,7 +5,7 @@
     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>
 
 ----------------------------------------------------------------------------------------
 */
@@ -15,21 +15,21 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
+    max_cpus                   = 2
+    max_memory                 = '6.GB'
+    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"
-    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"
-    transcript_fasta_host = "data/Human_gencode.v33_sub_transcriptome.fasta"
-    libtype = ""
+    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"
+    transcript_fasta_host      = "data/Human_gencode.v33_sub_transcriptome.fasta"
+    libtype                    = ""
 
-    fasta_pathogen = "data/SL1344*sub.fasta.gz"
-    gff_pathogen = "https://github.com/nf-core/test-datasets/raw/dualrnaseq/references/SL1344_sub.gff3"
+    fasta_pathogen             = "data/SL1344*sub.fasta.gz"
+    gff_pathogen               = "https://github.com/nf-core/test-datasets/raw/dualrnaseq/references/SL1344_sub.gff3"
 }
diff --git a/conf/test_full.config b/conf/test_full.config
@@ -17,8 +17,8 @@ params {
     // Input data for full size test
     // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
+    input                      = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
 
     // Genome references
-    genome = 'R64-1-1'
+    genome                     = 'R64-1-1'
 }
diff --git a/conf/test_local.config b/conf/test_local.config
@@ -5,7 +5,7 @@
     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>
 
 ----------------------------------------------------------------------------------------
 */
@@ -15,61 +15,60 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Ignore igenomes
-    igenomes_ignore = true
+    igenomes_ignore            = true
 
     //dockerImage  = 'nfcore/python:3.9.5'
 
     // input  = "https://raw.githubusercontent.com/nf-core/test-datasets/dualrnaseq/spreadsheet/spreadsheet.csv"
-    input = "data/samplesheet_test_local.csv"
+    input                      = "data/samplesheet_test_local.csv"
     //input = "data/samplesheet_validated.csv"
 
     // 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_gff = "data/Human_gencode.v33_sub.gff3"
+    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'
     pathogen_fasta_transcripts = "data/SL1344_sub_transcriptome.fasta"
-    host_fasta_transcripts = "data/Human_gencode.v33_sub_transcriptome.fasta"
-    libtype = ""
+    host_fasta_transcripts     = "data/Human_gencode.v33_sub_transcriptome.fasta"
+    libtype                    = ""
 
     // 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_gff = "data/SL1344_sub.gff3"
-
+    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'
     }
 }