validateParams is working, nf-schema plugins are working

number-25 · number-25 · commit 951dacc4b9c9 · 2026-01-13T15:55:30.000+10:00
diff --git a/assets/Dockerfile_bambu b/assets/Dockerfile_bambu
diff --git a/assets/Dockerfile_bambu_2 b/assets/Dockerfile_bambu_2
diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
@@ -1,2 +1,2 @@
-sample,replicate,read_path
+sample,replicate,reads
 COLOBL_RNA_600,,/mnt/hdd1/MedGen_RNA_datasets/COLOBL_RNA_600/fastq_pass/COLOBL_RNA_660.fastq.gz
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft/2020-12/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/number-25/LongTranscriptomics/dev/assets/schema_input.json",
     "title": "number-25/LongTranscriptomics pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
@@ -15,18 +15,18 @@
             },
             "replicate": {
                 "type": "integer",
-                "pattern": "\d+",
+                "pattern": "\\d+",
                 "errorMessage": "Replicate must be an integer",
                 "meta": ["replicate"]
             },
-            "fastq": {
+            "reads": {
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
                 "pattern": "^\\S+\\.f(ast)?q\\.gz$",
-                "errorMessage": "FastQ file must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
+                "errorMessage": "FastQ/BAM file must be provided, cannot contain spaces and must have extension '.fq.gz', '.fastq.gz' or '.bam'"
             }
         },
-        "required": ["sample", "fastq"]
+        "required": ["sample", "reads"]
     }
 }
diff --git a/conf/test.config b/conf/test.config
@@ -88,7 +88,7 @@ params {
 validation {
     help {
         enabled     = true
-        beforeText  = "Welcome to LongTranscriptomics, I see you are seeking help."
+        beforeText  = "Welcome to LongTranscriptomics, I see you are seeking help. "
         afterText   = "Farewell, hopefully this was helpful. Please cite the pipeline owners when using this pipeline."
         command     = "nextflow run . -profile <profile> --outdir <outdir>"
     }
diff --git a/main.nf b/main.nf
@@ -27,19 +27,19 @@ workflow{
     // nf-scheme validations
     //
 
-   // validateParameters()
+    validateParameters()
+
     log.info paramsSummaryLog(workflow)
 
     if (params.help) {
         log.info paramsHelp(
-            beforeText: "Welcome to LongTranscriptomics, I see you are seeking help.",
+            beforeText: "Welcome to LongTranscriptomics, I see you are seeking help. ",
             afterText: "Farewell, hopefully this was helpful.",
             command: "nextflow run . -profile <profile> --outdir <outdir>",
         )
         exit 0
     }
 
-
     DIRECTRNA ()
 }
 /*
@@ -52,18 +52,6 @@ workflow {
 
     main:
 
-    //
-    // SUBWORKFLOW: Run initialisation tasks
-    /*
-    PIPELINE_INITIALISATION (
-        params.version,
-        params.help,
-        params.validate_params,
-        params.monochrome_logs,
-        args,
-        params.outdir,
-        params.input
-    )
     PIPELINE_COMPLETION (
         params.email,
         params.email_on_fail,
diff --git a/modules.json b/modules.json
@@ -24,20 +24,10 @@
             },
             "subworkflows": {
                 "nf-core": {
-                    "utils_nextflow_pipeline": {
-                        "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
-                        "installed_by": ["subworkflows"]
-                    },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
                         "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["subworkflows"]
-                    },
-                    "utils_nfvalidation_plugin": {
-                        "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
-                        "installed_by": ["subworkflows"]
                     }
                 }
             }
diff --git a/modules/local/bambu/bambu/main.nf b/modules/local/bambu/bambu/main.nf
@@ -6,31 +6,18 @@ process BAMBU {
     'docker://number25/bambu:3.12.0' :
     'docker://quay.io/number_25/bambu:3.12.0' }"
 
-       // 'docker://quay.io/biocontainers/bioconductor-bambu:3.0.8--r42hc247a5b_0' }"
-       // 'docker://quay.io/biocontainers/bioconductor-bambu:3.0.8--r42hc247a5b_0' }"
-   //containerOptions = '-u $(id -u):$(id -g)'
-        //'number25/bambu:3.8.0':
-        //'docker://quay.io/number_25/bambu:latest' }"
-        // 'https://depot.galaxyproject.org/singularity/bioconductor-bambu:3.4.0--r43hf17093f_1' :
-        //'quay.io/biocontainers/bioconductor-bambu:3.4.0--r43hf17093f_1' }"
-
     input:
     path(genome_fasta)
     path(annotation_gtf)
     tuple val(meta), path(bam)
 
     output:
-    //path "counts_gene.txt"                                  , emit: ch_gene_counts
-    //path "counts_transcript.txt"                            , emit: ch_transcript_counts
-    path "extended_annotations.gtf"
-    path "allTranscriptModels.gtf"
-    path "novelTranscripts.gtf"
+    path "*.gtf"
     tuple val(meta), path("supportedTranscriptModels.gtf")  , emit: bambu_supported_gtf
     path "versions.yml"                                     , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
-    //def prefix = task.ext.prefix ?: "${meta.id}_${meta.replicate}_bambu"
 
     script:
     """
diff --git a/nextflow b/nextflow
@@ -196,8 +196,8 @@ function launch_nextflow() {
     for x in "${launcher[@]}"; do
         x="${x%\"}"
         x="${x#\"}"
-        cmdline+=("$x") 
-    done 
+        cmdline+=("$x")
+    done
 
     if [[ "$bg" ]]; then
       local pid_file="${NXF_PID_FILE:-.nextflow.pid}"
diff --git a/nextflow.config b/nextflow.config
@@ -7,7 +7,7 @@
 */
 //Plugins
 plugins {
-  id 'nf-schema@2.6.1'
+  id 'nf-schema@2.5.1'
 }
 
 // Global default params, used in configs
@@ -294,11 +294,6 @@ docker.registry      = 'quay.io'
 podman.registry      = 'quay.io'
 singularity.registry = 'quay.io'
 
-// Nextflow plugins
-plugins {
-    id 'nf-schema@2.0.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
-}
-
 // Load igenomes.config if required
 //if (!params.igenomes_ignore) {
 //includeConfig 'conf/igenomes.config'
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -74,7 +74,6 @@
                 },
                 "help": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Show the help message for the pipeline.",
                     "fa_icon": "fas fa-question-circle",
                     "help_text": "Welcome to LongTranscriptomics, I see you are seeking help, these are  a list of basic parameters."
diff --git a/nxf-tmp.h6mnQz b/nxf-tmp.h6mnQz
diff --git a/subworkflows/local/input_check/main.nf b/subworkflows/local/input_check/main.nf
@@ -1,30 +1,18 @@
 /* Checks the input channel and creates channel map */
 
-// can't use this until julia script is refined and fixed
-//include { CHECK_SAMPLESHEET } from '../../modules/local/check_samplesheet.nf'
-
 workflow INPUT_CHECK {
     take:
     samplesheet // file: /path/to/samplesheet
 
     main:
-    //CHECK_SAMPLESHEET( samplesheet )
-    //.csv  - access csv output from check_samplesheet module - not used at the moment
     ch_samplesheet = Channel.fromPath(samplesheet, checkIfExists: true)
     ch_samplesheet
         .splitCsv ( header:true, sep:',' )
         .map { get_sample_info(it) }
         .set { ch_sample }
-        /*.map { row -> tuple(row.sample, row.replicate,
-        file(row.sequencing_summary_path, checkIfExists: false),
-        file(row.read_path, checkIfExists: false)) }
-        //.view()
-        .set { ch_sample }
-        ch_sample.view() */
 
     emit:
     ch_sample // [ sample, replicate, path_to_reads ]
-    //ch_versions = ch_versions.mix(CHECK_SAMPLESHEET.out.versions.first())
 }
 
 // Create a meta map from the samplesheet
@@ -33,18 +21,17 @@ def get_sample_info(LinkedHashMap row) {
     def meta = [:]
     meta.id           = row.sample
     meta.replicate    = row.replicate
-    //meta.fastq = row.read_path
 
     // add path(s) of the fastq file to the meta map
     def fastq_meta = []
     //if (!file(row.read_path).exists()) {
     //    exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}"
     //}
     //if (meta.single_end) {
-    fastq_meta = [ meta, [ file(row.read_path) ] ]
+    fastq_meta = [ meta, [ file(row.reads) ] ]
     //} else {
     //    if (!file(row.fastq_2).exists()) {
-    //         exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
+    //         exit 1, "ERROR: Pl since most the trains are down ease check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
     //     }
     return fastq_meta
     //return meta
diff --git a/subworkflows/local/mapping/main.nf b/subworkflows/local/mapping/main.nf
@@ -32,12 +32,7 @@ workflow MAPPING {
         ch_versions         = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first())
 
     emit:
-    // do I need the index for anything else?
-    //bam      = SAMTOOLS_SORT.out.bam           // channel: [ val(meta), [ bam ] ]
     bam      = ch_sample_bam           // channel: [ val(meta), [ bam ] ]
-    //bai      = SAMTOOLS_INDEX.out.bam           // channel: [ val(meta), [ bam ] ]
     bai      = ch_sample_bam_idx          // channel: [ val(meta), [ bai ] ]
-    //csi      = SAMTOOLS_INDEX.out.csi          // channel: [ val(meta), [ csi ] ]
-
     versions = ch_versions                     // channel: [ versions.yml ]
 }
diff --git a/subworkflows/local/prepare_reference/main.nf b/subworkflows/local/prepare_reference/main.nf
@@ -12,12 +12,10 @@ include { SQANTI_PREPARE_REFERENCE                  } from '../../local/sqanti/s
 include { JAFFAL_PREPARE_REFERENCE                  } from '../../local/jaffal_prepare_reference'
 include { UNZIP                                     } from '../../../modules/local/unzip/unzip'
 
-// prepare additional files
-//TO-DO make these modules
+//optional modules down the line
 //include { GXF2BED as GTF_TO_BED } from '../../../modules/local/gxf2bed' // gxf2bed module
 //include { BIGWIG_TO_WIG } from '../../../modules/local/bigwigtowig'
 //include { BEDOPS as WIG_TO_BED } from '../../../modules/local/bedops'
-//include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main'
 
 workflow PREPARE_REFERENCE{
 
@@ -60,8 +58,6 @@ workflow PREPARE_REFERENCE{
             ch_genome_fasta = GUNZIP_FASTA( [ [:], file(genome_fasta, checkIfExists: true) ]).gunzip.map { it[1] }
             ch_versions = ch_versions.mix(GUNZIP_FASTA.out.versions)
         } else {
-    //which one below?
-            //ch_genome_fasta = Channel.value(file(genome_fasta), checkIfExists: true)
             ch_genome_fasta = Channel.fromPath(genome_fasta, checkIfExists: true)
         }
     }
@@ -91,7 +87,6 @@ workflow PREPARE_REFERENCE{
             ch_transcriptome_fasta = GUNZIP_TRANSCRIPTOME( [ [:], file(transcriptome_fasta, checkIfExists: true) ] ).gunzip.map { it[1] }
             ch_versions = ch_versions.mix(GUNZIP_TRANSCRIPTOME.out.versions)
 } else {
-            //ch_transcriptome_fasta = Channel.value(file(transcriptome_fasta), checkIfExists: true)
             ch_transcriptome_fasta = Channel.fromPath(params.transcriptome_fasta, checkIfExists: true)
         }
     }
@@ -103,21 +98,18 @@ workflow PREPARE_REFERENCE{
             ch_annotation_gtf = GUNZIP_ANNOTATION_GTF( [ [:], file(annotation_gtf, checkIfExists: true) ] ).gunzip.map { it[1] }
             ch_versions = ch_versions.mix(GUNZIP_ANNOTATION_GTF.out.versions)
         } else {
-//            ch_annotation_gtf = Channel.value(file(annotation_gtf), checkIfExists: true)
             ch_annotation_gtf = Channel.fromPath(params.annotation_gtf, checkIfExists: true)
         }
     }
 
     // Initialise genome minimap2 index if provided
     // If bam input is provided, skip minimap2 genome indexing
     if (!bam_input) {
-        //if (genome_minimap2_index == null) {
         if (!genome_minimap2_index) {
             MINIMAP2_GENOME_INDEX( ch_genome_fasta )
             ch_genome_minimap2_index = MINIMAP2_GENOME_INDEX.out.index
             ch_versions = ch_versions.mix(MINIMAP2_GENOME_INDEX.out.versions)
         } else {
-            //ch_genome_minimap2_index = Channel.value(file(genome_minimap2_index), checkIfExists: true)
             ch_genome_minimap2_index = Channel.fromPath(params.genome_minimap2_index, checkIfExists: true)
         }
     } else {
@@ -127,13 +119,11 @@ workflow PREPARE_REFERENCE{
     // Initialise transcriptome minimap2 index if provided
     // If bam input is provided, skip minimap2 transcriptome indexing
     if (!skip_transcript_quantification) {
-        //if (genome_minimap2_index == null) {
         if (!transcriptome_minimap2_index) {
             MINIMAP2_TXOME_INDEX( ch_transcriptome_fasta )
             ch_transcriptome_minimap2_index = MINIMAP2_TXOME_INDEX.out.index
             ch_versions = ch_versions.mix(MINIMAP2_TXOME_INDEX.out.versions)
         } else {
-            //ch_genome_minimap2_index = Channel.value(file(genome_minimap2_index), checkIfExists: true)
             ch_transcriptome_minimap2_index = Channel.fromPath(params.transcriptome_minimap2_index, checkIfExists: true)
         }
     } else {
@@ -184,7 +174,6 @@ workflow PREPARE_REFERENCE{
         ch_jaffal_reference_dir = null
     }
 
-
     emit:
     genome_fasta                    = ch_genome_fasta
     genome_fasta_index              = ch_genome_fasta_index
diff --git a/test/samplesheets/samplesheet_test_dRNA.csv b/test/samplesheets/samplesheet_test_dRNA.csv
@@ -1,2 +1,2 @@
-sample,replicate,read_path
+sample,replicate,reads
 KCMF1,1,assets/test_data/sample_nobc_dx.fastq.gz
diff --git a/test/samplesheets/samplesheet_test_local.csv b/test/samplesheets/samplesheet_test_local.csv
@@ -1,2 +1,2 @@
-sample,replicate,read_path
+sample,replicate,reads
 COLOBL_RNA600,1,assets/fulltest_data/COLOBL_RNA_660.fastq.gz
diff --git a/workflows/directrna.nf b/workflows/directrna.nf

Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,2 @@`
`1`		`-sample,replicate,read_path`
	`1`	`+sample,replicate,reads`
`2`	`2`	`COLOBL_RNA_600,,/mnt/hdd1/MedGen_RNA_datasets/COLOBL_RNA_600/fastq_pass/COLOBL_RNA_660.fastq.gz`
Original file line number	Diff line number	Diff line change
`@@ -88,7 +88,7 @@ params {`
`88`	`88`	`validation {`
`89`	`89`	`help {`
`90`	`90`	`enabled = true`
`91`		`- beforeText = "Welcome to LongTranscriptomics, I see you are seeking help."`
	`91`	`+ beforeText = "Welcome to LongTranscriptomics, I see you are seeking help. "`
`92`	`92`	`afterText = "Farewell, hopefully this was helpful. Please cite the pipeline owners when using this pipeline."`
`93`	`93`	`command = "nextflow run . -profile <profile> --outdir <outdir>"`
`94`	`94`	`}`