Merge pull request #368 from JoseEspinosa/dev

Update code after nf-validation adoption
nf-core · Oct 17, 2023 · 42b50c3 · 42b50c3
2 parents f9d6e65 + 60ecfe4
commit 42b50c3
Show file tree

Hide file tree

Showing 5 changed files with 36 additions and 43 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -20,7 +20,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Fix untar of `chromap` index when using `--chromap_index` param.
 - [nf-core/tools#2286](https://github.com/nf-core/tools/issues/2286) - Set default container registry outside profile scope.
 - [[#343](https://github.com/nf-core/chipseq/issues/343)] - Provide replicate information explicitly in samplesheet.
-- Updated pipeline template to [nf-core/tools 2.10](https://github.com/nf-core/tools/releases/tag/2.10)
+- Updated pipeline template to [nf-core/tools 2.10](https://github.com/nf-core/tools/releases/tag/2.10).
+- [[#367](https://github.com/nf-core/chipseq/issues/367)] - Get rid of `CheckIfExists` for params paths.
 
 ### Software dependencies
 

diff --git a/lib/WorkflowChipseq.groovy b/lib/WorkflowChipseq.groovy
@@ -10,14 +10,9 @@ class WorkflowChipseq {
     //
     // Check and validate parameters
     //
-    public static void initialise(params, log, valid_params) {
+    public static void initialise(params, log) {
         genomeExistsError(params, log)
 
-
-        if (!params.fasta) {
-            Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
-        }
-
         if (!params.gtf && !params.gff) {
             def error_string = "No GTF or GFF3 annotation specified! The pipeline requires at least one of these files."
             Nextflow.error(error_string)
@@ -35,13 +30,6 @@ class WorkflowChipseq {
             def error_string = "Both '--read_length' and '--macs_gsize' not specified! Please specify either to infer MACS2 genome size for peak calling."
             Nextflow.error(error_string)
         }
-
-        if (params.aligner) {
-            if (!valid_params['aligners'].contains(params.aligner)) {
-                    def error_string = "Invalid option: '${params.aligner}'. Valid options for '--aligner': ${valid_params['aligners'].join(', ')}."
-                    Nextflow.error(error_string)
-            }
-        }
     }
 
     //

diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
@@ -41,11 +41,6 @@ class WorkflowMain {
 
         // Check AWS batch settings
         NfcoreTemplate.awsBatch(workflow, params)
-
-        // Check input has been provided
-        if (!params.input) {
-            Nextflow.error("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'")
-        }
     }
     //
     // Get attribute from genome config file e.g. fasta

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -10,7 +10,7 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": ["outdir"],
+            "required": ["input", "outdir"],
             "properties": {
                 "input": {
                     "type": "string",
@@ -85,6 +85,7 @@
                 "gtf": {
                     "type": "string",
                     "format": "file-path",
+                    "exists": true,
                     "mimetype": "text/plain",
                     "pattern": "^\\S+\\.gtf(\\.gz)?$",
                     "description": "Path to GTF annotation file.",
@@ -94,6 +95,7 @@
                 "gff": {
                     "type": "string",
                     "format": "file-path",
+                    "exists": true,
                     "mimetype": "text/plain",
                     "pattern": "^\\S+\\.gff(\\.gz)?$",
                     "fa_icon": "fas fa-code-branch",
@@ -102,30 +104,36 @@
                 },
                 "bwa_index": {
                     "type": "string",
+                    "format": "path",
+                    "exists": true,
                     "description": "Path to directory or tar.gz archive for pre-built BWA index.",
                     "fa_icon": "fas fa-bezier-curve"
                 },
                 "bowtie2_index": {
                     "type": "string",
                     "format": "path",
+                    "exists": true,
                     "fa_icon": "fas fa-bezier-curve",
                     "description": "Path to directory or tar.gz archive for pre-built Bowtie2 index."
                 },
                 "chromap_index": {
                     "type": "string",
                     "format": "path",
+                    "exists": true,
                     "fa_icon": "fas fa-bezier-curve",
                     "description": "Path to directory or tar.gz archive for pre-built Chromap index."
                 },
                 "star_index": {
                     "type": "string",
                     "format": "path",
+                    "exists": true,
                     "fa_icon": "fas fa-bezier-curve",
                     "description": "Path to directory or tar.gz archive for pre-built STAR index."
                 },
                 "gene_bed": {
                     "type": "string",
                     "format": "file-path",
+                    "exists": true,
                     "mimetype": "text/plain",
                     "pattern": "^\\S+\\.bed(\\.gz)?$",
                     "fa_icon": "fas fa-procedures",
@@ -139,6 +147,8 @@
                 },
                 "blacklist": {
                     "type": "string",
+                    "format": "path",
+                    "exists": true,
                     "description": "Path to blacklist regions in BED format, used for filtering alignments.",
                     "help_text": "If provided, alignments that overlap with the regions in this file will be filtered out (see [ENCODE blacklists](https://sites.google.com/site/anshulkundaje/projects/blacklists)). The file should be in BED format. Blacklisted regions for *GRCh37*, *GRCh38*, *GRCm38*, *hg19*, *hg38*, *mm10* are bundled with the pipeline in the [`/assets/blacklists`](https://github.com/nf-core/chipseq/tree/master/assets/blacklists) directory, and as such will be automatically used if any of those genomes are specified with the `--genome` parameter.",
                     "fa_icon": "fas fa-book-dead"
@@ -164,7 +174,8 @@
                     "hidden": true,
                     "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`."
                 }
-            }
+            },
+            "required": ["fasta"]
         },
         "adapter_trimming_options": {
             "title": "Adapter trimming options",
@@ -254,13 +265,17 @@
                 },
                 "bamtools_filter_pe_config": {
                     "type": "string",
+                    "format": "path",
+                    "exists": true,
                     "default": "$projectDir/assets/bamtools_filter_pe.json",
                     "hidden": true,
                     "description": "BAMTools JSON file with custom filters for paired-end data.",
                     "fa_icon": "fas fa-cog"
                 },
                 "bamtools_filter_se_config": {
                     "type": "string",
+                    "format": "path",
+                    "exists": true,
                     "default": "$projectDir/assets/bamtools_filter_se.json",
                     "hidden": true,
                     "description": "BAMTools JSON file with custom filters for single-end data.",
@@ -546,18 +561,25 @@
                 "multiqc_config": {
                     "type": "string",
                     "format": "file-path",
+                    "exists": true,
+                    "mimetype": "text/plain",
                     "description": "Custom config file to supply to MultiQC.",
                     "fa_icon": "fas fa-cog",
                     "hidden": true
                 },
                 "multiqc_logo": {
                     "type": "string",
+                    "format": "file-path",
+                    "exists": true,
                     "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
                     "fa_icon": "fas fa-image",
                     "hidden": true
                 },
                 "multiqc_methods_description": {
                     "type": "string",
+                    "format": "file-path",
+                    "exists": true,
+                    "mimetype": "text/plain",
                     "description": "Custom MultiQC yaml file containing HTML including a methods description.",
                     "fa_icon": "fas fa-cog"
                 },
@@ -580,7 +602,7 @@
                     "fa_icon": "far fa-check-circle",
                     "description": "Validation of parameters fails when an unrecognised parameter is found.",
                     "hidden": true,
-                    "help_text": "By default, when an unrecognised parameter is found, it returns a warinig."
+                    "help_text": "By default, when an unrecognised parameter is found, it returns a warning."
                 },
                 "validationLenientMode": {
                     "type": "boolean",

diff --git a/workflows/chipseq.nf b/workflows/chipseq.nf
@@ -13,23 +13,10 @@ def summary_params = paramsSummaryMap(workflow)
 // Print parameter summary log to screen
 log.info logo + paramsSummaryLog(workflow) + citation
 
-def valid_params = [
-    aligners       : [ 'bwa', 'bowtie2', 'chromap', 'star' ]
-]
-
 // Validate input parameters
-WorkflowChipseq.initialise(params, log, valid_params)
-
-// Check input path parameters to see if they exist
-def checkPathParamList = [
-    params.input, params.multiqc_config,
-    params.fasta,
-    params.gtf, params.gff, params.gene_bed,
-    params.bwa_index, params.bowtie2_index, params.chromap_index, params.star_index,
-    params.blacklist,
-    params.bamtools_filter_pe_config, params.bamtools_filter_se_config
-]
-for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
+WorkflowChipseq.initialise(params, log)
+
+ch_input = file(params.input)
 
 // Save AWS IGenomes file containing annotation version
 def anno_readme = params.genomes[ params.genome ]?.readme
@@ -45,13 +32,13 @@ if (anno_readme && file(anno_readme).exists()) {
 */
 
 ch_multiqc_config          = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-ch_multiqc_custom_config   = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty()
-ch_multiqc_logo            = params.multiqc_logo   ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty()
-ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
+ch_multiqc_custom_config   = params.multiqc_config ? Channel.fromPath( params.multiqc_config ): Channel.empty()
+ch_multiqc_logo            = params.multiqc_logo   ? Channel.fromPath( params.multiqc_logo )  : Channel.empty()
+ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
 
 // JSON files required by BAMTools for alignment filtering
-ch_bamtools_filter_se_config = file(params.bamtools_filter_se_config, checkIfExists: true)
-ch_bamtools_filter_pe_config = file(params.bamtools_filter_pe_config, checkIfExists: true)
+ch_bamtools_filter_se_config = file(params.bamtools_filter_se_config)
+ch_bamtools_filter_pe_config = file(params.bamtools_filter_pe_config)
 
 // Header files for MultiQC
 ch_spp_nsc_header           = file("$projectDir/assets/multiqc/spp_nsc_header.txt", checkIfExists: true)