Merge pull request #434 from JoseEspinosa/fixes

Prevent pipeline fails from erroneous param validation when igenomes is used

Author: bjlang

CHANGELOG.md

@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
+[[PR #434](https://github.com/nf-core/chipseq/pull/434)] - Prevent pipeline fails from erroneous param validation when igenomes is used.
+
 ### Parameters
 
 | Old parameter | New parameter |

main.nf

@@ -9,17 +9,6 @@
 ----------------------------------------------------------------------------------------
 */
 
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-include { CHIPSEQ                 } from './workflows/chipseq'
-include { PREPARE_GENOME          } from './subworkflows/local/prepare_genome'
-include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_chipseq_pipeline'
-include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_chipseq_pipeline'
-include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_chipseq_pipeline'
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     GENOME PARAMETER VALUES
@@ -37,6 +26,17 @@ params.gene_bed      = getGenomeAttribute('gene_bed')
 params.blacklist     = getGenomeAttribute('blacklist')
 params.macs_gsize    = getMacsGsize(params)
 
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+include { CHIPSEQ                 } from './workflows/chipseq'
+include { PREPARE_GENOME          } from './subworkflows/local/prepare_genome'
+include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_chipseq_pipeline'
+include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_chipseq_pipeline'
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     NAMED WORKFLOWS FOR PIPELINE
@@ -138,6 +138,18 @@ workflow {
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
+//
+// Get attribute from genome config file e.g. fasta
+//
+def getGenomeAttribute(attribute) {
+    if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
+        if (params.genomes[params.genome].containsKey(attribute)) {
+            return params.genomes[params.genome][attribute]
+        }
+    }
+    return null
+}
+
 //
 // Get macs genome size (macs_gsize)
 //

subworkflows/local/utils_nfcore_chipseq_pipeline/main.nf

@@ -158,33 +158,6 @@ def validateInputParameters() {
     }
 }
 
-//
-// Validate channels from input samplesheet
-//
-def validateInputSamplesheet(input) {
-    def (metas, fastqs) = input[1..2]
-
-    // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
-    def endedness_ok = metas.collect { meta -> meta.single_end }.unique().size == 1
-    if (!endedness_ok) {
-        error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}")
-    }
-
-    return [metas[0], fastqs]
-}
-
-//
-// Get attribute from genome config file e.g. fasta
-//
-def getGenomeAttribute(attribute) {
-    if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
-        if (params.genomes[params.genome].containsKey(attribute)) {
-            return params.genomes[params.genome][attribute]
-        }
-    }
-    return null
-}
-
 //
 // Exit pipeline if incorrect --genome key provided
 //