Address review comments

main.nf

@@ -80,7 +80,7 @@ workflow NFCORE_ATACSEQ {
     ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)
 
     //
-    // WORKFLOW: Run nf-core/rnaseq workflow
+    // WORKFLOW: Run nf-core/atacseq workflow
     //
     ch_samplesheet = Channel.value(file(params.input, checkIfExists: true))
 

subworkflows/local/utils_nfcore_atacseq_pipeline/main.nf

@@ -111,6 +111,10 @@ workflow PIPELINE_COMPLETION {
             imNotification(summary_params, hook_url)
         }
     }
+
+    workflow.onError {
+        log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting"
+    }
 }
 
 /*
@@ -119,27 +123,6 @@ workflow PIPELINE_COMPLETION {
 ========================================================================================
 */
 
-//
-// Function to 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 strandedness
-    def strandedness_ok = metas.collect{ it.strandedness }.unique().size == 1
-    if (!strandedness_ok) {
-        error("Please check input samplesheet -> Multiple runs of a sample must have the same strandedness!: ${metas[0].id}")
-    }
-
-    // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
-    def endedness_ok = metas.collect{ it.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 ]
-}
-
 //
 // Check and validate pipeline parameters
 //
@@ -158,6 +141,14 @@ def validateInputParameters() {
     if (params.gtf && params.gff) {
         gtfGffWarn(log)
     }
+
+    if (!params.macs_gsize) {
+        macsGsizeWarn(log)
+    }
+
+    if (!params.read_length && !params.macs_gsize) {
+        error ("Both '--read_length' and '--macs_gsize' not specified! Please specify either to infer MACS2 genome size for peak calling.")
+    }
 }
 
 //

workflows/atacseq.nf

@@ -684,7 +684,7 @@ workflow ATACSEQ {
     // Collate and save software versions
     //
     softwareVersionsToYAML(ch_versions)
-        .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_rnaseq_software_mqc_versions.yml', sort: true, newLine: true)
+        .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_atacseq_software_mqc_versions.yml', sort: true, newLine: true)
         .set { ch_collated_versions }
 
     //