Remove samplesheet read from schema

Author: JoseEspinosa

main.nf

@@ -20,14 +20,13 @@ include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_chip
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_chipseq_pipeline'
 include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_chipseq_pipeline'
 
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     GENOME PARAMETER VALUES
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-params.fasta         = getGenomeAttribute('fasta') // TODO check if the function ways with the include
+params.fasta         = getGenomeAttribute('fasta')
 params.bwa_index     = getGenomeAttribute('bwa')
 params.bowtie2_index = getGenomeAttribute('bowtie2')
 params.chromap_index = getGenomeAttribute('chromap')
@@ -70,10 +69,23 @@ workflow NFCORE_CHIPSEQ {
     ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)
 
     //
-    // WORKFLOW: Run pipeline
+    // WORKFLOW: Run nf-core/chipseq workflow
     //
-    CHIPSEQ (
-        samplesheet
+    ch_input = Channel.value(file(params.input, checkIfExists: true))
+
+    CHIPSEQ(
+        ch_input,
+        ch_versions,
+        PREPARE_GENOME.out.fasta,
+        PREPARE_GENOME.out.fai,
+        PREPARE_GENOME.out.gtf,
+        PREPARE_GENOME.out.gene_bed,
+        PREPARE_GENOME.out.chrom_sizes,
+        PREPARE_GENOME.out.filtered_bed,
+        PREPARE_GENOME.out.bwa_index,
+        PREPARE_GENOME.out.bowtie2_index,
+        PREPARE_GENOME.out.chromap_index,
+        PREPARE_GENOME.out.star_index
     )
 
     emit:
@@ -104,9 +116,7 @@ workflow {
     //
     // WORKFLOW: Run main workflow
     //
-    NFCORE_CHIPSEQ (
-        PIPELINE_INITIALISATION.out.samplesheet //TODO check whether it works
-    )
+    NFCORE_CHIPSEQ ( )
 
     //
     // SUBWORKFLOW: Run completion tasks

subworkflows/local/utils_nfcore_chipseq_pipeline/main.nf

@@ -34,6 +34,8 @@ workflow PIPELINE_INITIALISATION {
 
     main:
 
+    ch_versions = Channel.empty()
+
     //
     // Print version and exit if required and dump pipeline parameters to JSON file
     //
@@ -48,30 +50,33 @@ workflow PIPELINE_INITIALISATION {
     //
     // Validate parameters and generate parameter summary to stdout
     //
-    pre_help_text = nfCoreLogo(monochrome_logs)
-    post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs)
-    def String workflow_command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --genome GRCh37 --outdir <OUTDIR>"
-    UTILS_NFVALIDATION_PLUGIN (
-        help,
-        workflow_command,
-        pre_help_text,
-        post_help_text,
+    UTILS_NFSCHEMA_PLUGIN (
+        workflow,
         validate_params,
         null
     )
 
-
     //
     // Check config provided to the pipeline
     //
     UTILS_NFCORE_PIPELINE (
         nextflow_cli_args
     )
+
     //
     // Custom validation for pipeline parameters
     //
     validateInputParameters()
 
+    //
+    // Create channel from input file provided through params.input
+    //
+
+    ch_samplesheet = Channel.fromList(samplesheetToList(params.input, "assets/schema_input.json"))
+
+    emit:
+    samplesheet = ch_samplesheet
+    versions    = ch_versions
 }
 
 /*

workflows/chipseq.nf

@@ -89,7 +89,7 @@ if (anno_readme && file(anno_readme).exists()) {
 workflow CHIPSEQ {
 
     take:
-    ch_samplesheet // channel: samplesheet read in from --input //TODO
+    // ch_samplesheet // channel: samplesheet read in from --input //TODO
     ch_input         // channel: path(sample_sheet.csv)
     ch_versions      // channel: [ path(versions.yml) ]
     ch_fasta         // channel: path(genome.fa)