remove redundant sample sheet parsing

nf-core · Mar 19, 2024 · 656c56c · 656c56c
1 parent db4ec6b
commit 656c56c
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Showing 3 changed files with 4 additions and 41 deletions.
diff --git a/main.nf b/main.nf
@@ -32,17 +32,12 @@ include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_ampl
 //
 workflow NFCORE_AMPLISEQ {
 
-    take:
-    samplesheet // channel: samplesheet read in from --input
-
     main:
 
     //
     // WORKFLOW: Run pipeline
     //
-    AMPLISEQ (
-        samplesheet
-    )
+    AMPLISEQ ()
 
     emit:
     multiqc_report = AMPLISEQ.out.multiqc_report // channel: /path/to/multiqc_report.html
@@ -67,16 +62,13 @@ workflow {
         params.validate_params,
         params.monochrome_logs,
         args,
-        params.outdir,
-        params.input
+        params.outdir
     )
 
     //
     // WORKFLOW: Run main workflow
     //
-    NFCORE_AMPLISEQ (
-        PIPELINE_INITIALISATION.out.samplesheet
-    )
+    NFCORE_AMPLISEQ ()
 
     //
     // SUBWORKFLOW: Run completion tasks

diff --git a/subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf
@@ -35,7 +35,6 @@ workflow PIPELINE_INITIALISATION {
     monochrome_logs   // boolean: Do not use coloured log outputs
     nextflow_cli_args //   array: List of positional nextflow CLI args
     outdir            //  string: The output directory where the results will be saved
-    input             //  string: Path to input samplesheet
 
     main:
 
@@ -94,31 +93,7 @@ workflow PIPELINE_INITIALISATION {
         sidlereftaxonomyExistsError()
     }
 
-    //
-    // Create channel from input file provided through params.input
-    //
-    Channel
-        .fromSamplesheet("input")
-        .map {
-            meta, fastq_1, fastq_2 ->
-                if (!fastq_2) {
-                    return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ]
-                } else {
-                    return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ]
-                }
-        }
-        .groupTuple()
-        .map {
-            validateInputSamplesheet(it)
-        }
-        .map {
-            meta, fastqs ->
-                return [ meta, fastqs.flatten() ]
-        }
-        .set { ch_samplesheet }
-
     emit:
-    samplesheet = ch_samplesheet
     versions    = ch_versions
 }
 

diff --git a/workflows/ampliseq.nf b/workflows/ampliseq.nf
@@ -255,9 +255,6 @@ include { makeComplement         } from '../subworkflows/local/utils_nfcore_ampl
 
 workflow AMPLISEQ {
 
-    take:
-    ch_samplesheet // channel: samplesheet read in from --input
-
     main:
 
     ch_versions = Channel.empty()
@@ -266,7 +263,6 @@ workflow AMPLISEQ {
     //
     // Create input channels
     //
-    //TODO: --input, --input_folder, --input_fasts, --metadata, --multiregion might need adjustments, because above under "tae:" it is supposed to be coming from!
     ch_input_fasta = Channel.empty()
     ch_input_reads = Channel.empty()
     if ( params.input ) {
@@ -905,7 +901,7 @@ workflow AMPLISEQ {
             ch_metadata.ifEmpty( [] ),
             params.input ? file(params.input) : [], // samplesheet input
             ch_input_fasta.ifEmpty( [] ), // fasta input
-            !params.input_fasta && !params.skip_fastqc && !params.skip_multiqc ? MULTIQC.out.plots : [], //.collect().flatten().collectFile(name: "mqc_fastqc_per_sequence_quality_scores_plot_1.svg")
+            !params.input_fasta && !params.skip_fastqc && !params.skip_multiqc ? MULTIQC.out.plots : [], //.collect().flatten().collectFile(name: "fastqc_per_sequence_quality_scores_plot.svg")
             !params.skip_cutadapt ? CUTADAPT_WORKFLOW.out.summary.collect().ifEmpty( [] ) : [],
             find_truncation_values,
             DADA2_PREPROCESSING.out.args.first().ifEmpty( [] ),