From 691720b05b93762d192d91195a6f957aa9b4fcca Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 23 Feb 2023 12:59:24 +0100
Subject: [PATCH] remove unused module and subworkflow

---
 .../modules/local/samplesheet_check.nf        | 27 ------------
 .../subworkflows/local/input_check.nf         | 44 -------------------
 2 files changed, 71 deletions(-)
 delete mode 100644 nf_core/pipeline-template/modules/local/samplesheet_check.nf
 delete mode 100644 nf_core/pipeline-template/subworkflows/local/input_check.nf

diff --git a/nf_core/pipeline-template/modules/local/samplesheet_check.nf b/nf_core/pipeline-template/modules/local/samplesheet_check.nf
deleted file mode 100644
index ccfdfecc2..000000000
--- a/nf_core/pipeline-template/modules/local/samplesheet_check.nf
+++ /dev/null
@@ -1,27 +0,0 @@
-process SAMPLESHEET_CHECK {
-    tag "$samplesheet"
-
-    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/python:3.8.3' :
-        'quay.io/biocontainers/python:3.8.3' }"
-
-    input:
-    path samplesheet
-
-    output:
-    path '*.csv'       , emit: csv
-    path "versions.yml", emit: versions
-
-    script: // This script is bundled with the pipeline, in {{ name }}/bin/
-    """
-    check_samplesheet.py \\
-        $samplesheet \\
-        samplesheet.valid.csv
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        python: \$(python --version | sed 's/Python //g')
-    END_VERSIONS
-    """
-}
diff --git a/nf_core/pipeline-template/subworkflows/local/input_check.nf b/nf_core/pipeline-template/subworkflows/local/input_check.nf
deleted file mode 100644
index 0aecf87fb..000000000
--- a/nf_core/pipeline-template/subworkflows/local/input_check.nf
+++ /dev/null
@@ -1,44 +0,0 @@
-//
-// Check input samplesheet and get read channels
-//
-
-include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check'
-
-workflow INPUT_CHECK {
-    take:
-    samplesheet // file: /path/to/samplesheet.csv
-
-    main:
-    SAMPLESHEET_CHECK ( samplesheet )
-        .csv
-        .splitCsv ( header:true, sep:',' )
-        .map { create_fastq_channel(it) }
-        .set { reads }
-
-    emit:
-    reads                                     // channel: [ val(meta), [ reads ] ]
-    versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ]
-}
-
-// Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
-def create_fastq_channel(LinkedHashMap row) {
-    // create meta map
-    def meta = [:]
-    meta.id         = row.sample
-    meta.single_end = row.single_end.toBoolean()
-
-    // add path(s) of the fastq file(s) to the meta map
-    def fastq_meta = []
-    if (!file(row.fastq_1).exists()) {
-        exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}"
-    }
-    if (meta.single_end) {
-        fastq_meta = [ meta, [ file(row.fastq_1) ] ]
-    } else {
-        if (!file(row.fastq_2).exists()) {
-            exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
-        }
-        fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
-    }
-    return fastq_meta
-}