From 27bfe82d3404e14bc266622046c1be22319f679d Mon Sep 17 00:00:00 2001
From: subwaystation <simon.heumos@qbic.uni-tuebingen.de>
Date: Wed, 21 Jun 2023 14:06:08 +0200
Subject: [PATCH] delete unused samplesheet files

---
 assets/samplesheet.csv             |  3 ---
 assets/schema_input.json           | 36 ------------------------------
 modules/local/samplesheet_check.nf | 31 -------------------------
 3 files changed, 70 deletions(-)
 delete mode 100644 assets/samplesheet.csv
 delete mode 100644 assets/schema_input.json
 delete mode 100644 modules/local/samplesheet_check.nf

diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
deleted file mode 100644
index 5f653ab7..00000000
--- a/assets/samplesheet.csv
+++ /dev/null
@@ -1,3 +0,0 @@
-sample,fastq_1,fastq_2
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,
diff --git a/assets/schema_input.json b/assets/schema_input.json
deleted file mode 100644
index 89256bdf..00000000
--- a/assets/schema_input.json
+++ /dev/null
@@ -1,36 +0,0 @@
-{
-    "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "https://raw.githubusercontent.com/nf-core/pangenome/master/assets/schema_input.json",
-    "title": "nf-core/pangenome pipeline - params.input schema",
-    "description": "Schema for the file provided with params.input",
-    "type": "array",
-    "items": {
-        "type": "object",
-        "properties": {
-            "sample": {
-                "type": "string",
-                "pattern": "^\\S+$",
-                "errorMessage": "Sample name must be provided and cannot contain spaces"
-            },
-            "fastq_1": {
-                "type": "string",
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
-                "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
-            },
-            "fastq_2": {
-                "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
-                "anyOf": [
-                    {
-                        "type": "string",
-                        "pattern": "^\\S+\\.f(ast)?q\\.gz$"
-                    },
-                    {
-                        "type": "string",
-                        "maxLength": 0
-                    }
-                ]
-            }
-        },
-        "required": ["sample", "fastq_1"]
-    }
-}
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
deleted file mode 100644
index d17dedff..00000000
--- a/modules/local/samplesheet_check.nf
+++ /dev/null
@@ -1,31 +0,0 @@
-process SAMPLESHEET_CHECK {
-    tag "$samplesheet"
-    label 'process_single'
-
-    conda "conda-forge::python=3.8.3"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/python:3.8.3' :
-        'biocontainers/python:3.8.3' }"
-
-    input:
-    path samplesheet
-
-    output:
-    path '*.csv'       , emit: csv
-    path "versions.yml", emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script: // This script is bundled with the pipeline, in nf-core/pangenome/bin/
-    """
-    check_samplesheet.py \\
-        $samplesheet \\
-        samplesheet.valid.csv
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        python: \$(python --version | sed 's/Python //g')
-    END_VERSIONS
-    """
-}