From 8c4d201dd53ac1f5cae3cd0fb064e6eacc7a5d01 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Tue, 16 Feb 2021 11:27:25 +0100
Subject: [PATCH] chores: remove deprecated bwamem2/index modules cf #166

---
 deprecated/bwa-mem2/index/main.nf             | 16 ------------
 deprecated/bwa-mem2/index/meta.yml            | 26 -------------------
 deprecated/bwa-mem2/index/test/main.nf        | 16 ------------
 .../bwa-mem2/index/test/nextflow.config       |  2 --
 4 files changed, 60 deletions(-)
 delete mode 100644 deprecated/bwa-mem2/index/main.nf
 delete mode 100644 deprecated/bwa-mem2/index/meta.yml
 delete mode 100644 deprecated/bwa-mem2/index/test/main.nf
 delete mode 100644 deprecated/bwa-mem2/index/test/nextflow.config

diff --git a/deprecated/bwa-mem2/index/main.nf b/deprecated/bwa-mem2/index/main.nf
deleted file mode 100644
index 7dd459e4..00000000
--- a/deprecated/bwa-mem2/index/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-process bwa-mem2_index {
-    tag {fasta}
-
-    container 'quay.io/biocontainers/bwa-mem2:2.0--he513fc3_0'
-
-    input:
-        path(fasta)
-
-    output:
-        path("${fasta}.*")
-
-    script:
-    """
-    bwa-mem2 index ${fasta}
-    """
-}
diff --git a/deprecated/bwa-mem2/index/meta.yml b/deprecated/bwa-mem2/index/meta.yml
deleted file mode 100644
index 97d6e854..00000000
--- a/deprecated/bwa-mem2/index/meta.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-name: bwa-mem2 index
-description: create indexes for BWA from a fasta file
-keywords:
-    - index
-tools:
-    - bwa:
-        description: |
-            Bwa-mem2 is the next version of the bwa-mem algorithm in bwa.
-            It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine.
-        homepage: https://github.com/bwa-mem2/bwa-mem2
-        documentation: https://github.com/bwa-mem2/bwa-mem2
-        arxiv: arXiv:1303.3997
-input:
-    -
-        - input:
-            type: file
-            description: Input fasta file
-            pattern: "*.{fasta,fa}"
-output:
-    -
-        - index:
-            type: file
-            description: bwa indexes file
-            pattern: "*.{fasta,fa}.{amb,ann,bwt,pac,sa}"
-authors:
-    - "@maxulysse"
diff --git a/deprecated/bwa-mem2/index/test/main.nf b/deprecated/bwa-mem2/index/test/main.nf
deleted file mode 100644
index 6acb4d61..00000000
--- a/deprecated/bwa-mem2/index/test/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-nextflow.preview.dsl = 2
-include '../../../nf-core/module_testing/check_process_outputs.nf' params(params)
-include '../main.nf' params(params)
-
-// Define input channels
-input = '../../../test-datasets/tools/bwa/index/input/reference.fasta'
-Channel
-  .from(input)
-  .set { ch_input }
-
-// Run the workflow
-workflow {
-    fastqc(ch_input)
-    // .check_output()
-}
diff --git a/deprecated/bwa-mem2/index/test/nextflow.config b/deprecated/bwa-mem2/index/test/nextflow.config
deleted file mode 100644
index c137a138..00000000
--- a/deprecated/bwa-mem2/index/test/nextflow.config
+++ /dev/null
@@ -1,2 +0,0 @@
-docker.enabled = true
-params.outdir = './results'