From 989dc55ce107ae01331727eb9678a0d41e22de03 Mon Sep 17 00:00:00 2001
From: sofstam <sofia.stamouli@scilifelab.se>
Date: Mon, 11 Apr 2022 17:42:38 +0200
Subject: [PATCH] Delete extra nf-core directory

---
 nf-core/modules/centrifuge/centrifuge/main.nf | 61 -----------------
 .../modules/centrifuge/centrifuge/meta.yml    | 66 -------------------
 2 files changed, 127 deletions(-)
 delete mode 100644 nf-core/modules/centrifuge/centrifuge/main.nf
 delete mode 100644 nf-core/modules/centrifuge/centrifuge/meta.yml

diff --git a/nf-core/modules/centrifuge/centrifuge/main.nf b/nf-core/modules/centrifuge/centrifuge/main.nf
deleted file mode 100644
index 3d23fc9..0000000
--- a/nf-core/modules/centrifuge/centrifuge/main.nf
+++ /dev/null
@@ -1,61 +0,0 @@
-process CENTRIFUGE_CENTRIFUGE {
-    tag "$meta.id"
-    label 'process_high'
-
-    conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6' :
-        'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }"
-
-    input:
-    tuple val(meta), path(reads)
-    path db
-    val save_unaligned
-    val save_aligned
-    val sam_format
-
-    output:
-    tuple val(meta), path('*report.txt')                 , emit: report
-    tuple val(meta), path('*results.txt')                , emit: results
-    tuple val(meta), path('*.sam')                       , optional: true, emit: sam
-    tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz')   , optional: true, emit: fastq_mapped
-    tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_unmapped
-    path "versions.yml"                                  , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def paired = meta.single_end ? "-U ${reads}" :  "-1 ${reads[0]} -2 ${reads[1]}"
-    def unaligned = ''
-    def aligned = ''
-    if (meta.single_end) {
-        unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
-        aligned = save_aligned ? "--al-gz ${prefix}.mapped.fastq.gz" : ''
-    } else {
-        unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
-        aligned = save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : ''
-    }
-    def sam_output = sam_format ? "--out-fmt 'sam'" : ''
-    """
-    ## we add "-no-name ._" to ensure silly Mac OSX metafiles files aren't included
-    db_name=`find -L ${db} -name "*.1.cf" -not -name "._*"  | sed 's/.1.cf//'`
-    centrifuge \\
-        -x \$db_name \\
-        -p $task.cpus \\
-        $paired \\
-        --report-file ${prefix}.report.txt \\
-        -S ${prefix}.results.txt \\
-        $unaligned \\
-        $aligned \\
-        $sam_output \\
-        $args
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        centrifuge: \$( centrifuge --version  | sed -n 1p | sed 's/^.*centrifuge-class version //')
-    END_VERSIONS
-    """
-}
diff --git a/nf-core/modules/centrifuge/centrifuge/meta.yml b/nf-core/modules/centrifuge/centrifuge/meta.yml
deleted file mode 100644
index a252c00..0000000
--- a/nf-core/modules/centrifuge/centrifuge/meta.yml
+++ /dev/null
@@ -1,66 +0,0 @@
-name: centrifuge_centrifuge
-description: Classifies metagenomic sequence data
-keywords:
-  - classify
-  - metagenomics
-  - fastq
-  - db
-tools:
-  - centrifuge:
-      description: Centrifuge is a classifier for metagenomic sequences.
-      homepage: https://ccb.jhu.edu/software/centrifuge/
-      documentation: https://ccb.jhu.edu/software/centrifuge/manual.shtml
-      doi: 10.1101/gr.210641.116
-      licence: ["GPL v3"]
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: |
-        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-        respectively.
-  - db:
-      type: directory
-      description: Path to directory containing centrifuge database files
-  - save_unaligned:
-      type: value
-      description: If true unmapped fastq files are saved
-  - save_aligned:
-      type: value
-      description: If true mapped fastq files are saved
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - report:
-      type: file
-      description: |
-        File containing a classification summary
-      pattern: "*.{report.txt}"
-  - results:
-      type: file
-      description: |
-        File containing classification results
-      pattern: "*.{results.txt}"
-  - fastq_unmapped:
-      type: file
-      description: Unmapped fastq files
-      pattern: "*.unmapped.fastq.gz"
-  - fastq_mapped:
-      type: file
-      description: Mapped fastq files
-      pattern: "*.mapped.fastq.gz"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-authors:
-  - "@sofstam"
-  - "@jfy133"
-  - "@sateeshperi"