From 289f9aa3bb1cc47bee724a17044e516aa605619a Mon Sep 17 00:00:00 2001
From: atrigila <18577080+atrigila@users.noreply.github.com>
Date: Fri, 27 Sep 2024 14:46:23 +0000
Subject: [PATCH] remove local mirdeep

---
 modules/local/mirdeep2_mapper.nf | 43 --------------------------------
 modules/local/mirdeep2_run.nf    | 42 -------------------------------
 subworkflows/local/mirdeep2.nf   | 31 -----------------------
 workflows/smrnaseq.nf            |  1 -
 4 files changed, 117 deletions(-)
 delete mode 100644 modules/local/mirdeep2_mapper.nf
 delete mode 100644 modules/local/mirdeep2_run.nf
 delete mode 100644 subworkflows/local/mirdeep2.nf

diff --git a/modules/local/mirdeep2_mapper.nf b/modules/local/mirdeep2_mapper.nf
deleted file mode 100644
index e810c736..00000000
--- a/modules/local/mirdeep2_mapper.nf
+++ /dev/null
@@ -1,43 +0,0 @@
-def VERSION = '2.0.1'
-
-process MIRDEEP2_MAPPER {
-    label 'process_medium'
-    tag "$meta.id"
-
-    conda 'bioconda::mirdeep2=2.0.1.2'
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mirdeep2:2.0.1.3--hdfd78af_1' :
-        'biocontainers/mirdeep2:2.0.1.3--hdfd78af_1' }"
-
-    input:
-    tuple val(meta), path(reads)
-    path index
-
-    output:
-    tuple val(meta), path('*_collapsed.fa'), path('*reads_vs_refdb.arf'), emit: mirdeep2_inputs
-    path "versions.yml"                                                 , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def index_base = index.toString().tokenize(' ')[0].tokenize('.')[0]
-    """
-    mapper.pl \\
-    $reads \\
-        -e \\
-        -h \\
-        -i \\
-        -j \\
-        -m \\
-        -p $index_base \\
-        -s ${meta.id}_collapsed.fa \\
-        -t ${meta.id}_reads_vs_refdb.arf \\
-        -o 4
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        mapper: \$(echo "$VERSION")
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/mirdeep2_run.nf b/modules/local/mirdeep2_run.nf
deleted file mode 100644
index a65dd175..00000000
--- a/modules/local/mirdeep2_run.nf
+++ /dev/null
@@ -1,42 +0,0 @@
-def VERSION = '2.0.1'
-
-process MIRDEEP2_RUN {
-    label 'process_medium'
-    errorStrategy 'ignore' //TODO why was it set like this?
-
-    conda 'bioconda::mirdeep2=2.0.1.2'
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mirdeep2:2.0.1.3--hdfd78af_1' :
-        'biocontainers/mirdeep2:2.0.1.3--hdfd78af_1' }"
-
-    input:
-    path(fasta)
-    tuple val(meta), path(reads), path(arf)
-    path(hairpin)
-    path(mature)
-
-    output:
-    tuple val(meta), path('result*.{bed,csv,html}'), emit: result
-    path "versions.yml"                            , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    """
-    miRDeep2.pl  \\
-        $reads   \\
-        $fasta   \\
-        $arf     \\
-        $mature  \\
-        none     \\
-        $hairpin \\
-        -d       \\
-        -z _${reads.simpleName}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        mirdeep2: \$(echo "$VERSION")
-    END_VERSIONS
-    """
-}
diff --git a/subworkflows/local/mirdeep2.nf b/subworkflows/local/mirdeep2.nf
deleted file mode 100644
index 40dd9f29..00000000
--- a/subworkflows/local/mirdeep2.nf
+++ /dev/null
@@ -1,31 +0,0 @@
-//
-// Quantify mirna with bowtie and mirtop
-//
-
-include { PIGZ_UNCOMPRESS } from '../../modules/nf-core/pigz/uncompress/main'
-include { MIRDEEP2_MAPPER } from '../../modules/local/mirdeep2_mapper'
-include { MIRDEEP2_RUN    } from '../../modules/local/mirdeep2_run'
-
-workflow MIRDEEP2 {
-    take:
-    reads        // channel: [ val(meta), [ reads ] ]
-    fasta        // channel: [ val(meta), path(fasta) ]
-    index        // channel: [genome.1.ebwt, genome.2.ebwt, genome.3.ebwt, genome.4.ebwt, genome.rev.1.ebwt, genome.rev.2.ebwt]
-    hairpin      // channel: [ path(hairpin.fa) ]
-    mature       // channel: [ path(mature.fa)  ]
-
-    main:
-    ch_versions = Channel.empty()
-
-    PIGZ_UNCOMPRESS ( reads )
-    ch_versions = ch_versions.mix(PIGZ_UNCOMPRESS.out.versions.first())
-
-    MIRDEEP2_MAPPER ( PIGZ_UNCOMPRESS.out.file, index )
-    ch_versions = ch_versions.mix(MIRDEEP2_MAPPER.out.versions.first())
-
-    MIRDEEP2_RUN ( fasta.map{meta,file->file}, MIRDEEP2_MAPPER.out.mirdeep2_inputs, hairpin, mature )
-    ch_versions = ch_versions.mix(MIRDEEP2_RUN.out.versions.first())
-
-    emit:
-    versions = ch_versions // channel: [ versions.yml ]
-}
diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf
index 23f876d8..fd3e31aa 100644
--- a/workflows/smrnaseq.nf
+++ b/workflows/smrnaseq.nf
@@ -22,7 +22,6 @@ include { FASTQ_FIND_MIRNA_MIRDEEP2        } from '../subworkflows/nf-core/fastq
 include { CONTAMINANT_FILTER               } from '../subworkflows/local/contaminant_filter/main'
 include { GENOME_QUANT                     } from '../subworkflows/local/genome_quant'
 include { MIRNA_QUANT                      } from '../subworkflows/local/mirna_quant'
-include { MIRDEEP2                         } from '../subworkflows/local/mirdeep2'
 // plugins
 include { paramsSummaryMap                 } from 'plugin/nf-validation'