From 0ada1f5217183b620768b0cf4b562063333ad32b Mon Sep 17 00:00:00 2001
From: LilyAnderssonLee <lilili2011me@gmail.com>
Date: Thu, 9 Jan 2025 15:31:05 +0100
Subject: [PATCH] remove old local modules

---
 modules/local/extract_viral_taxid.nf    | 44 -------------------------
 modules/local/extractcentrifugereads.nf | 42 -----------------------
 modules/local/extractdiamondreads.nf    | 43 ------------------------
 modules/local/rm_empty_fastq.nf         | 27 ---------------
 modules/local/subset_bam.nf             | 34 -------------------
 5 files changed, 190 deletions(-)
 delete mode 100644 modules/local/extract_viral_taxid.nf
 delete mode 100644 modules/local/extractcentrifugereads.nf
 delete mode 100644 modules/local/extractdiamondreads.nf
 delete mode 100644 modules/local/rm_empty_fastq.nf
 delete mode 100644 modules/local/subset_bam.nf

diff --git a/modules/local/extract_viral_taxid.nf b/modules/local/extract_viral_taxid.nf
deleted file mode 100644
index 0c4e9ac..0000000
--- a/modules/local/extract_viral_taxid.nf
+++ /dev/null
@@ -1,44 +0,0 @@
-process EXTRACT_VIRAL_TAXID {
-
-    tag "$meta.id"
-    label 'process_low'
-
-    conda "bioconda::seqkit=2.8.2"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.8.2--h9ee0642_1':
-        'biocontainers/seqkit:2.8.2--h9ee0642_1' }"
-
-    input:
-    val evalue // e-vaule threshold to filter the diamond report
-    tuple val(meta), path(taxpasta_standardised_profile)
-    tuple val(meta), path(report) // classification report
-
-    output:
-    tuple val(meta), path("*viral_taxids.tsv"), optional:true, emit: viral_taxid
-    path "versions.yml"                                      , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def prefix = task.ext.prefix ?: "${meta.id}_${meta.tool}"
-
-    """
-    if grep -qi "virus" $taxpasta_standardised_profile; then
-        grep -i "virus" $taxpasta_standardised_profile | cut -f 1 > taxpasta_viral_taxid.txt
-        if [[ "${meta.tool}" == "kraken2" || "${meta.tool}" == "centrifuge" ]]; then
-            awk -F'\t' '\$3 != 0 {print \$5}' ${report} > detected_taxid.txt
-            grep -F -w -f taxpasta_viral_taxid.txt detected_taxid.txt > ${prefix}_viral_taxids.tsv
-        elif [[ "${meta.tool}" == "diamond" ]]; then
-            awk '\$3 < ${evalue}' ${report} | cut -f 2 | uniq > detected_taxid.txt
-            grep -F -w -f taxpasta_viral_taxid.txt detected_taxid.txt | uniq > ${prefix}_viral_taxids.tsv
-        fi
-    else
-        echo "No viral taxids found." > "no_viral_taxid.txt"
-    fi
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        seqkit: \$( seqkit version | sed 's/seqkit v//' )
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/extractcentrifugereads.nf b/modules/local/extractcentrifugereads.nf
deleted file mode 100644
index 43c7e18..0000000
--- a/modules/local/extractcentrifugereads.nf
+++ /dev/null
@@ -1,42 +0,0 @@
-process EXTRACTCENTRIFUGEREADS {
-
-    tag "$meta.id"
-    label 'process_low'
-
-    conda "bioconda::seqkit=2.8.2"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.8.2--h9ee0642_1':
-        'biocontainers/seqkit:2.8.2--h9ee0642_1' }"
-
-    input:
-    val taxid
-    tuple val (meta), path(results)
-    tuple val (meta), path(fastq) // bowtie2/align *unmapped_{1,2}.fastq.gz
-
-    output:
-    tuple val(meta), path("*.fastq"), optional:true, emit: extracted_centrifuge_reads
-    path "versions.yml"                            , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    """
-    awk -v taxID=$taxid '\$3 == taxID && \$8 == 1 {print \$1}' $results > readID.txt
-    if [ "${meta.single_end}" == 'true' ]; then
-        seqkit grep -f readID.txt $fastq > ${prefix}_${taxid}.extracted_centrifuge_read.fastq
-    elif [ "${meta.single_end}" == 'false' ]; then
-        seqkit grep -f readID.txt ${fastq[0]} > ${prefix}_${taxid}.extracted_centrifuge_read1.fastq
-        seqkit grep -f readID.txt ${fastq[1]} > ${prefix}_${taxid}.extracted_centrifuge_read2.fastq
-    fi
-
-    rm readID.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        seqkit: \$( seqkit version | sed 's/seqkit v//' )
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/extractdiamondreads.nf b/modules/local/extractdiamondreads.nf
deleted file mode 100644
index 337be8b..0000000
--- a/modules/local/extractdiamondreads.nf
+++ /dev/null
@@ -1,43 +0,0 @@
-process EXTRACTCDIAMONDREADS {
-
-    tag "$meta.id"
-    label 'process_medium'
-
-    conda "bioconda::seqkit=2.8.2"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.8.2--h9ee0642_1':
-        'biocontainers/seqkit:2.8.2--h9ee0642_1' }"
-
-    input:
-    val taxid
-    tuple val (meta), path(tsv)
-    tuple val (meta), path(fastq) // bowtie2/align *unmapped_{1,2}.fastq.gz
-
-    output:
-    tuple val(meta), path("*.fastq"), optional:true, emit: extracted_diamond_reads
-    path "versions.yml"                            , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-
-    """
-    awk -v taxID=$taxid '\$2 == taxID {print \$1}' $tsv > readID.txt
-    if [ ${meta.single_end} == 'true' ]; then
-        seqkit grep -f readID.txt $fastq > ${prefix}_${taxid}.extracted_diamond_read.fastq
-    elif [ "${meta.single_end}" == 'false' ]; then
-        seqkit grep -f readID.txt ${fastq[0]} > ${prefix}_${taxid}.extracted_diamond_read1.fastq
-        seqkit grep -f readID.txt ${fastq[1]} > ${prefix}_${taxid}.extracted_diamond_read2.fastq
-    fi
-
-    rm readID.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        seqkit: \$( seqkit version | sed 's/seqkit v//' )
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/rm_empty_fastq.nf b/modules/local/rm_empty_fastq.nf
deleted file mode 100644
index f00463f..0000000
--- a/modules/local/rm_empty_fastq.nf
+++ /dev/null
@@ -1,27 +0,0 @@
-process RM_EMPTY_FASTQ {
-
-    label 'process_low'
-
-    input:
-    path folder
-
-    output:
-    path folder, optional: true
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    """
-    if [ -d ${folder} ]; then
-        for f in ${folder}/*.fastq; do
-            if [ ! -s \$f ]; then
-                rm \$f
-            fi
-        done
-    else
-        echo "Folder ${folder} doesn't exist."
-    fi
-    """
-}
diff --git a/modules/local/subset_bam.nf b/modules/local/subset_bam.nf
deleted file mode 100644
index 01a58fd..0000000
--- a/modules/local/subset_bam.nf
+++ /dev/null
@@ -1,34 +0,0 @@
-process SUBSET_BAM {
-
-    tag "$meta.id"
-    label 'process_low'
-
-    conda "bioconda::samtools:1.21"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0':
-        'biocontainers/samtools:1.21--h50ea8bc_0' }"
-
-    input:
-    tuple val(meta), path(bam), path(bai)
-    val taxid_accession
-
-    output:
-    tuple val(meta), path("*.bam"), emit: bam
-    path "versions.yml"           , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def accessions = taxid_accession.join(" ")
-
-    """
-    samtools view $bam $accessions -o ${prefix}.bam
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(samtools --version |& sed '1!d ; s/samtools //')
-    END_VERSIONS
-    """
-}