From f4abbe280ab6497a220fde116f606d588b49bf73 Mon Sep 17 00:00:00 2001
From: ljmesi <37740329+ljmesi@users.noreply.github.com>
Date: Tue, 3 May 2022 12:56:49 +0200
Subject: [PATCH] Fix back to nf-core modules version

---
 .../nf-core/modules/samtools/bam2fq/main.nf   |  2 +-
 nf-core/modules/samtools/bam2fq/main.nf       | 56 -------------------
 nf-core/modules/samtools/bam2fq/meta.yml      | 55 ------------------
 3 files changed, 1 insertion(+), 112 deletions(-)
 delete mode 100644 nf-core/modules/samtools/bam2fq/main.nf
 delete mode 100644 nf-core/modules/samtools/bam2fq/meta.yml

diff --git a/modules/nf-core/modules/samtools/bam2fq/main.nf b/modules/nf-core/modules/samtools/bam2fq/main.nf
index 0dd1da9..5d6aa79 100644
--- a/modules/nf-core/modules/samtools/bam2fq/main.nf
+++ b/modules/nf-core/modules/samtools/bam2fq/main.nf
@@ -45,7 +45,7 @@ process SAMTOOLS_BAM2FQ {
             bam2fq \\
             $args \\
             -@ $task.cpus \\
-            $inputbam > ${prefix}_interleaved.fq.gz
+            $inputbam >${prefix}_interleaved.fq.gz
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
diff --git a/nf-core/modules/samtools/bam2fq/main.nf b/nf-core/modules/samtools/bam2fq/main.nf
deleted file mode 100644
index 5d6aa79..0000000
--- a/nf-core/modules/samtools/bam2fq/main.nf
+++ /dev/null
@@ -1,56 +0,0 @@
-process SAMTOOLS_BAM2FQ {
-    tag "$meta.id"
-    label 'process_low'
-
-    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
-        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
-
-    input:
-    tuple val(meta), path(inputbam)
-    val split
-
-    output:
-    tuple val(meta), path("*.fq.gz"), emit: reads
-    path "versions.yml"             , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-
-    if (split){
-        """
-        samtools \\
-            bam2fq \\
-            $args \\
-            -@ $task.cpus \\
-            -1 ${prefix}_1.fq.gz \\
-            -2 ${prefix}_2.fq.gz \\
-            -0 ${prefix}_other.fq.gz \\
-            -s ${prefix}_singleton.fq.gz \\
-            $inputbam
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-        END_VERSIONS
-        """
-    } else {
-        """
-        samtools \\
-            bam2fq \\
-            $args \\
-            -@ $task.cpus \\
-            $inputbam >${prefix}_interleaved.fq.gz
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-        END_VERSIONS
-        """
-    }
-}
diff --git a/nf-core/modules/samtools/bam2fq/meta.yml b/nf-core/modules/samtools/bam2fq/meta.yml
deleted file mode 100644
index 319a60c..0000000
--- a/nf-core/modules/samtools/bam2fq/meta.yml
+++ /dev/null
@@ -1,55 +0,0 @@
-name: samtools_bam2fq
-description: |
-  The module uses bam2fq method from samtools to
-  convert a SAM, BAM or CRAM file to FASTQ format
-keywords:
-  - bam2fq
-  - samtools
-  - fastq
-tools:
-  - samtools:
-      description: Tools for dealing with SAM, BAM and CRAM files
-      homepage: None
-      documentation: http://www.htslib.org/doc/1.1/samtools.html
-      tool_dev_url: None
-      doi: ""
-      licence: ["MIT"]
-
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - inputbam:
-      type: file
-      description: BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
-  - split:
-      type: boolean
-      description: |
-        TRUE/FALSE value to indicate if reads should be separated into
-        /1, /2 and if present other, or singleton.
-        Note: choosing TRUE will generate 4 different files.
-        Choosing FALSE will produce a single file, which will be interleaved in case
-        the input contains paired reads.
-
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-  - reads:
-      type: file
-      description: |
-        FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton)
-        or a single interleaved .fq.gz file if the user chooses not to split the reads.
-      pattern: "*.fq.gz"
-
-authors:
-  - "@lescai"