From 4f590ff2397cc3ad3f0b1d5e534d70052c13982d Mon Sep 17 00:00:00 2001
From: drpatelh <drhpatel@gmail.com>
Date: Wed, 5 Aug 2020 17:25:34 +0100
Subject: [PATCH] Remove some more modules

---
 deprecated/bwa/index/main.nf                  | 16 -------
 deprecated/bwa/index/meta.yml                 | 25 -----------
 deprecated/bwa/index/test/main.nf             | 16 -------
 deprecated/bwa/index/test/nextflow.config     |  2 -
 deprecated/bwa/mem/Dockerfile                 |  7 ----
 deprecated/bwa/mem/environment.yml            | 10 -----
 deprecated/bwa/mem/main.nf                    | 27 ------------
 deprecated/bwa/mem/meta.yml                   | 42 -------------------
 deprecated/bwa/mem/test/main.nf               | 13 ------
 deprecated/bwa/mem/test/nextflow.config       |  2 -
 deprecated/samtools/Dockerfile                |  8 ----
 deprecated/samtools/environment.yml           |  9 ----
 deprecated/samtools/index/main.nf             | 21 ----------
 deprecated/samtools/index/meta.yml            | 27 ------------
 deprecated/samtools/index/test/main.nf        | 13 ------
 .../samtools/index/test/nextflow.config       |  2 -
 16 files changed, 240 deletions(-)
 delete mode 100644 deprecated/bwa/index/main.nf
 delete mode 100644 deprecated/bwa/index/meta.yml
 delete mode 100644 deprecated/bwa/index/test/main.nf
 delete mode 100644 deprecated/bwa/index/test/nextflow.config
 delete mode 100644 deprecated/bwa/mem/Dockerfile
 delete mode 100644 deprecated/bwa/mem/environment.yml
 delete mode 100644 deprecated/bwa/mem/main.nf
 delete mode 100644 deprecated/bwa/mem/meta.yml
 delete mode 100644 deprecated/bwa/mem/test/main.nf
 delete mode 100644 deprecated/bwa/mem/test/nextflow.config
 delete mode 100644 deprecated/samtools/Dockerfile
 delete mode 100644 deprecated/samtools/environment.yml
 delete mode 100644 deprecated/samtools/index/main.nf
 delete mode 100644 deprecated/samtools/index/meta.yml
 delete mode 100644 deprecated/samtools/index/test/main.nf
 delete mode 100644 deprecated/samtools/index/test/nextflow.config

diff --git a/deprecated/bwa/index/main.nf b/deprecated/bwa/index/main.nf
deleted file mode 100644
index 1f67a886..00000000
--- a/deprecated/bwa/index/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-process bwa_index {
-    tag "$fasta"
-
-    container 'quay.io/biocontainers/bwa:0.7.17--hed695b0_7'
-
-    input:
-        path fasta
-
-    output:
-        path "${fasta}.*"
-
-    script:
-    """
-    bwa index ${fasta}
-    """
-}
diff --git a/deprecated/bwa/index/meta.yml b/deprecated/bwa/index/meta.yml
deleted file mode 100644
index 49fa3c44..00000000
--- a/deprecated/bwa/index/meta.yml
+++ /dev/null
@@ -1,25 +0,0 @@
-name: bwa index
-description: create indexes for BWA from a fasta file
-keywords:
-    - index
-tools:
-    - bwa:
-        description: |
-            BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
-        homepage: http://bio-bwa.sourceforge.net/
-        documentation: http://www.htslib.org/doc/samtools.html
-        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/index/test/main.nf b/deprecated/bwa/index/test/main.nf
deleted file mode 100644
index 8e36c9ac..00000000
--- a/deprecated/bwa/index/test/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-nextflow.preview.dsl = 2
-include '../../../tests/functions/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/index/test/nextflow.config b/deprecated/bwa/index/test/nextflow.config
deleted file mode 100644
index c137a138..00000000
--- a/deprecated/bwa/index/test/nextflow.config
+++ /dev/null
@@ -1,2 +0,0 @@
-docker.enabled = true
-params.outdir = './results'
diff --git a/deprecated/bwa/mem/Dockerfile b/deprecated/bwa/mem/Dockerfile
deleted file mode 100644
index 9a3e0caa..00000000
--- a/deprecated/bwa/mem/Dockerfile
+++ /dev/null
@@ -1,7 +0,0 @@
-FROM nfcore/base
-LABEL authors="Jeremy Guntoro" \
-    description="Docker image containing all requirements for nf-core/modules/bwa/mem module"
-
-COPY environment.yml /
-RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-bwa-mem/bin:$PATH
diff --git a/deprecated/bwa/mem/environment.yml b/deprecated/bwa/mem/environment.yml
deleted file mode 100644
index b48b7c2d..00000000
--- a/deprecated/bwa/mem/environment.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-# You can use this file to create a conda environment for this pipeline:
-#   conda env create -f environment.yml
-name: nf-core-bwa-mem
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - bioconda::bwa=0.7.17
-  - bioconda::samtools=1.9
diff --git a/deprecated/bwa/mem/main.nf b/deprecated/bwa/mem/main.nf
deleted file mode 100644
index 780b7293..00000000
--- a/deprecated/bwa/mem/main.nf
+++ /dev/null
@@ -1,27 +0,0 @@
-params.bwa_options = "-M -B 2"
-params.sequencer = "ILLUMINA"
-
-process bwa_mem {
-    tag "$id"
-
-    publishDir "${params.outdir}/bwa_mem", mode: 'copy'
-
-    //TO-DO: Change container declaration, for now a test container is present in my personal docker acccount
-    container 'jeremy1805/bwa-mem-img'
-
-    input:
-        tuple val(id), path(reads)
-        path genomeindex
-        val indexprefix
-
-    output:
-        tuple path("*.bam"), path("*.bai")
-
-    script:
-    """
-    bwa mem -t ${task.cpus} -R "@RG\\tID:${id}\\tLB:${id}\\tSM:${id}\\tPL:${params.sequencer}" \\
-    ${params.bwa_options} ${indexprefix} ${reads} | samtools sort -@8 -O BAM -o ${id}.bam -
-
-    samtools index ${id}.bam
-    """
-}
diff --git a/deprecated/bwa/mem/meta.yml b/deprecated/bwa/mem/meta.yml
deleted file mode 100644
index d8ae9a7d..00000000
--- a/deprecated/bwa/mem/meta.yml
+++ /dev/null
@@ -1,42 +0,0 @@
-name: bwa mem
-description: Performs fastq alignment to a fasta reference using the burrows-wheeler aligner
-keywords:
-    - mem
-    - bwa
-    - alignment
-tools:
-    - bwa:
-        description: |
-            BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
-        homepage: http://bio-bwa.sourceforge.net/
-        documentation: http://www.htslib.org/doc/samtools.html
-        arxiv: arXiv:1303.3997
-input:
-    -
-        - id:
-            type: val
-            description: read/read pair id
-        - reads:
-            type: file
-            description: Input fastq file
-            pattern: "*.{fastq,fq}"
-        - index:
-            type: file
-            description: bwa indexes file
-            pattern: "*.{amb,ann,bwt,pac,sa}"
-        - prefix:
-            type: val
-            description: bwa index prefix, equivalent to index file names without extensions. Usually the reference genome file name unless otherwise specified.
-output:
-    -
-        - bam:
-            type: file
-            description: Output bam file
-            pattern: "*.bam"
-        - bamindex:
-            type: file
-            description: Output bam index file
-            pattern: "*.bai"
-
-authors:
-    - "@jeremy1805"
diff --git a/deprecated/bwa/mem/test/main.nf b/deprecated/bwa/mem/test/main.nf
deleted file mode 100644
index 3a609477..00000000
--- a/deprecated/bwa/mem/test/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-nextflow.preview.dsl = 2
-include '../../../../tests/functions/check_process_outputs.nf' params(params)
-include '../main.nf' params(params)
-
-reads = '../../../../test-datasets/tools/bwa/mem/reads/*_R{1,2}_001.fastq.gz'
-index = '../../../../test-datasets/tools/bwa/mem/index/H3N2.{amb,ann,bwt,pac,sa}'
-prefix = 'H3N2'
-
-workflow {
-  read_input=Channel.fromFilePairs(reads)
-  bwa_mem(read_input,file(index),prefix)
-}
diff --git a/deprecated/bwa/mem/test/nextflow.config b/deprecated/bwa/mem/test/nextflow.config
deleted file mode 100644
index c137a138..00000000
--- a/deprecated/bwa/mem/test/nextflow.config
+++ /dev/null
@@ -1,2 +0,0 @@
-docker.enabled = true
-params.outdir = './results'
diff --git a/deprecated/samtools/Dockerfile b/deprecated/samtools/Dockerfile
deleted file mode 100644
index ff8c7c64..00000000
--- a/deprecated/samtools/Dockerfile
+++ /dev/null
@@ -1,8 +0,0 @@
-FROM nfcore/base:1.7
-LABEL authors="phil.ewels@scilifelab.se" \
-    description="Docker image for nf-core modules samtools"
-
-# foobar
-COPY environment.yml /
-RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-modules-samtools/bin:$PATH
diff --git a/deprecated/samtools/environment.yml b/deprecated/samtools/environment.yml
deleted file mode 100644
index 1a909c80..00000000
--- a/deprecated/samtools/environment.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-# You can use this file to create a conda environment for this pipeline:
-#   conda env create -f environment.yml
-name: nf-core-modules-samtools
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - samtools=1.9
diff --git a/deprecated/samtools/index/main.nf b/deprecated/samtools/index/main.nf
deleted file mode 100644
index bf3c5095..00000000
--- a/deprecated/samtools/index/main.nf
+++ /dev/null
@@ -1,21 +0,0 @@
-process samtools_index {
-    tag "${bam.baseName}"
-
-    container 'quay.io/biocontainers/samtools:1.9--h10a08f8_12'
-
-    input:
-    path bam
-
-    output:
-    path "*.bai"
-
-    script:
-    def suff_mem = ("${(task.memory.toBytes() - 6000000000) / task.cpus}" > 2000000000) ? 'true' : 'false'
-    def avail_mem = (task.memory && suff_mem) ? "-m" + "${(task.memory.toBytes() - 6000000000) / task.cpus}" : ''
-    """
-    samtools index $bam \\
-        -@ ${task.cpus} ${avail_mem}
-
-    samtools --version &> v_samtools.txt
-    """
-}
diff --git a/deprecated/samtools/index/meta.yml b/deprecated/samtools/index/meta.yml
deleted file mode 100644
index 35d34802..00000000
--- a/deprecated/samtools/index/meta.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-name: samtools index
-description: index a BAM or CRAM file
-keywords:
-    - index
-tools:
-    - samtools:
-        description: |
-            SAMtools is a set of utilities for interacting with and post-processing
-            short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
-            These files are generated as output by short read aligners like BWA.
-        homepage: http://www.htslib.org/
-        documentation: hhttp://www.htslib.org/doc/samtools.html
-        doi: 10.1093/bioinformatics/btp352
-input:
-    -
-        - input:
-            type: file
-            description: Input BAM or CRAM file
-            pattern: "*.{bam,cram}"
-output:
-    -
-        - index:
-            type: file
-            description: BAM or CRAM index file
-            pattern: "*.{bai}"
-authors:
-    - "@ewels"
diff --git a/deprecated/samtools/index/test/main.nf b/deprecated/samtools/index/test/main.nf
deleted file mode 100644
index 5fb89109..00000000
--- a/deprecated/samtools/index/test/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-echo true
-
-cheers = Channel.from 'Bonjour', 'Ciao', 'Hello', 'Hola'
-
-process sayHello {
-  input:
-    val x from cheers
-  script:
-    """
-    echo '$x world!'
-    """
-}
diff --git a/deprecated/samtools/index/test/nextflow.config b/deprecated/samtools/index/test/nextflow.config
deleted file mode 100644
index c137a138..00000000
--- a/deprecated/samtools/index/test/nextflow.config
+++ /dev/null
@@ -1,2 +0,0 @@
-docker.enabled = true
-params.outdir = './results'