From e4e4f8090caa7c2f3fd71caa62792a1ea9ff4b59 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Thu, 5 May 2022 23:59:12 +0200
Subject: [PATCH 1/9] combine multiple pytor

---
 modules/cnvpytor/view/main.nf       | 16 +++++++++-------
 tests/modules/cnvpytor/view/main.nf |  6 +++---
 2 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/modules/cnvpytor/view/main.nf b/modules/cnvpytor/view/main.nf
index ad2249b8..1bb61a38 100644
--- a/modules/cnvpytor/view/main.nf
+++ b/modules/cnvpytor/view/main.nf
@@ -8,7 +8,7 @@ process CNVPYTOR_VIEW {
         'quay.io/biocontainers/cnvpytor:1.2.1--pyhdfd78af_0' }"
 
     input:
-    tuple val(meta), path(pytor)
+    tuple val(meta), path(pytor_files)
     val bin_sizes
     val output_format
 
@@ -23,17 +23,18 @@ process CNVPYTOR_VIEW {
 
     script:
     def output_suffix = output_format ?: 'vcf'
-    def bins = bin_sizes ?: '1000'
+    def bins   = bin_sizes ?: '1000'
+    def input  = pytor_files.join(" ")
+    def prefix = task.ext.prefix ?: "${meta.id}"
     """
 
     python3 <<CODE
     import cnvpytor,os
-    from pathlib import Path
-    pytor_file = Path("$pytor")
     binsizes = "${bins}".split(" ")
     for binsize in binsizes:
-        app = cnvpytor.Viewer(["$pytor"], params={} )
-        outputfile = "{}_{}.{}".format(pytor_file.stem,binsize.strip(),"${output_suffix}")
+        file_list = "${input}".split(" ")
+        app = cnvpytor.Viewer(file_list, params={} )
+        outputfile = "{}_{}.{}".format("${prefix}",binsize.strip(),"${output_suffix}")
         app.print_filename = outputfile
         app.bin_size = int(binsize)
         app.print_calls_file()
@@ -47,8 +48,9 @@ process CNVPYTOR_VIEW {
 
     stub:
     def output_suffix = output_format ?: 'vcf'
+    def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${pytor.baseName}.${output_suffix}
+    touch ${prefix}.${output_suffix}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/tests/modules/cnvpytor/view/main.nf b/tests/modules/cnvpytor/view/main.nf
index b865dd6d..3b99c314 100644
--- a/tests/modules/cnvpytor/view/main.nf
+++ b/tests/modules/cnvpytor/view/main.nf
@@ -8,7 +8,7 @@ workflow test_cnvpytor_view {
 
     input = [
         [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
+        [file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)]
     ]
 
     bin_sizes = "10000 100000"
@@ -20,7 +20,7 @@ workflow test_cnvpytor_view_tsvout {
 
     input = [
         [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
+        [file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)]
     ]
 
     output_suffix = "tsv"
@@ -32,7 +32,7 @@ workflow test_cnvpytor_view_stub {
 
     input = [
         [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
+        [file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)]
     ]
 
     bin_sizes = []

From af73544010cc9563ec7d7160aeb825ae28ec217f Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Fri, 6 May 2022 00:13:49 +0200
Subject: [PATCH 2/9] update meta

---
 modules/cnvpytor/view/meta.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/cnvpytor/view/meta.yml b/modules/cnvpytor/view/meta.yml
index 1392e90e..e4e68fad 100644
--- a/modules/cnvpytor/view/meta.yml
+++ b/modules/cnvpytor/view/meta.yml
@@ -17,9 +17,9 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test' ]
-  - pytor:
+  - pytor_files:
       type: file
-      description: pytor file containing read depth data
+      description: pytor file containing cnv calls. To merge calls from multiple samples use a list of files.
       pattern: "*.{pytor}"
   - bin_sizes:
       type: string

From 313d76e00525c8e975dabce0c34973fd53c3f4dd Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Fri, 6 May 2022 00:18:16 +0200
Subject: [PATCH 3/9] update svdb version

---
 modules/svdb/merge/main.nf | 6 +++---
 modules/svdb/query/main.nf | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/svdb/merge/main.nf b/modules/svdb/merge/main.nf
index 4a39940c..0d56fea2 100644
--- a/modules/svdb/merge/main.nf
+++ b/modules/svdb/merge/main.nf
@@ -2,10 +2,10 @@ process SVDB_MERGE {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::svdb=2.6.0" : null)
+    conda (params.enable_conda ? "bioconda::svdb=2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/svdb:2.6.0--py39h5371cbf_0':
-        'quay.io/biocontainers/svdb:2.6.0--py39h5371cbf_0' }"
+        'https://depot.galaxyproject.org/singularity/svdb:2.6.1--py39h5371cbf_0':
+        'quay.io/biocontainers/svdb:2.6.1--py39h5371cbf_0' }"
 
     input:
     tuple val(meta), path(vcfs)
diff --git a/modules/svdb/query/main.nf b/modules/svdb/query/main.nf
index c669b5a5..dbab5259 100644
--- a/modules/svdb/query/main.nf
+++ b/modules/svdb/query/main.nf
@@ -2,10 +2,10 @@ process SVDB_QUERY {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::svdb=2.6.0" : null)
+    conda (params.enable_conda ? "bioconda::svdb=2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/svdb:2.6.0--py39h5371cbf_0':
-        'quay.io/biocontainers/svdb:2.6.0--py39h5371cbf_0' }"
+        'https://depot.galaxyproject.org/singularity/svdb:2.6.1--py39h5371cbf_0':
+        'quay.io/biocontainers/svdb:2.6.1--py39h5371cbf_0' }"
 
     input:
     tuple val(meta), path(vcf)

From 853b623969357753468365aa538eb92b2bcb8ce9 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 6 May 2022 09:20:40 +0200
Subject: [PATCH 4/9] new module: md5sum

---
 modules/md5sum/main.nf               | 35 +++++++++++++++++++++++++
 modules/md5sum/meta.yml              | 39 ++++++++++++++++++++++++++++
 tests/config/pytest_modules.yml      | 12 ++++++---
 tests/modules/md5sum/main.nf         | 15 +++++++++++
 tests/modules/md5sum/nextflow.config |  3 +++
 tests/modules/md5sum/test.yml        |  8 ++++++
 6 files changed, 108 insertions(+), 4 deletions(-)
 create mode 100644 modules/md5sum/main.nf
 create mode 100644 modules/md5sum/meta.yml
 create mode 100644 tests/modules/md5sum/main.nf
 create mode 100644 tests/modules/md5sum/nextflow.config
 create mode 100644 tests/modules/md5sum/test.yml

diff --git a/modules/md5sum/main.nf b/modules/md5sum/main.nf
new file mode 100644
index 00000000..0b101811
--- /dev/null
+++ b/modules/md5sum/main.nf
@@ -0,0 +1,35 @@
+process MD5SUM {
+    tag "$meta.id"
+    label 'process_low'
+
+    if (params.enable_conda) {
+        exit 1, "Conda environments cannot be used when using bcl-convert. Please use docker or singularity containers."
+    }
+    container "debian:bullseye-slim"
+
+    input:
+    tuple val(meta), path(file)
+
+    output:
+    tuple val(meta), path("*.md5"), emit: checksum
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    md5sum \\
+        $args \\
+        ${file} \\
+        > ${file}.md5
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        md5sum: \$(echo \$(md5sum --version 2>&1 | head -n 1| sed 's/^.*) //;' ))
+    END_VERSIONS
+    """
+}
diff --git a/modules/md5sum/meta.yml b/modules/md5sum/meta.yml
new file mode 100644
index 00000000..d4f1939d
--- /dev/null
+++ b/modules/md5sum/meta.yml
@@ -0,0 +1,39 @@
+name: "md5sum"
+description: Create an MD5 (128-bit) checksum
+keywords:
+  - checksum
+tools:
+  - "md5sum":
+      description: Create an MD5 (128-bit) checksum
+      homepage: "https://www.gnu.org"
+      documentation: "https://man7.org/linux/man-pages/man1/md5sum.1.html"
+      licence: GPLv3+
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - file:
+      type: file
+      description: Any file
+      pattern: "*.*"
+
+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"
+  - checksum:
+      type: file
+      description: File containing checksum
+      pattern: "*.md5"
+
+authors:
+  - "@matthdsm"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 81f98d59..a5a7c083 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1058,10 +1058,6 @@ krona/kronadb:
   - modules/krona/kronadb/**
   - tests/modules/krona/kronadb/**
 
-krona/ktupdatetaxonomy:
-  - modules/krona/ktupdatetaxonomy/**
-  - tests/modules/krona/ktupdatetaxonomy/**
-
 krona/ktimporttaxonomy:
   - modules/krona/ktimporttaxonomy/**
   - tests/modules/krona/ktimporttaxonomy/**
@@ -1070,6 +1066,10 @@ krona/ktimporttext:
   - modules/krona/ktimporttext/**
   - tests/modules/krona/ktimporttext/**
 
+krona/ktupdatetaxonomy:
+  - modules/krona/ktupdatetaxonomy/**
+  - tests/modules/krona/ktupdatetaxonomy/**
+
 last/dotplot:
   - modules/last/dotplot/**
   - tests/modules/last/dotplot/**
@@ -1190,6 +1190,10 @@ maxbin2:
   - modules/maxbin2/**
   - tests/modules/maxbin2/**
 
+md5sum:
+  - modules/md5sum/**
+  - tests/modules/md5sum/**
+
 medaka:
   - modules/medaka/**
   - tests/modules/medaka/**
diff --git a/tests/modules/md5sum/main.nf b/tests/modules/md5sum/main.nf
new file mode 100644
index 00000000..f90642b6
--- /dev/null
+++ b/tests/modules/md5sum/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MD5SUM } from '../../../modules/md5sum/main.nf'
+
+workflow test_md5sum {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    MD5SUM ( input )
+}
diff --git a/tests/modules/md5sum/nextflow.config b/tests/modules/md5sum/nextflow.config
new file mode 100644
index 00000000..0293c16f
--- /dev/null
+++ b/tests/modules/md5sum/nextflow.config
@@ -0,0 +1,3 @@
+process {
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+}
diff --git a/tests/modules/md5sum/test.yml b/tests/modules/md5sum/test.yml
new file mode 100644
index 00000000..1e6517a7
--- /dev/null
+++ b/tests/modules/md5sum/test.yml
@@ -0,0 +1,8 @@
+- name: md5sum test_md5sum
+  command: nextflow run tests/modules/md5sum -entry test_md5sum -c tests/config/nextflow.config
+  tags:
+    - md5sum
+  files:
+    - path: output/md5sum/test.paired_end.bam.md5
+      md5sum: 1163095be8fdfb2acb3cc6c027389c4b
+    - path: output/md5sum/versions.yml

From 09e729ad414bc51d91b487edf720e7bb9b80abb7 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 6 May 2022 10:28:14 +0200
Subject: [PATCH 5/9] added sha256sum

---
 modules/shasum/main.nf               | 35 ++++++++++++++++++++++++
 modules/shasum/meta.yml              | 40 ++++++++++++++++++++++++++++
 tests/config/pytest_modules.yml      |  4 +++
 tests/modules/shasum/main.nf         | 15 +++++++++++
 tests/modules/shasum/nextflow.config |  5 ++++
 tests/modules/shasum/test.yml        |  8 ++++++
 6 files changed, 107 insertions(+)
 create mode 100644 modules/shasum/main.nf
 create mode 100644 modules/shasum/meta.yml
 create mode 100644 tests/modules/shasum/main.nf
 create mode 100644 tests/modules/shasum/nextflow.config
 create mode 100644 tests/modules/shasum/test.yml

diff --git a/modules/shasum/main.nf b/modules/shasum/main.nf
new file mode 100644
index 00000000..a2c37da7
--- /dev/null
+++ b/modules/shasum/main.nf
@@ -0,0 +1,35 @@
+process SHASUM {
+    tag "$meta.id"
+    label 'process_low'
+
+    if (params.enable_conda) {
+        exit 1, "Conda environments cannot be used when using bcl-convert. Please use docker or singularity containers."
+    }
+    container "debian:bullseye-slim"
+
+    input:
+    tuple val(meta), path(file)
+
+    output:
+    tuple val(meta), path("*.sha256"), emit: checksum
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    sha256sum \\
+        $args \\
+        ${file} \\
+        > ${file}.sha256
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sha256sum: \$(echo \$(sha256sum --version 2>&1 | head -n 1| sed 's/^.*) //;' ))
+    END_VERSIONS
+    """
+}
diff --git a/modules/shasum/meta.yml b/modules/shasum/meta.yml
new file mode 100644
index 00000000..f16e0771
--- /dev/null
+++ b/modules/shasum/meta.yml
@@ -0,0 +1,40 @@
+name: "shasum"
+description: Print SHA256 (256-bit) checksums.
+keywords:
+  - checksum
+  - sha256
+tools:
+  - "md5sum":
+      description: Create an SHA256 (256-bit) checksum.
+      homepage: "https://www.gnu.org"
+      documentation: "https://linux.die.net/man/1/shasum"
+      licence: GPLv3+
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - file:
+      type: file
+      description: Any file
+      pattern: "*.*"
+
+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"
+  - checksum:
+      type: file
+      description: File containing checksum
+      pattern: "*.sha256"
+
+authors:
+  - "@matthdsm"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index a5a7c083..effe6fe2 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1739,6 +1739,10 @@ seqwish/induce:
   - modules/seqwish/induce/**
   - tests/modules/seqwish/induce/**
 
+shasum:
+  - modules/shasum/**
+  - tests/modules/shasum/**
+
 shigatyper:
   - modules/shigatyper/**
   - tests/modules/shigatyper/**
diff --git a/tests/modules/shasum/main.nf b/tests/modules/shasum/main.nf
new file mode 100644
index 00000000..817ea6f0
--- /dev/null
+++ b/tests/modules/shasum/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SHASUM } from '../../../modules/shasum/main.nf'
+
+workflow test_shasum {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    SHASUM ( input )
+}
diff --git a/tests/modules/shasum/nextflow.config b/tests/modules/shasum/nextflow.config
new file mode 100644
index 00000000..50f50a7a
--- /dev/null
+++ b/tests/modules/shasum/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}
\ No newline at end of file
diff --git a/tests/modules/shasum/test.yml b/tests/modules/shasum/test.yml
new file mode 100644
index 00000000..6778d156
--- /dev/null
+++ b/tests/modules/shasum/test.yml
@@ -0,0 +1,8 @@
+- name: shasum test_shasum
+  command: nextflow run tests/modules/shasum -entry test_shasum -c tests/config/nextflow.config
+  tags:
+    - shasum
+  files:
+    - path: output/shasum/test.paired_end.bam.sha256
+      md5sum: 138a19e100f09fc975ea1b717da9b6dd
+    - path: output/shasum/versions.yml

From 77d825e0439c4d9a1d68a329c97012e4b99f3e40 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 6 May 2022 10:39:13 +0200
Subject: [PATCH 6/9] fix copy paste errors

---
 modules/md5sum/main.nf | 2 +-
 modules/shasum/main.nf | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/md5sum/main.nf b/modules/md5sum/main.nf
index 0b101811..2cdb8bf6 100644
--- a/modules/md5sum/main.nf
+++ b/modules/md5sum/main.nf
@@ -3,7 +3,7 @@ process MD5SUM {
     label 'process_low'
 
     if (params.enable_conda) {
-        exit 1, "Conda environments cannot be used when using bcl-convert. Please use docker or singularity containers."
+        exit 1, "Conda environments cannot be used when using md5sum. Please use docker or singularity containers."
     }
     container "debian:bullseye-slim"
 
diff --git a/modules/shasum/main.nf b/modules/shasum/main.nf
index a2c37da7..e7a18da6 100644
--- a/modules/shasum/main.nf
+++ b/modules/shasum/main.nf
@@ -3,7 +3,7 @@ process SHASUM {
     label 'process_low'
 
     if (params.enable_conda) {
-        exit 1, "Conda environments cannot be used when using bcl-convert. Please use docker or singularity containers."
+        exit 1, "Conda environments cannot be used when using sha256sum. Please use docker or singularity containers."
     }
     container "debian:bullseye-slim"
 

From 1c7205d68389a899ee6b4f8c11343701c2c07ce8 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 6 May 2022 10:44:51 +0200
Subject: [PATCH 7/9] fixed container definitions

---
 modules/md5sum/main.nf | 8 ++++----
 modules/shasum/main.nf | 8 ++++----
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/modules/md5sum/main.nf b/modules/md5sum/main.nf
index 2cdb8bf6..7b66625e 100644
--- a/modules/md5sum/main.nf
+++ b/modules/md5sum/main.nf
@@ -2,10 +2,10 @@ process MD5SUM {
     tag "$meta.id"
     label 'process_low'
 
-    if (params.enable_conda) {
-        exit 1, "Conda environments cannot be used when using md5sum. Please use docker or singularity containers."
-    }
-    container "debian:bullseye-slim"
+    conda (params.enable_conda ? "conda-forge::coreutils=8.25" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/coreutils:8.31--h14c3975_0' :
+        'quay.io/biocontainers/coreutils:8.31--h14c3975_0' }"
 
     input:
     tuple val(meta), path(file)
diff --git a/modules/shasum/main.nf b/modules/shasum/main.nf
index e7a18da6..11f9376c 100644
--- a/modules/shasum/main.nf
+++ b/modules/shasum/main.nf
@@ -2,10 +2,10 @@ process SHASUM {
     tag "$meta.id"
     label 'process_low'
 
-    if (params.enable_conda) {
-        exit 1, "Conda environments cannot be used when using sha256sum. Please use docker or singularity containers."
-    }
-    container "debian:bullseye-slim"
+    conda (params.enable_conda ? "conda-forge::coreutils=8.25" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/coreutils:8.31--h14c3975_0' :
+        'quay.io/biocontainers/coreutils:8.31--h14c3975_0' }"
 
     input:
     tuple val(meta), path(file)

From 1ccea5ff4d3dffbf9a8e53032481cc9246d4e23d Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Fri, 6 May 2022 10:56:58 +0200
Subject: [PATCH 8/9] remove prefix def in callcnvs

---
 modules/cnvpytor/callcnvs/main.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/cnvpytor/callcnvs/main.nf b/modules/cnvpytor/callcnvs/main.nf
index 092f6def..69c9d40e 100644
--- a/modules/cnvpytor/callcnvs/main.nf
+++ b/modules/cnvpytor/callcnvs/main.nf
@@ -20,7 +20,6 @@ process CNVPYTOR_CALLCNVS {
 
     script:
     def bins = bin_sizes ?: '1000'
-    def prefix = task.ext.prefix ?: "${meta.id}"
     """
     cnvpytor \\
         -root $pytor \\

From bd1b80f36e1b9a978e598e4b47f6705ede34da37 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 6 May 2022 11:07:05 +0200
Subject: [PATCH 9/9] fix software definitions

---
 modules/md5sum/main.nf | 6 +++---
 modules/shasum/main.nf | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/md5sum/main.nf b/modules/md5sum/main.nf
index 7b66625e..2b516f1b 100644
--- a/modules/md5sum/main.nf
+++ b/modules/md5sum/main.nf
@@ -2,10 +2,10 @@ process MD5SUM {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::coreutils=8.25" : null)
+    conda (params.enable_conda ? "conda-forge::coreutils=9.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/coreutils:8.31--h14c3975_0' :
-        'quay.io/biocontainers/coreutils:8.31--h14c3975_0' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(file)
diff --git a/modules/shasum/main.nf b/modules/shasum/main.nf
index 11f9376c..0e288435 100644
--- a/modules/shasum/main.nf
+++ b/modules/shasum/main.nf
@@ -2,10 +2,10 @@ process SHASUM {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::coreutils=8.25" : null)
+    conda (params.enable_conda ? "conda-forge::coreutils=9.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/coreutils:8.31--h14c3975_0' :
-        'quay.io/biocontainers/coreutils:8.31--h14c3975_0' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(file)