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] 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