added sha256sum

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
+    """
+}

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"

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/**

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 )
+}

tests/modules/shasum/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}

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