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