From c7a5ae140b984c6bca051d9b0dc6975b2497fcd1 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 14 Jul 2022 18:40:58 -0500 Subject: [PATCH] Initial `nf-core modules emboss/seqret` --- modules/emboss/seqret/main.nf | 75 +++++++++++++++++++++ modules/emboss/seqret/meta.yml | 51 ++++++++++++++ tests/config/pytest_modules.yml | 4 ++ tests/modules/emboss/seqret/main.nf | 15 +++++ tests/modules/emboss/seqret/nextflow.config | 5 ++ tests/modules/emboss/seqret/test.yml | 14 ++++ 6 files changed, 164 insertions(+) create mode 100644 modules/emboss/seqret/main.nf create mode 100644 modules/emboss/seqret/meta.yml create mode 100644 tests/modules/emboss/seqret/main.nf create mode 100644 tests/modules/emboss/seqret/nextflow.config create mode 100644 tests/modules/emboss/seqret/test.yml diff --git a/modules/emboss/seqret/main.nf b/modules/emboss/seqret/main.nf new file mode 100644 index 00000000..7869ea72 --- /dev/null +++ b/modules/emboss/seqret/main.nf @@ -0,0 +1,75 @@ +// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :) +// https://github.com/nf-core/modules/tree/master/modules +// You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace: +// https://nf-co.re/join +// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters. +// All other parameters MUST be provided using the "task.ext" directive, see here: +// https://www.nextflow.io/docs/latest/process.html#ext +// where "task.ext" is a string. +// Any parameters that need to be evaluated in the context of a particular sample +// e.g. single-end/paired-end data MUST also be defined and evaluated appropriately. +// TODO nf-core: Software that can be piped together SHOULD be added to separate module files +// unless there is a run-time, storage advantage in implementing in this way +// e.g. it's ok to have a single module for bwa to output BAM instead of SAM: +// bwa mem | samtools view -B -T ref.fasta +// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty +// list (`[]`) instead of a file can be used to work around this issue. + +process EMBOSS_SEQRET { + tag "$meta.id" + label 'process_low' + + // TODO nf-core: List required Conda package(s). + // Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10"). + // For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems. + // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below. + conda (params.enable_conda ? "bioconda::emboss=6.6.0" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/emboss:6.6.0--hf657eab_5': + 'quay.io/biocontainers/emboss:6.6.0--h440b012_4' }" + + input: + // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group" + // MUST be provided as an input via a Groovy Map called "meta". + // This information may not be required in some instances e.g. indexing reference genome files: + // https://github.com/nf-core/modules/blob/master/modules/bwa/index/main.nf + // TODO nf-core: Where applicable please provide/convert compressed files as input/output + // e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc. + tuple val(meta), path(bam) + + output: + // TODO nf-core: Named file extensions MUST be emitted for ALL output channels + tuple val(meta), path("*.bam"), emit: bam + // TODO nf-core: List additional required output channels/values here + 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}" + // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10 + // If the software is unable to output a version number on the command-line then it can be manually specified + // e.g. https://github.com/nf-core/modules/blob/master/modules/homer/annotatepeaks/main.nf + // Each software used MUST provide the software name and version number in the YAML version file (versions.yml) + // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive + // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter + // using the Nextflow "task" variable e.g. "--threads $task.cpus" + // TODO nf-core: Please replace the example samtools command below with your module's command + // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;) + """ + samtools \\ + sort \\ + $args \\ + -@ $task.cpus \\ + -o ${prefix}.bam \\ + -T $prefix \\ + $bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + emboss: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' )) + END_VERSIONS + """ +} diff --git a/modules/emboss/seqret/meta.yml b/modules/emboss/seqret/meta.yml new file mode 100644 index 00000000..f4734ebe --- /dev/null +++ b/modules/emboss/seqret/meta.yml @@ -0,0 +1,51 @@ +name: "emboss_seqret" +## TODO nf-core: Add a description of the module and list keywords +description: write your description here +keywords: + - sort +tools: + - "emboss": + ## TODO nf-core: Add a description and other details for the software below + description: "The European Molecular Biology Open Software Suite" + homepage: "None" + documentation: "None" + tool_dev_url: "None" + doi: "" + licence: "['GPL']" + +## TODO nf-core: Add a description of all of the variables used as input +input: + # Only when we have meta + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + # + ## TODO nf-core: Delete / customise this example input + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + +## TODO nf-core: Add a description of all of the variables used as output +output: + #Only when we have meta + - 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" + ## TODO nf-core: Delete / customise this example output + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + +authors: + - "@MillironX" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index cae10d10..0043375b 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -723,6 +723,10 @@ elprep/split: - modules/elprep/split/** - tests/modules/elprep/split/** +emboss/seqret: + - modules/emboss/seqret/** + - tests/modules/emboss/seqret/** + emmtyper: - modules/emmtyper/** - tests/modules/emmtyper/** diff --git a/tests/modules/emboss/seqret/main.nf b/tests/modules/emboss/seqret/main.nf new file mode 100644 index 00000000..2275c6c0 --- /dev/null +++ b/tests/modules/emboss/seqret/main.nf @@ -0,0 +1,15 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { EMBOSS_SEQRET } from '../../../../modules/emboss/seqret/main.nf' + +workflow test_emboss_seqret { + + input = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) + ] + + EMBOSS_SEQRET ( input ) +} diff --git a/tests/modules/emboss/seqret/nextflow.config b/tests/modules/emboss/seqret/nextflow.config new file mode 100644 index 00000000..50f50a7a --- /dev/null +++ b/tests/modules/emboss/seqret/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/emboss/seqret/test.yml b/tests/modules/emboss/seqret/test.yml new file mode 100644 index 00000000..f8e0d2a3 --- /dev/null +++ b/tests/modules/emboss/seqret/test.yml @@ -0,0 +1,14 @@ +## TODO nf-core: Please run the following command to build this file: +# nf-core modules create-test-yml emboss/seqret +- name: "emboss seqret" + command: nextflow run ./tests/modules/emboss/seqret -entry test_emboss_seqret -c ./tests/config/nextflow.config -c ./tests/modules/emboss/seqret/nextflow.config + tags: + - "emboss" + # + - "emboss/seqret" + # + files: + - path: "output/emboss/test.bam" + md5sum: e667c7caad0bc4b7ac383fd023c654fc + - path: output/emboss/versions.yml + md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b