From 927dbfed048469e945f93236d213011e45672fba Mon Sep 17 00:00:00 2001 From: Sateesh <33637490+sateeshperi@users.noreply.github.com> Date: Fri, 18 Feb 2022 21:17:58 -0500 Subject: [PATCH] Picard cleansam (#1306) * add picard-cleansam * add picard/cleansam * update test yml with output * picard 2.26.10 -> 2.26.9 * add output to test yml Co-authored-by: Peri Co-authored-by: Robert A. Petit III --- modules/picard/cleansam/main.nf | 44 ++++++++++++++++++ modules/picard/cleansam/meta.yml | 46 +++++++++++++++++++ tests/config/pytest_modules.yml | 4 ++ tests/modules/picard/cleansam/main.nf | 15 ++++++ tests/modules/picard/cleansam/nextflow.config | 5 ++ tests/modules/picard/cleansam/test.yml | 10 ++++ 6 files changed, 124 insertions(+) create mode 100644 modules/picard/cleansam/main.nf create mode 100644 modules/picard/cleansam/meta.yml create mode 100644 tests/modules/picard/cleansam/main.nf create mode 100644 tests/modules/picard/cleansam/nextflow.config create mode 100644 tests/modules/picard/cleansam/test.yml diff --git a/modules/picard/cleansam/main.nf b/modules/picard/cleansam/main.nf new file mode 100644 index 00000000..2eb171d5 --- /dev/null +++ b/modules/picard/cleansam/main.nf @@ -0,0 +1,44 @@ +process PICARD_CLEANSAM { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::picard=2.26.9" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }" + + input: + tuple val(meta), path(sam) + + output: + tuple val(meta), path("*.sam"), emit: sam + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def STRINGENCY = task.ext.stringency ?: "STRICT" + def avail_mem = 3 + if (!task.memory) { + log.info '[Picard CleanSam] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' + } else { + avail_mem = task.memory.giga + } + """ + picard \\ + -Xmx${avail_mem}g \\ + CleanSam \\ + ${args} \\ + -I ${sam} \\ + -O ${prefix}.sam \\ + --VALIDATION_STRINGENCY ${STRINGENCY} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + picard: \$(picard CleanSam --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:) + END_VERSIONS + """ +} diff --git a/modules/picard/cleansam/meta.yml b/modules/picard/cleansam/meta.yml new file mode 100644 index 00000000..d22e1742 --- /dev/null +++ b/modules/picard/cleansam/meta.yml @@ -0,0 +1,46 @@ +name: picard_cleansam +description: Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads +keywords: + - clean + - sam + - bam +tools: + - picard: + description: | + A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) + data and formats such as SAM/BAM/CRAM and VCF. + homepage: https://broadinstitute.github.io/picard/ + documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360036491452-CleanSam-Picard- + tool_dev_url: https://github.com/broadinstitute/picard + licence: ["MIT"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sam: + type: file + description: SAM file + pattern: "*.{sam}" + +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" + - sam: + type: file + description: Cleaned SAM file + pattern: "*.{sam}" + +authors: + - "@sateeshperi" + - "@mjcipriano" + - "@hseabolt" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 52f8d625..3d857d2c 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -1157,6 +1157,10 @@ phyloflash: - modules/phyloflash/** - tests/modules/phyloflash/** +picard/cleansam: + - modules/picard/cleansam/** + - tests/modules/picard/cleansam/** + picard/collecthsmetrics: - modules/picard/collecthsmetrics/** - tests/modules/picard/collecthsmetrics/** diff --git a/tests/modules/picard/cleansam/main.nf b/tests/modules/picard/cleansam/main.nf new file mode 100644 index 00000000..f189b0f3 --- /dev/null +++ b/tests/modules/picard/cleansam/main.nf @@ -0,0 +1,15 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { PICARD_CLEANSAM } from '../../../../modules/picard/cleansam/main.nf' + +workflow test_picard_cleansam { + + input = [ + [ id:'test', single_end:true ], // meta map + file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) + ] + + PICARD_CLEANSAM ( input ) +} diff --git a/tests/modules/picard/cleansam/nextflow.config b/tests/modules/picard/cleansam/nextflow.config new file mode 100644 index 00000000..50f50a7a --- /dev/null +++ b/tests/modules/picard/cleansam/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/picard/cleansam/test.yml b/tests/modules/picard/cleansam/test.yml new file mode 100644 index 00000000..716dfe6a --- /dev/null +++ b/tests/modules/picard/cleansam/test.yml @@ -0,0 +1,10 @@ +- name: picard cleansam test_picard_cleansam + command: nextflow run tests/modules/picard/cleansam -entry test_picard_cleansam -c tests/config/nextflow.config + tags: + - picard/cleansam + - picard + files: + - path: output/picard/test.sam + md5sum: e314171a6060eb79947c13ad126ddf00 + - path: output/picard/versions.yml + md5sum: e6457d7c6de51bf6f4b577eda65e57ac