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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,59 @@ | ||
| #! /usr/bin/env python3 | ||
| """ | ||
| Create a simple before and after report from scrubbing | ||
| """ | ||
| PROGRAM = "scrubber-summary" | ||
| VERSION = "3.0.1" | ||
| import json | ||
| import sys | ||
|
|
||
| def read_json(json_file): | ||
| json_data = None | ||
| with open(json_file, 'rt') as json_fh: | ||
| json_data = json.load(json_fh) | ||
| return json_data | ||
|
|
||
| if __name__ == '__main__': | ||
| import argparse as ap | ||
|
|
||
| parser = ap.ArgumentParser( | ||
| prog=PROGRAM, | ||
| conflict_handler='resolve', | ||
| description=( | ||
| f'{PROGRAM} (v{VERSION}) - Create a simple before and after report from scrubbing' | ||
| ) | ||
| ) | ||
| parser.add_argument('sample', metavar="SAMPLE", type=str, | ||
| help='the name of the sample') | ||
| parser.add_argument('original', metavar="ORIGINAL", type=str, | ||
| help='A summary of the original FASTQs in JSON format') | ||
| parser.add_argument('scrubbed', metavar="SCRUBBED", type=str, | ||
| help='A summary of the scrubbed FASTQs in JSON format') | ||
| parser.add_argument('--version', action='version', | ||
| version=f'{PROGRAM} {VERSION}') | ||
|
|
||
| if len(sys.argv) == 1: | ||
| parser.print_help() | ||
| sys.exit(0) | ||
|
|
||
| args = parser.parse_args() | ||
|
|
||
| original_json = read_json(args.original) | ||
| scrubbed_json = read_json(args.scrubbed) | ||
|
|
||
| # Summary | ||
| cols = [ | ||
| 'sample', | ||
| 'original_read_total', | ||
| 'scrubbed_read_total', | ||
| 'host_read_total', | ||
| ] | ||
| results = [ | ||
| args.sample, | ||
| str(original_json['qc_stats']['read_total']), | ||
| str(scrubbed_json['qc_stats']['read_total']), | ||
| str(original_json['qc_stats']['read_total'] - scrubbed_json['qc_stats']['read_total']), | ||
| ] | ||
|
|
||
| print('\t'.join(cols)) | ||
| print('\t'.join(results)) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| // Import generic module functions | ||
| include { get_resources; initOptions; saveFiles } from '../../../../lib/nf/functions' | ||
| RESOURCES = get_resources(workflow.profile, params.max_memory, params.max_cpus) | ||
| options = initOptions(params.containsKey("options") ? params.options : [:], 'custom_wget') | ||
| options.btype = options.btype ?: "comparative" | ||
| conda_tools = "bioconda::gnu-wget=1.18" | ||
| conda_name = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-") | ||
| conda_env = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools | ||
|
|
||
| process CUSTOM_WGET { | ||
| label 'process_low' | ||
| storeDir params.datasets_cache | ||
| publishDir params.datasets_cache | ||
|
|
||
| conda (params.enable_conda ? conda_env : null) | ||
| container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/gnu-wget:1.18--h36e9172_9' : | ||
| 'quay.io/biocontainers/gnu-wget:1.18--h36e9172_9' }" | ||
|
|
||
| output: | ||
| path "${options.args2}", emit: download | ||
| path "*.{log,err}" , emit: logs, optional: true | ||
| path ".command.*" , emit: nf_logs | ||
| path "versions.yml" ,emit: versions | ||
|
|
||
| script: | ||
| """ | ||
| wget $options.args | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| wget: \$(echo \$( wget --version 2>&1) | sed "s/GNU Wget //;s/ .*//;" ) | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| name: custom_wget | ||
| description: Custom module used to download files using wget | ||
| keywords: | ||
| - wget | ||
| - custom | ||
| - version | ||
| tools: | ||
| - custom: | ||
| description: Custom module used to download files using wget | ||
| homepage: https://github.com/nf-core/tools | ||
| documentation: https://github.com/nf-core/tools | ||
|
|
||
| output: | ||
| - download: | ||
| type: file | ||
| description: Downloaded file from input URL | ||
| pattern: "*" | ||
| - versions: | ||
| type: file | ||
| description: File containing software versions | ||
| pattern: "versions.yml" | ||
|
|
||
| authors: | ||
| - "@rpetit3" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,90 @@ | ||
| { | ||
| "$schema": "http://json-schema.org/draft-07/schema", | ||
| "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/kraken2/params.json", | ||
| "title": "Kraken2 Module", | ||
| "description": "A module for taxonomic classification of sequence reads", | ||
| "type": "object", | ||
| "definitions": { | ||
| "kraken2_parameters": { | ||
| "title": "Scrubber (Kraken2) Parameters", | ||
| "type": "object", | ||
| "description": "", | ||
| "default": "", | ||
| "fa_icon": "fas fa-exclamation-circle", | ||
| "properties": { | ||
| "quick_mode": { | ||
| "type": "boolean", | ||
| "default": false, | ||
| "description": "Quick operation (use first hit or hits)", | ||
| "fa_icon": "fas fa-expand-arrows-alt", | ||
| "hidden": true | ||
| }, | ||
| "confidence": { | ||
| "type": "number", | ||
| "default": 0.0, | ||
| "description": "Confidence score threshold between 0 and 1", | ||
| "fa_icon": "fas fa-expand-arrows-alt" | ||
| }, | ||
| "minimum_base_quality": { | ||
| "type": "integer", | ||
| "default": 0, | ||
| "description": "Minimum base quality used in classification", | ||
| "fa_icon": "fas fa-expand-arrows-alt", | ||
| "hidden": true | ||
| }, | ||
| "use_mpa_style": { | ||
| "type": "boolean", | ||
| "default": false, | ||
| "description": "Format report output like Kraken 1's kraken-mpa-report", | ||
| "fa_icon": "fas fa-expand-arrows-alt" | ||
| }, | ||
| "report_zero_counts": { | ||
| "type": "boolean", | ||
| "default": false, | ||
| "description": "Report counts for ALL taxa, even if counts are zero", | ||
| "fa_icon": "fas fa-expand-arrows-alt" | ||
| }, | ||
| "report_minimizer_data": { | ||
| "type": "boolean", | ||
| "default": false, | ||
| "description": "Include minimizer and distinct minimizer count information in report", | ||
| "fa_icon": "fas fa-expand-arrows-alt", | ||
| "hidden": true | ||
| }, | ||
| "use_names": { | ||
| "type": "boolean", | ||
| "default": false, | ||
| "description": "Print scientific names instead of just taxids", | ||
| "fa_icon": "fas fa-expand-arrows-alt", | ||
| "hidden": true | ||
| }, | ||
| "memory_mapping": { | ||
| "type": "boolean", | ||
| "default": false, | ||
| "description": "Avoid loading database into RAM", | ||
| "fa_icon": "fas fa-expand-arrows-alt", | ||
| "hidden": true | ||
| }, | ||
| "minimum_hit_groups": { | ||
| "type": "integer", | ||
| "default": 2, | ||
| "description": "Minimum number of hit groups needed to make a call", | ||
| "fa_icon": "fas fa-expand-arrows-alt", | ||
| "hidden": true | ||
| }, | ||
| "remove_filtered_reads": { | ||
| "type": "boolean", | ||
| "default": false, | ||
| "description": "Discard the classified and unclassified FASTQs prduced by Kraken2", | ||
| "fa_icon": "fas fa-expand-arrows-alt", | ||
| "hidden": true | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| "allOf": [ | ||
| { | ||
| "$ref": "#/definitions/kraken2_parameters" | ||
| } | ||
| ] | ||
| } |
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