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This commit is contained in:
James Fellows Yates 2022-04-13 11:49:35 +02:00
parent 1ac5a129a8
commit de57340526
6 changed files with 146 additions and 10 deletions

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@ -30,6 +30,9 @@
"malt/run": {
"git_sha": "72b96f4e504eef673f2b5c13560a9d90b669129b"
},
"megan/rma2info": {
"git_sha": "2d38566eca4cc15142b2ffa7c11837569b39aece"
},
"metaphlan3": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
@ -47,4 +50,4 @@
}
}
}
}
}

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@ -0,0 +1,38 @@
process MEGAN_RMA2INFO {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::megan=6.21.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/megan:6.21.7--h9ee0642_0':
'quay.io/biocontainers/megan:6.21.7--h9ee0642_0' }"
input:
tuple val(meta), path(rma6)
val(megan_summary)
output:
tuple val(meta), path("*.txt.gz") , emit: txt
tuple val(meta), path("*.megan"), optional: true, emit: megan_summary
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 summary = megan_summary ? "-es ${prefix}.megan" : ""
"""
rma2info \\
-i ${rma6} \\
-o ${prefix}.txt.gz \\
${summary} \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
megan: \$(echo \$(rma2info 2>&1) | grep version | sed 's/.*version //g;s/, built.*//g')
END_VERSIONS
"""
}

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@ -0,0 +1,51 @@
name: "megan_rma2info"
description: Analyses an RMA file and exports information in text format
keywords:
- megan
- rma6
- classification
- conversion
tools:
- "megan":
description: "A tool for studying the taxonomic content of a set of DNA reads"
homepage: "https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/megan6/"
documentation: "https://software-ab.informatik.uni-tuebingen.de/download/megan6/welcome.html"
tool_dev_url: "https://github.com/husonlab/megan-ce"
doi: "10.1371/journal.pcbi.1004957"
licence: "['GPL >=3']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- rma6:
type: file
description: RMA6 file from MEGAN or MALT
pattern: "*.rma6"
- megan_summary:
type: boolean
description: Specify whether to generate an MEGAN summary file
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"
- txt:
type: file
description: Compressed text file
pattern: "*.txt.gz"
- megan_summary:
type: file
description: Optionally generated MEGAN summary file
pattern: "*.megan"
authors:
- "@jfy133"

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@ -89,6 +89,7 @@ params {
centrifuge_save_unaligned = false
centrifuge_save_aligned = false
centrifuge_sam_format = false
// metaphlan3
run_metaphlan3 = false
}

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@ -14,8 +14,9 @@ workflow PROFILING {
databases // [ [ meta ], path ]
main:
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
ch_raw_profiles = Channel.empty()
/*
COMBINE READS WITH POSSIBLE DATABASES
@ -89,30 +90,33 @@ workflow PROFILING {
if ( params.run_malt ) {
MALT_RUN ( ch_input_for_malt.reads, params.malt_mode, ch_input_for_malt.db )
ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( MALT_RUN.out.versions.first() )
ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( MALT_RUN.out.versions.first() )
ch_raw_profiles = ch_raw_profiles.mix( MALT_RUN.out.rma6 )
}
if ( params.run_kraken2 ) {
KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db )
ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
ch_raw_profiles = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.txt )
}
if ( params.run_centrifuge ) {
CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_unaligned, params.centrifuge_save_aligned, params.centrifuge_sam_format )
ch_versions = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
ch_versions = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
ch_raw_profiles = ch_raw_profiles.mix( CENTRIFUGE_CENTRIFUGE.out.report )
}
if ( params.run_metaphlan3 ) {
METAPHLAN3 ( ch_input_for_metaphlan3.reads, ch_input_for_metaphlan3.db )
ch_versions = ch_versions.mix( METAPHLAN3.out.versions.first() )
ch_raw_profiles = ch_raw_profiles.mix( METAPHLAN3.out.biom )
}
emit:
// TODO work out if there is enough standardisation of output to export as one?
//output = ch_filtered_reads // channel: [ val(meta), [ reads ] ]
profiles = ch_raw_profiles // channel: [ val(meta), [ reads ] ]
versions = ch_versions // channel: [ versions.yml ]
mqc = ch_multiqc_files
}

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@ -0,0 +1,39 @@
//
// Perform read trimming and merging
//
include { SHORTREAD_FASTP } from './shortread_fastp'
include { SHORTREAD_ADAPTERREMOVAL } from './shortread_adapterremoval'
include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/modules/fastqc/main'
workflow SHORTREAD_POSTPROCESSING {
take:
input // [ [ meta ], [ taxon_table/file ] ]
main:
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
if ( params.shortread_clipmerge_tool == "fastp" ) {
ch_processed_reads = SHORTREAD_FASTP ( reads ).reads
ch_versions = ch_versions.mix( SHORTREAD_FASTP.out.versions )
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_FASTP.out.mqc )
} else if ( params.shortread_clipmerge_tool == "adapterremoval" ) {
ch_processed_reads = SHORTREAD_ADAPTERREMOVAL ( reads ).reads
ch_versions = ch_versions.mix( SHORTREAD_ADAPTERREMOVAL.out.versions )
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_ADAPTERREMOVAL.out.mqc )
} else {
ch_processed_reads = reads
}
FASTQC_PROCESSED ( ch_processed_reads )
ch_versions = ch_versions.mix( FASTQC_PROCESSED.out.versions )
ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip )
emit:
output = output // channel: [ val(meta), taxon_table ]
versions = ch_versions // channel: [ versions.yml ]
mqc = ch_multiqc_files
}