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Merge branch 'dev' into hostremoval

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James A. Fellows Yates 2022-04-07 14:00:10 +02:00 committed by GitHub
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19 changed files with 503 additions and 160 deletions
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8
.github/workflows/ci.yml vendored
View file

@ -29,8 +29,16 @@ jobs:
- NXF_VER: ""
NXF_EDGE: "1"
parameters:
- "--longread_clip false"
- "--shortread_clip false"
- "--shortread_clipmerge_tool fastp"
- "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged"
- "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs"
- "--shortread_clipmerge_tool adapterremoval"
- "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged"
- "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs"
- "--shortread_complexityfilter_tool bbduk"
- "--shortread_complexityfilter_tool prinseq"
steps:
- name: Check out pipeline code

14
CITATIONS.md
View file

@ -18,21 +18,27 @@
- [fastp](https://doi.org/10.1093/bioinformatics/bty560)
> Chen, Shifu, Yanqing Zhou, Yaru Chen, and Jia Gu. 2018. “Fastp: An Ultra-Fast All-in-One FASTQ Preprocessor.” Bioinformatics 34 (17): i884-90. 10.1093/bioinformatics/bty560.
> Chen, Shifu, Yanqing Zhou, Yaru Chen, and Jia Gu. 2018. Fastp: An Ultra-Fast All-in-One FASTQ Preprocessor. Bioinformatics 34 (17): i884-90. 10.1093/bioinformatics/bty560.
- [AdapterRemoval2](https://doi.org/10.1186/s13104-016-1900-2)
> Schubert, Mikkel, Stinus Lindgreen, and Ludovic Orlando. 2016. “AdapterRemoval v2: Rapid Adapter Trimming, Identification, and Read Merging.” BMC Research Notes 9 (February): 88. doi:10.1186/s13104-016-1900-2.
> Schubert, Mikkel, Stinus Lindgreen, and Ludovic Orlando. 2016. AdapterRemoval v2: Rapid Adapter Trimming, Identification, and Read Merging. BMC Research Notes 9 (February): 88. doi:10.1186/s13104-016-1900-2.
- [Porechop](https://github.com/rrwick/Porechop)
- [BBTools](http://sourceforge.net/projects/bbmap/)
- [PRINSEQ++](https://doi.org/10.7287/peerj.preprints.27553v1)
> Cantu, Vito Adrian, Jeffrey Sadural, and Robert Edwards. 2019. PRINSEQ++, a Multi-Threaded Tool for Fast and Efficient Quality Control and Preprocessing of Sequencing Datasets. e27553v1. PeerJ Preprints. doi: 10.7287/peerj.preprints.27553v1.
- [Kraken2](https://doi.org/10.1186/s13059-019-1891-0)
> Wood, Derrick E., Jennifer Lu, and Ben Langmead. 2019. “Improved Metagenomic Analysis with Kraken 2.” Genome Biology 20 (1): 257. doi: 10.1186/s13059-019-1891-0.
> Wood, Derrick E., Jennifer Lu, and Ben Langmead. 2019. Improved Metagenomic Analysis with Kraken 2. Genome Biology 20 (1): 257. doi: 10.1186/s13059-019-1891-0.
- [MALT](https://doi.org/10.1038/s41559-017-0446-6)
> Vågene, Åshild J., Alexander Herbig, Michael G. Campana, Nelly M. Robles García, Christina Warinner, Susanna Sabin, Maria A. Spyrou, et al. 2018. “Salmonella Enterica Genomes from Victims of a Major Sixteenth-Century Epidemic in Mexico.” Nature Ecology & Evolution 2 (3): 520-28. doi: 10.1038/s41559-017-0446-6.
> Vågene, Åshild J., Alexander Herbig, Michael G. Campana, Nelly M. Robles García, Christina Warinner, Susanna Sabin, Maria A. Spyrou, et al. 2018. Salmonella Enterica Genomes from Victims of a Major Sixteenth-Century Epidemic in Mexico. Nature Ecology & Evolution 2 (3): 520-28. doi: 10.1038/s41559-017-0446-6.
- [MetaPhlAn3](https://doi.org/10.7554/eLife.65088)

80
conf/modules.config
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@ -12,12 +12,6 @@
process {
publishDir = [
path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
withName: SAMPLESHEET_CHECK {
publishDir = [
path: { "${params.outdir}/pipeline_info" },
@ -34,20 +28,12 @@ process {
]
}
withName: UNTAR {
publishDir = [
path: { "${params.outdir}/databases" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: FASTQC {
ext.args = '--quiet'
ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
publishDir = [
path: { "${params.outdir}/fastqc/raw" },
mode: 'copy',
mode: params.publish_dir_mode,
pattern: '*.html'
]
}
@ -57,7 +43,7 @@ process {
ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
publishDir = [
path: { "${params.outdir}/fastqc/processed" },
mode: 'copy',
mode: params.publish_dir_mode,
pattern: '*.html'
]
}
@ -73,8 +59,9 @@ process {
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/fastp" },
mode: 'copy',
pattern: '*.fastq.gz'
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
]
}
@ -92,8 +79,9 @@ process {
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/fastp" },
mode: 'copy',
pattern: '*.fastq.gz'
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
]
}
@ -108,8 +96,9 @@ process {
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/adapterremoval" },
mode: 'copy',
pattern: '*.fastq.gz'
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
]
}
@ -127,8 +116,9 @@ process {
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/adapterremoval" },
mode: 'copy',
pattern: '*.fastq.gz'
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
]
}
@ -136,8 +126,9 @@ process {
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/porechop" },
mode: 'copy',
pattern: '*.fastq.gz'
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
]
}
@ -145,7 +136,7 @@ process {
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/bowtie2/build" },
mode: 'copy',
mode: params.publish_dir_mode,
pattern: '*.bt2'
]
}
@ -154,16 +145,37 @@ process {
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/bowtie2/align" },
mode: 'copy',
mode: params.publish_dir_mode,
pattern: '*.{fastq.gz,bam}'
]
}
withName: CAT_FASTQ {
withName: BBMAP_BBDUK {
ext.args = [
"entropy=${params.shortread_complexityfilter_entropy}",
"entropywindow=${params.shortread_complexityfilter_bbduk_windowsize}",
params.shortread_complexityfilter_bbduk_mask ? "entropymask=t" : "entropymask=f"
].join(' ').trim()
ext.prefix = { "${meta.id}-${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/prepared_sequences" },
mode: 'copy',
pattern: '*.fastq.gz'
path: { "${params.outdir}/bbduk/" },
mode: params.publish_dir_mode,
pattern: '*.{fastq.gz,log}',
enabled: params.save_complexityfiltered_reads
]
}
withName: PRINSEQPLUSPLUS {
ext.args = [
params.shortread_complexityfilter_prinseqplusplus_mode == 'dust' ? "-lc_dust=${params.shortread_complexityfilter_prinseqplusplus_dustscore}" : "-lc_entropy=${params.shortread_complexityfilter_entropy}",
"-trim_qual_left=0 -trim_qual_left=0 -trim_qual_window=0 -trim_qual_step=0"
].join(' ').trim()
ext.prefix = { "${meta.id}-${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/prinseqplusplus/" },
mode: params.publish_dir_mode,
pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz,log}',
enabled: params.save_complexityfiltered_reads
]
}
@ -172,7 +184,7 @@ process {
ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/malt/${meta.db_name}" },
mode: 'copy',
mode: params.publish_dir_mode,
pattern: '*.{rma6,tab,text,sam,log}'
]
}
@ -182,7 +194,7 @@ process {
ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/kraken2/${meta.db_name}" },
mode: 'copy',
mode: params.publish_dir_mode,
pattern: '*.{fastq.gz,txt}'
]
}

4
conf/test.config
View file

@ -28,7 +28,9 @@ params {
run_malt = true
run_metaphlan3 = true
shortread_clipmerge = true
longread_clip = false
shortread_complexityfilter = true
shortread_clipmerge = true
shortread_hostremoval = true
shortread_hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
}

8
modules.json
View file

@ -4,7 +4,10 @@
"repos": {
"nf-core/modules": {
"adapterremoval": {
"git_sha": "f0800157544a82ae222931764483331a81812012"
"git_sha": "879d42c5e28661fe0a5e744c9e2c515868f9e08a"
},
"bbmap/bbduk": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"bowtie2/align": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
@ -39,6 +42,9 @@
"porechop": {
"git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
},
"prinseqplusplus": {
"git_sha": "f1c5384c31e985591716afdd732cf8c2ae29d05b"
},
"untar": {
"git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
}

42
modules/nf-core/modules/adapterremoval/main.nf generated
View file

@ -12,14 +12,13 @@ process ADAPTERREMOVAL {
path(adapterlist)
output:
tuple val(meta), path("${prefix}.truncated.gz") , optional: true, emit: singles_truncated
tuple val(meta), path("${prefix}.discarded.gz") , optional: true, emit: discarded
tuple val(meta), path("${prefix}.pair1.truncated.gz") , optional: true, emit: pair1_truncated
tuple val(meta), path("${prefix}.pair2.truncated.gz") , optional: true, emit: pair2_truncated
tuple val(meta), path("${prefix}.collapsed.gz") , optional: true, emit: collapsed
tuple val(meta), path("${prefix}.collapsed.truncated.gz") , optional: true, emit: collapsed_truncated
tuple val(meta), path("${prefix}.paired.gz") , optional: true, emit: paired_interleaved
tuple val(meta), path('*.log') , emit: log
tuple val(meta), path("${prefix}.truncated.fastq.gz") , optional: true, emit: singles_truncated
tuple val(meta), path("${prefix}.discarded.fastq.gz") , optional: true, emit: discarded
tuple val(meta), path("${prefix}.pair{1,2}.truncated.fastq.gz") , optional: true, emit: paired_truncated
tuple val(meta), path("${prefix}.collapsed.fastq.gz") , optional: true, emit: collapsed
tuple val(meta), path("${prefix}.collapsed.truncated.fastq.gz") , optional: true, emit: collapsed_truncated
tuple val(meta), path("${prefix}.paired.fastq.gz") , optional: true, emit: paired_interleaved
tuple val(meta), path('*.settings') , emit: settings
path "versions.yml" , emit: versions
when:
@ -38,10 +37,19 @@ process ADAPTERREMOVAL {
$adapterlist \\
--basename ${prefix} \\
--threads ${task.cpus} \\
--settings ${prefix}.log \\
--seed 42 \\
--gzip
ensure_fastq() {
if [ -f "\${1}" ]; then
mv "\${1}" "\${1::-3}.fastq.gz"
fi
}
ensure_fastq '${prefix}.truncated.gz'
ensure_fastq '${prefix}.discarded.gz'
cat <<-END_VERSIONS > versions.yml
"${task.process}":
adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
@ -56,10 +64,24 @@ process ADAPTERREMOVAL {
$adapterlist \\
--basename ${prefix} \\
--threads $task.cpus \\
--settings ${prefix}.log \\
--seed 42 \\
--gzip
ensure_fastq() {
if [ -f "\${1}" ]; then
mv "\${1}" "\${1::-3}.fastq.gz"
fi
}
ensure_fastq '${prefix}.truncated.gz'
ensure_fastq '${prefix}.discarded.gz'
ensure_fastq '${prefix}.pair1.truncated.gz'
ensure_fastq '${prefix}.pair2.truncated.gz'
ensure_fastq '${prefix}.collapsed.gz'
ensure_fastq '${prefix}.collapsed.truncated.gz'
ensure_fastq '${prefix}.paired.gz'
cat <<-END_VERSIONS > versions.yml
"${task.process}":
adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")

14
modules/nf-core/modules/adapterremoval/meta.yml generated
View file

@ -43,43 +43,43 @@ output:
Adapter trimmed FastQ files of either single-end reads, or singleton
'orphaned' reads from merging of paired-end data (i.e., one of the pair
was lost due to filtering thresholds).
pattern: "*.truncated.gz"
pattern: "*.truncated.fastq.gz"
- discarded:
type: file
description: |
Adapter trimmed FastQ files of reads that did not pass filtering
thresholds.
pattern: "*.discarded.gz"
pattern: "*.discarded.fastq.gz"
- pair1_truncated:
type: file
description: |
Adapter trimmed R1 FastQ files of paired-end reads that did not merge
with their respective R2 pair due to long templates. The respective pair
is stored in 'pair2_truncated'.
pattern: "*.pair1.truncated.gz"
pattern: "*.pair1.truncated.fastq.gz"
- pair2_truncated:
type: file
description: |
Adapter trimmed R2 FastQ files of paired-end reads that did not merge
with their respective R1 pair due to long templates. The respective pair
is stored in 'pair1_truncated'.
pattern: "*.pair2.truncated.gz"
pattern: "*.pair2.truncated.fastq.gz"
- collapsed:
type: file
description: |
Collapsed FastQ of paired-end reads that successfully merged with their
respective R1 pair but were not trimmed.
pattern: "*.collapsed.gz"
pattern: "*.collapsed.fastq.gz"
- collapsed_truncated:
type: file
description: |
Collapsed FastQ of paired-end reads that successfully merged with their
respective R1 pair and were trimmed of adapter due to sufficient overlap.
pattern: "*.collapsed.truncated.gz"
pattern: "*.collapsed.truncated.fastq.gz"
- log:
type: file
description: AdapterRemoval log file
pattern: "*.log"
pattern: "*.settings"
- versions:
type: file
description: File containing software versions

43
modules/nf-core/modules/bbmap/bbduk/main.nf generated Normal file
View file

@ -0,0 +1,43 @@
process BBMAP_BBDUK {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::bbmap=38.90" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bbmap:38.90--he522d1c_1' :
'quay.io/biocontainers/bbmap:38.90--he522d1c_1' }"
input:
tuple val(meta), path(reads)
path contaminants
output:
tuple val(meta), path('*.fastq.gz'), emit: reads
tuple val(meta), path('*.log') , emit: log
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def raw = meta.single_end ? "in=${reads[0]}" : "in1=${reads[0]} in2=${reads[1]}"
def trimmed = meta.single_end ? "out=${prefix}.fastq.gz" : "out1=${prefix}_1.fastq.gz out2=${prefix}_2.fastq.gz"
def contaminants_fa = contaminants ? "ref=$contaminants" : ''
"""
maxmem=\$(echo \"$task.memory\"| sed 's/ GB/g/g')
bbduk.sh \\
-Xmx\$maxmem \\
$raw \\
$trimmed \\
threads=$task.cpus \\
$args \\
$contaminants_fa \\
&> ${prefix}.bbduk.log
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bbmap: \$(bbversion.sh)
END_VERSIONS
"""
}

52
modules/nf-core/modules/bbmap/bbduk/meta.yml generated Normal file
View file

@ -0,0 +1,52 @@
name: bbmap_bbduk
description: Adapter and quality trimming of sequencing reads
keywords:
- trimming
- adapter trimming
- quality trimming
tools:
- bbmap:
description: BBMap is a short read aligner, as well as various other bioinformatic tools.
homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
tool_dev_url: None
doi: ""
licence: ["UC-LBL license (see package)"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- contaminants:
type: file
description: |
Reference files containing adapter and/or contaminant sequences for sequence kmer matching
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: The trimmed/modified fastq reads
pattern: "*fastq.gz"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- log:
type: file
description: Bbduk log file
pattern: "*bbduk.log"
authors:
- "@MGordon09"

61
modules/nf-core/modules/prinseqplusplus/main.nf generated Normal file
View file

@ -0,0 +1,61 @@
process PRINSEQPLUSPLUS {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::prinseq-plus-plus=1.2.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/prinseq-plus-plus:1.2.3--hc90279e_1':
'quay.io/biocontainers/prinseq-plus-plus:1.2.3--hc90279e_1' }"
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path("*_good_out*.fastq.gz") , emit: good_reads
tuple val(meta), path("*_single_out*.fastq.gz"), optional: true, emit: single_reads
tuple val(meta), path("*_bad_out*.fastq.gz") , optional: true, emit: bad_reads
tuple val(meta), path("*.log") , emit: log
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}"
if (meta.single_end) {
"""
prinseq++ \\
-threads $task.cpus \\
-fastq ${reads} \\
-out_name ${prefix} \\
-out_gz \\
-VERBOSE 1 \\
$args \\
| tee ${prefix}.log
cat <<-END_VERSIONS > versions.yml
"${task.process}":
prinseqplusplus: \$(echo \$(prinseq++ --version | cut -f 2 -d ' ' ))
END_VERSIONS
"""
} else {
"""
prinseq++ \\
-threads $task.cpus \\
-fastq ${reads[0]} \\
-fastq2 ${reads[1]} \\
-out_name ${prefix} \\
-out_gz \\
-VERBOSE 1 \\
$args \\
| tee ${prefix}.log
cat <<-END_VERSIONS > versions.yml
"${task.process}":
prinseqplusplus: \$(echo \$(prinseq++ --version | cut -f 2 -d ' ' ))
END_VERSIONS
"""
}
}

60
modules/nf-core/modules/prinseqplusplus/meta.yml generated Normal file
View file

@ -0,0 +1,60 @@
name: "prinseqplusplus"
description: PRINSEQ++ is a C++ implementation of the prinseq-lite.pl program. It can be used to filter, reformat or trim genomic and metagenomic sequence data
keywords:
- fastq
- fasta
- filter
- trim
tools:
- "prinseqplusplus":
description: "PRINSEQ++ - Multi-threaded C++ sequence cleaning"
homepage: "https://github.com/Adrian-Cantu/PRINSEQ-plus-plus"
documentation: "https://github.com/Adrian-Cantu/PRINSEQ-plus-plus"
tool_dev_url: "https://github.com/Adrian-Cantu/PRINSEQ-plus-plus"
doi: "10.7287/peerj.preprints.27553v1"
licence: "['GPL v2']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end
data, respectively.
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"
- good_reads:
type: file
description: Reads passing filter(s) in gzipped FASTQ format
pattern: "*_good_out_{R1,R2}.fastq.gz"
- single_reads:
type: file
description: |
Single reads without the pair passing filter(s) in gzipped FASTQ format
pattern: "*_single_out_{R1,R2}.fastq.gz"
- bad_reads:
type: file
description: |
Reads without not passing filter(s) in gzipped FASTQ format
pattern: "*_bad_out_{R1,R2}.fastq.gz"
- log:
type: file
description: |
Verbose level 2 STDOUT information in a log file
pattern: "*.log"
authors:
- "@jfy133"

14
nextflow.config
View file

@ -51,7 +51,7 @@ params {
max_cpus = 16
max_time = '240.h'
// Databaess
// Databases
databases = null
// FASTQ preprocessing
@ -64,6 +64,18 @@ params {
shortread_clipmerge_adapter2 = null
shortread_clipmerge_minlength = 15
longread_clip = false
save_preprocessed_reads = false
// Complexity filtering
shortread_complexityfilter = false
shortread_complexityfilter_tool = 'bbduk'
shortread_complexityfilter_entropy = 0.3
shortread_complexityfilter_bbduk_windowsize = 50
shortread_complexityfilter_bbduk_mask = false
shortread_complexityfilter_prinseqplusplus_mode = 'entropy'
shortread_complexityfilter_prinseqplusplus_dustscore = 0.5
save_complexityfiltered_reads = false
// Host Removal
shortread_hostremoval = false

35
nextflow_schema.json
View file

@ -308,6 +308,41 @@
"type": "integer",
"default": 15
},
"save_preprocessed_reads": {
"type": "boolean",
"default": false
},
"shortread_complexityfilter_tool": {
"type": "string",
"default": "bbduk"
},
"shortread_complexityfilter_bbduk_windowsize": {
"type": "integer",
"default": 50
},
"shortread_complexityfilter_bbduk_mask": {
"type": "boolean"
},
"shortread_complexityfilter": {
"type": "boolean"
},
"shortread_complexityfilter_entropy": {
"type": "number",
"default": 0.3
},
"shortread_complexityfilter_prinseqplusplus_mode": {
"type": "string",
"default": "entropy",
"enum": ["entropy", "dust"]
},
"shortread_complexityfilter_prinseqplusplus_dustscore": {
"type": "number",
"default": 0.5
},
"save_complexityfiltered_reads": {
"type": "boolean",
"default": false
},
"shortread_hostremoval": {
"type": "boolean"
},

8
subworkflows/local/longread_preprocessing.nf
View file

@ -1,6 +1,6 @@
/*
Process long raw reads with porechop
*/
//
// Process long raw reads with porechop
//
include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/modules/fastqc/main'
include { PORECHOP } from '../../modules/nf-core/modules/porechop/main'
@ -25,7 +25,7 @@ workflow LONGREAD_PREPROCESSING {
FASTQC_PROCESSED ( PORECHOP.out.reads )
ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip.collect{it[1]} )
ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip )
emit:

89
subworkflows/local/shortread_adapterremoval.nf
View file

@ -1,15 +1,10 @@
/*
Process short raw reads with AdapterRemoval
*/
//
// Process short raw reads with AdapterRemoval
//
include { ADAPTERREMOVAL as ADAPTERREMOVAL_SINGLE } from '../../modules/nf-core/modules/adapterremoval/main'
include { ADAPTERREMOVAL as ADAPTERREMOVAL_PAIRED } from '../../modules/nf-core/modules/adapterremoval/main'
include { CAT_FASTQ } from '../../modules/nf-core/modules/cat/fastq/main'
include {
ENSURE_FASTQ_EXTENSION as ENSURE_FASTQ_EXTENSION1;
ENSURE_FASTQ_EXTENSION as ENSURE_FASTQ_EXTENSION2;
ENSURE_FASTQ_EXTENSION as ENSURE_FASTQ_EXTENSION3;
} from '../../modules/local/ensure_fastq_extension'
workflow SHORTREAD_ADAPTERREMOVAL {
@ -36,89 +31,63 @@ workflow SHORTREAD_ADAPTERREMOVAL {
if ( params.shortread_clipmerge_mergepairs && !params.shortread_clipmerge_excludeunmerged ) {
ENSURE_FASTQ_EXTENSION1(
Channel.empty().mix(
ch_concat_fastq = Channel.empty()
.mix(
ADAPTERREMOVAL_PAIRED.out.collapsed,
ADAPTERREMOVAL_PAIRED.out.collapsed_truncated,
ADAPTERREMOVAL_PAIRED.out.singles_truncated,
ADAPTERREMOVAL_PAIRED.out.pair1_truncated,
ADAPTERREMOVAL_PAIRED.out.pair2_truncated
ADAPTERREMOVAL_PAIRED.out.paired_truncated
)
.map { meta, reads ->
meta.single_end = true
[meta, reads]
def meta_new = meta.clone()
meta_new.single_end = true
[meta_new, reads]
}
)
CAT_FASTQ(
ENSURE_FASTQ_EXTENSION1.out.reads
.groupTuple()
)
// Paired-end reads cause a nested tuple during grouping.
// We want to present a flat list of files to `CAT_FASTQ`.
.map { meta, fastq -> [meta, fastq.flatten()] }
ENSURE_FASTQ_EXTENSION2(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
CAT_FASTQ(ch_concat_fastq)
ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
.mix(ENSURE_FASTQ_EXTENSION2.out.reads)
.mix(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
} else if ( params.shortread_clipmerge_mergepairs && params.shortread_clipmerge_excludeunmerged ) {
ENSURE_FASTQ_EXTENSION1(
Channel.empty().mix(
ch_concat_fastq = Channel.empty()
.mix(
ADAPTERREMOVAL_PAIRED.out.collapsed,
ADAPTERREMOVAL_PAIRED.out.collapsed_truncated
)
.map { meta, reads ->
meta.single_end = true
[meta, reads]
def meta_new = meta.clone()
meta_new.single_end = true
[meta_new, reads]
}
)
CAT_FASTQ(
ENSURE_FASTQ_EXTENSION1.out.reads
.groupTuple()
)
.map { meta, fastq -> [meta, fastq.flatten()] }
ENSURE_FASTQ_EXTENSION2(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
CAT_FASTQ(ch_concat_fastq)
ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
.mix(ENSURE_FASTQ_EXTENSION2.out.reads)
.mix(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
} else {
ENSURE_FASTQ_EXTENSION1(
ADAPTERREMOVAL_PAIRED.out.pair1_truncated
.map { meta, reads ->
meta.single_end = true
[meta, reads]
}
)
ENSURE_FASTQ_EXTENSION2(
ADAPTERREMOVAL_PAIRED.out.pair2_truncated
.map { meta, reads ->
meta.single_end = true
[meta, reads]
}
)
ENSURE_FASTQ_EXTENSION3(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
ch_adapterremoval_reads_prepped = ENSURE_FASTQ_EXTENSION1.out.reads
.join(ENSURE_FASTQ_EXTENSION2.out.reads)
.groupTuple()
.map { meta, pair1, pair2 ->
meta.single_end = false
[ meta, [ pair1, pair2 ].flatten() ]
}
.mix(ENSURE_FASTQ_EXTENSION3.out.reads)
ch_adapterremoval_reads_prepped = ADAPTERREMOVAL_PAIRED.out.paired_truncated
.mix(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
}
ch_versions = ch_versions.mix( ADAPTERREMOVAL_SINGLE.out.versions.first() )
ch_versions = ch_versions.mix( ADAPTERREMOVAL_PAIRED.out.versions.first() )
ch_multiqc_files = ch_multiqc_files.mix(
ADAPTERREMOVAL_PAIRED.out.log.collect{it[1]},
ADAPTERREMOVAL_SINGLE.out.log.collect{it[1]}
ADAPTERREMOVAL_PAIRED.out.settings,
ADAPTERREMOVAL_SINGLE.out.settings
)
emit:

32
subworkflows/local/shortread_complexityfiltering.nf Normal file
View file

@ -0,0 +1,32 @@
//
// Check input samplesheet and get read channels
//
include { BBMAP_BBDUK } from '../../modules/nf-core/modules/bbmap/bbduk/main'
include { PRINSEQPLUSPLUS } from '../../modules/nf-core/modules/prinseqplusplus/main'
workflow SHORTREAD_COMPLEXITYFILTERING {
take:
reads // [ [ meta ], [ reads ] ]
main:
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
if ( params.shortread_complexityfilter_tool == 'bbduk' ) {
ch_filtered_reads = BBMAP_BBDUK ( reads, [] ).reads
ch_versions = ch_versions.mix( BBMAP_BBDUK.out.versions.first() )
ch_multiqc_files = ch_multiqc_files.mix( BBMAP_BBDUK.out.log )
} else if ( params.shortread_complexityfilter_tool == 'prinseqplusplus' ) {
ch_filtered_reads = PRINSEQPLUSPLUS ( reads ).good_reads
ch_versions = ch_versions.mix( PRINSEQPLUSPLUS.out.versions.first() )
} else {
ch_filtered_reads = reads
}
emit:
reads = ch_filtered_reads // channel: [ val(meta), [ reads ] ]
versions = ch_versions // channel: [ versions.yml ]
mqc = ch_multiqc_files
}

10
subworkflows/local/shortread_fastp.nf
View file

@ -1,6 +1,6 @@
/*
Process short raw reads with FastP
*/
//
// Process short raw reads with FastP
//
include { FASTP as FASTP_SINGLE } from '../../modules/nf-core/modules/fastp/main'
include { FASTP as FASTP_PAIRED } from '../../modules/nf-core/modules/fastp/main'
@ -44,8 +44,8 @@ workflow SHORTREAD_FASTP {
ch_processed_reads = ch_fastp_reads_prepped
ch_multiqc_files = ch_multiqc_files.mix( FASTP_SINGLE.out.json.collect{it[1]} )
ch_multiqc_files = ch_multiqc_files.mix( FASTP_PAIRED.out.json.collect{it[1]} )
ch_multiqc_files = ch_multiqc_files.mix( FASTP_SINGLE.out.json )
ch_multiqc_files = ch_multiqc_files.mix( FASTP_PAIRED.out.json )
emit:
reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]

6
subworkflows/local/shortread_preprocessing.nf
View file

@ -1,5 +1,5 @@
//
// Check input samplesheet and get read channels
// Perform read trimming and merging
//
@ -9,7 +9,7 @@ include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/modules
workflow SHORTREAD_PREPROCESSING {
take:
reads // file: /path/to/samplesheet.csv
reads // [ [ meta ], [ reads ] ]
main:
ch_versions = Channel.empty()
@ -29,7 +29,7 @@ workflow SHORTREAD_PREPROCESSING {
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.collect{it[1]} )
ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip )
emit:
reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]

69
workflows/taxprofiler.nf
View file

@ -18,8 +18,8 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
// Check mandatory parameters
if (params.input ) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
if (params.databases ) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] warning: MALT does not except uncollapsed paired-reads. Pairs will be profiled as separate files."
if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] warning: MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
if (params.shortread_clipmerge_excludeunmerged && !params.shortread_clipmerge_mergepairs) exit 1, "[nf-core/taxprofiler] error: cannot include unmerged reads when merging not turned on. Please specify --shortread_clipmerge_mergepairs"
// TODO Add check if index but no reference exit 1
@ -53,6 +53,7 @@ include { DB_CHECK } from '../subworkflows/local/db_check'
include { SHORTREAD_PREPROCESSING } from '../subworkflows/local/shortread_preprocessing'
include { LONGREAD_PREPROCESSING } from '../subworkflows/local/longread_preprocessing'
include { SHORTREAD_HOSTREMOVAL } from '../subworkflows/local/shortread_hostremoval'
include { SHORTREAD_COMPLEXITYFILTERING } from '../subworkflows/local/shortread_complexityfiltering'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@ -100,7 +101,7 @@ workflow TAXPROFILER {
/*
MODULE: Run FastQC
*/
ch_input_for_fastqc = INPUT_CHECK.out.fastq.mix( INPUT_CHECK.out.nanopore ).dump(tag: "input_to_fastq")
ch_input_for_fastqc = INPUT_CHECK.out.fastq.mix( INPUT_CHECK.out.nanopore )
FASTQC (
ch_input_for_fastqc
@ -108,10 +109,6 @@ workflow TAXPROFILER {
ch_versions = ch_versions.mix(FASTQC.out.versions.first())
CUSTOM_DUMPSOFTWAREVERSIONS (
ch_versions.unique().collectFile(name: 'collated_versions.yml')
)
/*
SUBWORKFLOW: PERFORM PREPROCESSING
*/
@ -125,15 +122,29 @@ workflow TAXPROFILER {
ch_longreads_preprocessed = LONGREAD_PREPROCESSING ( INPUT_CHECK.out.nanopore ).reads
.map { it -> [ it[0], [it[1]] ] }
ch_versions = ch_versions.mix(LONGREAD_PREPROCESSING.out.versions.first())
} else {SHORTREAD_HOSTREMOVAL
} else {
ch_longreads_preprocessed = INPUT_CHECK.out.nanopore
}
/*
SUBWORKFLOW: COMPLEXITY FILTERING
*/
if ( params.shortread_complexityfilter ) {
ch_shortreads_filtered = SHORTREAD_COMPLEXITYFILTERING ( ch_shortreads_preprocessed ).reads
} else {
ch_shortreads_filtered = ch_shortreads_preprocessed
}
/*
SUBWORKFLOW: HOST REMOVAL
*/
if ( params.shortread_hostremoval ) {
ch_shortreads_hostremoved = SHORTREAD_HOSTREMOVAL ( ch_shortreads_preprocessed, ch_reference, ch_reference_index ).reads
ch_shortreads_hostremoved = SHORTREAD_HOSTREMOVAL ( ch_shortreads_filtered, ch_reference, ch_reference_index ).reads
ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions.first())
} else {
ch_shortreads_hostremoved = ch_shortreads_preprocessed
ch_shortreads_hostremoved = ch_shortreads_filtered
}
/*
@ -182,7 +193,6 @@ workflow TAXPROFILER {
}
ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3
.dump(tag: "input_metaphlan3")
.multiMap {
it ->
reads: [it[0] + it[2], it[1]]
@ -207,6 +217,12 @@ workflow TAXPROFILER {
/*
MODULE: MultiQC
*/
CUSTOM_DUMPSOFTWAREVERSIONS (
ch_versions.unique().collectFile(name: 'collated_versions.yml')
)
workflow_summary = WorkflowTaxprofiler.paramsSummaryMultiqc(workflow, summary_params)
ch_workflow_summary = Channel.value(workflow_summary)
@ -218,27 +234,34 @@ workflow TAXPROFILER {
ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
if (params.shortread_clipmerge) {
ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_PREPROCESSING.out.mqc)
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( SHORTREAD_PREPROCESSING.out.versions )
}
if (params.longread_clip) {
ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( LONGREAD_PREPROCESSING.out.versions )
}
if (params.shortread_complexityfilter){
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_COMPLEXITYFILTERING.out.mqc.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
}
if (params.shortread_hostremoval) {
ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([]))
}
if (params.longread_clip) {
ch_multiqc_files = ch_multiqc_files.mix(LONGREAD_PREPROCESSING.out.mqc)
}
if (params.run_kraken2) {
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())
}
if (params.run_malt) {
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( KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
}
if (params.run_malt) {
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() )
}
// TODO MALT results overwriting per database?
// TODO Versions for Karken/MALT not report?
// TODO create multiQC module for metaphlan
MULTIQC (