1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-11-13 07:23:10 +00:00

Merge branch 'nf-core:dev' into update_output

This commit is contained in:
Sofia Stamouli 2022-12-20 15:30:19 +01:00 committed by GitHub
commit 3eb6a29fb0
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
30 changed files with 749 additions and 432 deletions

View file

@ -77,8 +77,6 @@ On release, automated continuous integration tests run the pipeline on a full-si
nextflow run nf-core/taxprofiler --input samplesheet.csv --databases database.csv --outdir <OUTDIR> --run_<TOOL1> --run_<TOOL1> -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
```
Note pipeline supports both CSV and PEP input sample sheets. Find out more [here](http://pep.databio.org/en/2.1.0/specification/).
## Documentation
The nf-core/taxprofiler pipeline comes with documentation about the pipeline [usage](https://nf-co.re/taxprofiler/usage), [parameters](https://nf-co.re/taxprofiler/parameters) and [output](https://nf-co.re/taxprofiler/output).

View file

@ -19,11 +19,20 @@ custom_logo_title: "nf-core/taxprofiler"
run_modules:
- fastqc
- adapterRemoval
- bbduk
- prinseqplusplus
- fastp
- filtlong
- bowtie2
- minimap2
- samtools
- kraken
- kaiju
- metaphlan
- diamond
- malt
- motus
- porechop
- custom_content
#extra_fn_clean_exts:
@ -36,16 +45,41 @@ top_modules:
name: "FastQC (pre-Trimming)"
path_filters:
- "*raw_*fastqc.zip"
- "fastqc":
name: "Falco (pre-Trimming)"
path_filters:
- "*_raw_falco_*_report.html"
- "fastp"
- "adapterRemoval"
- "porechop"
- "fastqc":
name: "FastQC (post-Trimming)"
path_filters:
- "*raw_*processed.zip"
- "*_processed_*fastqc.zip"
- "fastqc":
name: "Falco (post-Trimming)"
path_filters:
- "*_processed_falco_*_report.html"
- "bbduk"
- "prinseqplusplus"
- "filtlong"
- "bowtie2":
name: "bowtie2"
- "samtools":
name: "Samtools Stats"
- "kraken":
name: "Kraken"
path_filters:
- "*.kraken2.report.txt"
- "*.kraken2.kraken2.report.txt"
- "kraken":
name: "Bracken"
anchor: "bracken"
target: "Bracken"
doi: "10.7717/peerj-cs.104"
info: "Estimates species abundances in metagenomics samples by probabilistically re-distributing reads in the taxonomic tree."
extra: "Note: plot title will say Kraken2 due to the first step of bracken producing the same output format as Kraken. Abundance information is currently not supported in MultiQC."
path_filters:
- "*.bracken.kraken2.report.txt"
- "kraken":
name: "Centrifuge"
anchor: "centrifuge"
@ -55,3 +89,171 @@ top_modules:
extra: "Note: plot title will say Kraken2 due to Centrifuge producing the same output format as Kraken. If activated, see the actual Kraken2 results in the section above."
path_filters:
- "*.centrifuge.txt"
- "malt":
name: "MALT"
- "diamond"
- "kaiju":
name: "Kaiju"
- "motus"
#It is not possible to set placement for custom kraken and centrifuge columns.
table_columns_placement:
FastQC (pre-Trimming):
total_sequences: 100
avg_sequence_length: 110
percent_duplicates: 120
percent_gc: 130
percent_fails: 140
Falco (pre-Trimming):
total_sequences: 200
avg_sequence_length: 210
percent_duplicates: 220
percent_gc: 230
percent_fails: 240
fastp:
pct_adapter: 300
pct_surviving: 310
pct_duplication: 320
after_filtering_gc_content: 330
after_filtering_q30_rate: 340
after_filtering_q30_bases: 350
Adapter Removal:
aligned_total: 360
percent_aligned: 370
percent_collapsed: 380
percent_discarded: 390
FastQC (post-Trimming):
total_sequences: 400
avg_sequence_length: 410
percent_duplicates: 420
percent_gc: 430
percent_fails: 440
Falco (post-Trimming):
total_sequences: 500
avg_sequence_length: 510
percent_duplicates: 520
percent_gc: 530
percent_fails: 540
bowtie2:
overall_alignment_rate: 600
Samtools Stats:
raw_total_sequences: 700
reads_mapped: 710
reads_mapped_percent: 720
reads_properly_paired_percent: 730
non-primary_alignments: 740
reads_MQ0_percent: 750
error_rate: 760
MALT:
Num. of queries: 1000
Total reads: 1100
Mappability: 1200
Assig. Taxonomy: 1300
Taxonomic assignment success: 1400
Kaiju:
assigned: 2000
"% Assigned": 2100
"% Unclassified": 2200
table_columns_visible:
FastQC (pre-Trimming):
total_sequences: True
avg_sequence_length: True
percent_duplicates: True
percent_gc: True
percent_fails: False
Falco (pre-Trimming):
total_sequences: True
avg_sequence_length: True
percent_duplicates: True
percent_gc: True
percent_fails: False
fastp:
pct_adapter: True
pct_surviving: True
pct_duplication: False
after_filtering_gc_content: False
after_filtering_q30_rate: False
after_filtering_q30_bases: False
Adapter Removal:
aligned_total: True
percent_aligned: True
percent_collapsed: True
percent_discarded: False
FastQC (post-Trimming):
total_sequences: True
avg_sequence_length: True
percent_duplicates: False
percent_gc: False
percent_fails: False
Falco (post-Trimming):
total_sequences: True
avg_sequence_length: True
percent_duplicates: False
percent_gc: False
percent_fails: False
bowtie2:
overall_alignment_rate: True
Samtools Stats:
raw_total_sequences: True
reads_mapped: True
reads_mapped_percent: True
reads_properly_paired_percent: False
non-primary_alignments: False
reads_MQ0_percent: False
error_rate: False
Kraken:
"% Unclassified": True
"% Top 5": False
Bracken:
"% Unclassified": True
"% Top 5": False
Centrifuge:
"% Unclassified": True
"% Top 5": False
MALT:
Num. of queries: True
Total reads: True
Mappability: True
Assig. Taxonomy: False
Taxonomic assignment success: True
Kaiju:
assigned: False
"% Assigned": False
"% Unclassified": True
table_columns_name:
FastQC (pre-Trimming):
total_sequences: "Nr. Input Reads"
avg_sequence_length: "Length Input Reads"
percent_gc: "% GC Input Reads"
percent_duplicates: "% Dups Input Reads"
percent_fails: "% Failed Input Reads"
Falco (pre-Trimming):
total_sequences: "Nr. Input Reads"
avg_sequence_length: "Length Input Reads"
percent_gc: "% GC Input Reads"
percent_duplicates: "% Dups Input Reads"
percent_fails: "% Failed Input Reads"
FastQC (post-Trimming):
total_sequences: "Nr. Processed Reads"
avg_sequence_length: "Length Processed Reads"
percent_gc: "% GC Processed Reads"
percent_duplicates: "% Dups Processed Reads"
percent_fails: "% Failed Processed Reads"
Falco (post-Trimming):
total_sequences: "Nr. Processed Reads"
avg_sequence_length: "Length Processed Reads"
percent_gc: "% GC Processed Reads"
percent_duplicates: "% Dups Processed Reads"
percent_fails: "% Failed Processed Reads"
Samtools Stats:
raw_total_sequences: "Nr. Reads Into Mapping"
reads_mapped: "Nr. Mapped Reads"
reads_mapped_percent: "% Mapped Reads"
extra_fn_clean_exts:
- ".kraken2.kraken2.report.txt"
- ".centrifuge.txt"
- ".bracken.kraken2.report.txt"
- ".settings"

View file

@ -1,55 +0,0 @@
description: A schema for validation of samplesheet.csv for taxprofiler pipeline.
imports:
- https://schema.databio.org/pep/2.1.0.yaml
properties:
samples:
type: array
items:
type: object
properties:
sample:
type: string
description: "Sample identifier."
pattern: "^\\S*$"
run_accession:
type: string
description: "Run accession number."
instrument_platform:
type: string
description: "Name of the platform that sequenced the samples."
enum:
[
"ABI_SOLID",
"BGISEQ",
"CAPILLARY",
"COMPLETE_GENOMICS",
"DNBSEQ",
"HELICOS",
"ILLUMINA",
"ION_TORRENT",
"LS454",
"OXFORD_NANOPORE",
"PACBIO_SMRT",
]
fastq1:
type: ["string", "null"]
description: "Optional FASTQ file for read 1 of paired-end sequenced libraries."
pattern: "^[\\S]+.(fq\\.gz|fastq\\.gz)$"
fastq2:
type: ["string", "null"]
description: "Optional FASTQ file for read 2 of paired-end sequenced libraries."
pattern: "^[\\S]+.(fq\\.gz|fastq\\.gz)$"
fasta:
type: ["string", "null"]
description: "Optional FASTA file."
pattern: "^[\\S]+.(fa\\.gz|fasta\\.gz)$"
required:
- sample
- run_accession
- instrument_platform
files:
- fastq1
- fastq2
- fasta
required:
- samples

233
bin/check_samplesheet.py Executable file
View file

@ -0,0 +1,233 @@
#!/usr/bin/env python
from distutils import extension
import os
import sys
import errno
import argparse
def parse_args(args=None):
Description = "Reformat nf-core/taxprofiler samplesheet file and check its contents."
Epilog = "Example usage: python check_samplesheet.py <FILE_IN> <FILE_OUT>"
parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
parser.add_argument("FILE_IN", help="Input samplesheet file.")
parser.add_argument("FILE_OUT", help="Output file.")
return parser.parse_args(args)
def make_dir(path):
if len(path) > 0:
try:
os.makedirs(path)
except OSError as exception:
if exception.errno != errno.EEXIST:
raise exception
def print_error(error, context="Line", context_str=""):
error_str = "ERROR: Please check samplesheet -> {}".format(error)
if context != "" and context_str != "":
error_str = "ERROR: Please check samplesheet -> {}\n{}: '{}'".format(
error, context.strip(), context_str.strip()
)
print(error_str)
sys.exit(1)
def check_samplesheet(file_in, file_out):
"""
This function checks that the samplesheet follows the following structure:
sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta
2611,ERR5766174,ILLUMINA,,,ERX5474930_ERR5766174_1.fa.gz
2612,ERR5766176,ILLUMINA,ERX5474932_ERR5766176_1.fastq.gz,ERX5474932_ERR5766176_2.fastq.gz,
2612,ERR5766174,ILLUMINA,ERX5474936_ERR5766180_1.fastq.gz,,
2613,ERR5766181,ILLUMINA,ERX5474937_ERR5766181_1.fastq.gz,ERX5474937_ERR5766181_2.fastq.gz,
"""
FQ_EXTENSIONS = (".fq.gz", ".fastq.gz")
FA_EXTENSIONS = (
".fa.gz",
".fasta.gz",
".fna.gz",
".fas.gz",
)
INSTRUMENT_PLATFORMS = [
"ABI_SOLID",
"BGISEQ",
"CAPILLARY",
"COMPLETE_GENOMICS",
"DNBSEQ",
"HELICOS",
"ILLUMINA",
"ION_TORRENT",
"LS454",
"OXFORD_NANOPORE",
"PACBIO_SMRT",
]
sample_mapping_dict = {}
with open(file_in, "r") as fin:
## Check header
MIN_COLS = 4
HEADER = [
"sample",
"run_accession",
"instrument_platform",
"fastq_1",
"fastq_2",
"fasta",
]
header = [x.strip('"') for x in fin.readline().strip().split(",")]
## Check for missing mandatory columns
missing_columns = list(set(HEADER) - set(header))
if len(missing_columns) > 0:
print(
"ERROR: Missing required column header -> {}. Note some columns can otherwise be empty. See pipeline documentation (https://nf-co.re/taxprofiler/usage).".format(
",".join(missing_columns)
)
)
sys.exit(1)
## Find locations of mandatory columns
header_locs = {}
for i in HEADER:
header_locs[i] = header.index(i)
## Check sample entries
for line in fin:
## Pull out only relevant columns for downstream checking
line_parsed = [x.strip().strip('"') for x in line.strip().split(",")]
# Check valid number of columns per row
if len(line_parsed) < len(HEADER):
print_error(
"Invalid number of columns (minimum = {})!".format(len(HEADER)),
"Line",
line,
)
num_cols = len([x for x in line_parsed if x])
if num_cols < MIN_COLS:
print_error(
"Invalid number of populated columns (minimum = {})!".format(MIN_COLS),
"Line",
line,
)
lspl = [line_parsed[i] for i in header_locs.values()]
## Check sample name entries
(
sample,
run_accession,
instrument_platform,
fastq_1,
fastq_2,
fasta,
) = lspl[: len(HEADER)]
sample = sample.replace(" ", "_")
if not sample:
print_error("Sample entry has not been specified!", "Line", line)
## Check FastQ file extension
for fastq in [fastq_1, fastq_2]:
if fastq:
if fastq.find(" ") != -1:
print_error("FastQ file contains spaces!", "Line", line)
if not fastq.endswith(FQ_EXTENSIONS):
print_error(
f"FastQ file does not have extension {' or '.join(list(FQ_EXTENSIONS))} !",
"Line",
line,
)
if fasta:
if fasta.find(" ") != -1:
print_error("FastA file contains spaces!", "Line", line)
if not fasta.endswith(FA_EXTENSIONS):
print_error(
f"FastA file does not have extension {' or '.join(list(FA_EXTENSIONS))}!",
"Line",
line,
)
sample_info = []
# Check run_accession
if not run_accession:
print_error("Run accession has not been specified!", "Line", line)
else:
sample_info.append(run_accession)
# Check instrument_platform
if not instrument_platform:
print_error("Instrument platform has not been specified!", "Line", line)
else:
if instrument_platform not in INSTRUMENT_PLATFORMS:
print_error(
f"Instrument platform {instrument_platform} is not supported! "
f"List of supported platforms {', '.join(INSTRUMENT_PLATFORMS)}",
"Line",
line,
)
sample_info.append(instrument_platform)
## Auto-detect paired-end/single-end
if sample and fastq_1 and fastq_2: ## Paired-end short reads
sample_info.extend(["0", fastq_1, fastq_2, fasta])
elif sample and fastq_1 and not fastq_2: ## Single-end short/long fastq reads
sample_info.extend(["1", fastq_1, fastq_2, fasta])
elif sample and fasta and not fastq_1 and not fastq_2: ## Single-end long reads
sample_info.extend(["1", fastq_1, fastq_2, fasta])
elif fasta and (fastq_1 or fastq_2):
print_error(
"FastQ and FastA files cannot be specified together in the same library!",
"Line",
line,
)
else:
print_error("Invalid combination of columns provided!", "Line", line)
## Create sample mapping dictionary = { sample: [ run_accession, instrument_platform, single_end, fastq_1, fastq_2 , fasta ] }
if sample not in sample_mapping_dict:
sample_mapping_dict[sample] = [sample_info]
else:
if sample_info in sample_mapping_dict[sample]:
print_error("Samplesheet contains duplicate rows!", "Line", line)
else:
sample_mapping_dict[sample].append(sample_info)
## Write validated samplesheet with appropriate columns
HEADER_OUT = [
"sample",
"run_accession",
"instrument_platform",
"single_end",
"fastq_1",
"fastq_2",
"fasta",
]
if len(sample_mapping_dict) > 0:
out_dir = os.path.dirname(file_out)
make_dir(out_dir)
with open(file_out, "w") as fout:
fout.write(",".join(HEADER_OUT) + "\n")
for sample in sorted(sample_mapping_dict.keys()):
for idx, val in enumerate(sample_mapping_dict[sample]):
fout.write(f"{sample},{','.join(val)}\n")
else:
print_error("No entries to process!", "Samplesheet: {}".format(file_in))
def main(args=None):
args = parse_args(args)
check_samplesheet(args.FILE_IN, args.FILE_OUT)
if __name__ == "__main__":
sys.exit(main())

View file

@ -12,14 +12,6 @@
process {
withName: DATABASE_CHECK {
publishDir = [
path: { "${params.outdir}/pipeline_info" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: FASTQC {
ext.args = '--quiet'
ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
@ -41,7 +33,7 @@ process {
}
withName: FALCO {
ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
ext.prefix = { "${meta.id}_${meta.run_accession}_raw_falco" }
publishDir = [
path: { "${params.outdir}/falco/raw" },
mode: params.publish_dir_mode,
@ -50,7 +42,7 @@ process {
}
withName: FALCO_PROCESSED {
ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
ext.prefix = { "${meta.id}_${meta.run_accession}_processed_falco" }
publishDir = [
path: { "${params.outdir}/falco/processed" },
mode: params.publish_dir_mode,
@ -69,10 +61,17 @@ process {
].join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/fastp" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
[
path: { "${params.outdir}/fastp" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
],
[
path: { "${params.outdir}/fastp" },
mode: params.publish_dir_mode,
pattern: '*.{log,html,json}'
]
]
}
@ -90,10 +89,17 @@ process {
].join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/fastp" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
[
path: { "${params.outdir}/fastp" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
],
[
path: { "${params.outdir}/fastp" },
mode: params.publish_dir_mode,
pattern: '*.{log,html,json}'
]
]
}
@ -106,10 +112,17 @@ process {
].join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/adapterremoval" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
[
path: { "${params.outdir}/adapterremoval" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
],
[
path: { "${params.outdir}/adapterremoval" },
mode: params.publish_dir_mode,
pattern: '*.settings'
]
]
}
@ -125,20 +138,34 @@ process {
].join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/adapterremoval" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
[
path: { "${params.outdir}/adapterremoval" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
],
[
path: { "${params.outdir}/adapterremoval" },
mode: params.publish_dir_mode,
pattern: '*.settings'
]
]
}
withName: PORECHOP_PORECHOP {
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/porechop" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
[
path: { "${params.outdir}/porechop" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
],
[
path: { "${params.outdir}/porechop" },
mode: params.publish_dir_mode,
pattern: '*.log'
]
]
}
@ -151,10 +178,17 @@ process {
.join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}_filtered" }
publishDir = [
path: { "${params.outdir}/filtlong" },
mode: params.publish_dir_mode,
pattern: '*.{fastq.gz,log}',
enabled: params.save_preprocessed_reads
[
path: { "${params.outdir}/filtlong" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
],
[
path: { "${params.outdir}/filtlong" },
mode: params.publish_dir_mode,
pattern: '*.log'
]
]
}
@ -171,21 +205,21 @@ process {
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
[
path: { "${params.outdir}/bowtie2/align" },
mode: params.publish_dir_mode,
pattern: '*.log'
path: { "${params.outdir}/bowtie2/align" },
mode: params.publish_dir_mode,
pattern: '*.log'
],
[
path: { "${params.outdir}/bowtie2/align" },
mode: params.publish_dir_mode,
enabled: params.save_hostremoval_mapped,
pattern: '*.bam'
path: { "${params.outdir}/bowtie2/align" },
mode: params.publish_dir_mode,
enabled: params.save_hostremoval_mapped,
pattern: '*.bam'
],
[
path: { "${params.outdir}/bowtie2/align" },
mode: params.publish_dir_mode,
enabled: params.save_hostremoval_unmapped,
pattern: '*.fastq.gz'
path: { "${params.outdir}/bowtie2/align" },
mode: params.publish_dir_mode,
enabled: params.save_hostremoval_unmapped,
pattern: '*.fastq.gz'
]
]
}
@ -248,10 +282,17 @@ process {
].join(' ').trim()
ext.prefix = { "${meta.id}-${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/bbduk/" },
mode: params.publish_dir_mode,
pattern: '*.{fastq.gz,log}',
enabled: params.save_complexityfiltered_reads
[
path: { "${params.outdir}/bbduk/" },
mode: params.publish_dir_mode,
pattern: '*.{fastq.gz,log}',
enabled: params.save_complexityfiltered_reads
],
[
path: { "${params.outdir}/bbduk/" },
mode: params.publish_dir_mode,
pattern: '*.log'
]
]
}
@ -263,10 +304,17 @@ process {
].join(' ').trim()
ext.prefix = { "${meta.id}-${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/prinseqplusplus/" },
mode: params.publish_dir_mode,
pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz,log}',
enabled: params.save_complexityfiltered_reads
[
path: { "${params.outdir}/prinseqplusplus/" },
mode: params.publish_dir_mode,
pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz}',
enabled: params.save_complexityfiltered_reads
],
[
path: { "${params.outdir}/prinseqplusplus/" },
mode: params.publish_dir_mode,
pattern: '*.log'
]
]
}
@ -303,7 +351,7 @@ process {
withName: KRAKEN2_KRAKEN2 {
ext.args = params.kraken2_save_minimizers ? { "${meta.db_params} --report-minimizer-data" } : { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
ext.prefix = params.perform_runmerging ? { meta.tool == "bracken" ? "${meta.id}-${meta.db_name}.bracken" : "${meta.id}-${meta.db_name}" } : { meta.tool == "bracken" ? "${meta.id}-${meta.run_accession}-${meta.db_name}.bracken" : "${meta.id}-${meta.run_accession}-${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/kraken2/${meta.db_name}/" },
mode: params.publish_dir_mode,
@ -313,7 +361,7 @@ process {
withName: BRACKEN_BRACKEN {
errorStrategy = 'ignore'
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.bracken" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.bracken" }
publishDir = [
path: { "${params.outdir}/bracken/${meta.db_name}/" },
mode: params.publish_dir_mode,
@ -321,12 +369,21 @@ process {
]
}
withName: KRAKENTOOLS_COMBINEKREPORTS {
withName: BRACKEN_COMBINEBRACKENOUTPUTS {
ext.prefix = { "bracken_${meta.id}_combined_reports" }
publishDir = [
path: { "${params.outdir}/bracken/" },
mode: params.publish_dir_mode,
pattern: '*.txt'
]
}
withName: KRAKENTOOLS_COMBINEKREPORTS_KRAKEN {
ext.prefix = { "kraken2_${meta.id}_combined_reports" }
publishDir = [
path: { "${params.outdir}/kraken2/" },
mode: params.publish_dir_mode,
pattern: '*.{txt}'
pattern: '*.txt'
]
}
@ -495,12 +552,4 @@ process {
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: 'EIDO_VALIDATE' {
ext.args = '--st-index sample'
}
withName: 'EIDO_CONVERT' {
ext.args = '--st-index sample'
}
}

View file

@ -60,10 +60,4 @@ process {
withName: MEGAN_RMA2INFO_KRONA {
maxForks = 1
}
withName: 'EIDO_VALIDATE' {
ext.args = '--st-index sample'
}
withName: 'EIDO_CONVERT' {
ext.args = '--st-index sample'
}
}

View file

@ -63,10 +63,4 @@ process {
withName: MEGAN_RMA2INFO_KRONA {
maxForks = 1
}
withName: 'EIDO_VALIDATE' {
ext.args = '--st-index sample'
}
withName: 'EIDO_CONVERT' {
ext.args = '--st-index sample'
}
}

View file

@ -1,45 +0,0 @@
params {
config_profile_name = 'Test PEP profile'
config_profile_description = 'Minimal test dataset to check pipeline function with PEP file as an input.'
// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'
// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_pep_format_files/config.yaml'
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
perform_shortread_qc = true
perform_longread_qc = true
perform_shortread_complexityfilter = true
perform_shortread_hostremoval = true
perform_longread_hostremoval = true
perform_runmerging = true
hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
run_kaiju = true
run_kraken2 = true
run_bracken = true
run_malt = true
run_metaphlan3 = true
run_centrifuge = true
run_diamond = true
run_motus = false
run_krona = true
krona_taxonomy_directory = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
malt_save_reads = true
kraken2_save_reads = true
centrifuge_save_reads = true
diamond_save_reads = true
}
process {
withName: MALT_RUN {
maxForks = 1
ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
}
withName: MEGAN_RMA2INFO {
maxForks = 1
}
}

View file

@ -12,7 +12,7 @@
nf-core/taxprofiler can accept as input raw or preprocessed single- or paired-end short-read (e.g. Illumina) FASTQ files, long-read FASTQ files (e.g. Oxford Nanopore), or FASTA sequences (available for a subset of profilers).
> ⚠️ Input FASTQ files _must_ be gzipped, while FASTA files may optionally be uncompressed (although this is not recommended)
> ⚠️ Input FASTQ and FASTA files _must_ be gzipped
You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 6 columns, and a header row as shown in the examples below. Furthermother, nf-core/taxprofiler also requires a second comma-separated file of 3 columns with a header row as in the examples below.
@ -22,10 +22,6 @@ This samplesheet is then specified on the command line as follows:
--input '[path to samplesheet file]' --databases '[path to database sheet file]'
```
Note pipeline supports both CSV and PEP input sample sheets. Find out more [here](http://pep.databio.org/en/2.1.0/specification/).
When using PEP as an input, the `samplesheet.csv` must be placed in the same folder
as `config.yaml` file. A path to `samplesheet.csv` within the config must be absolute.
### Multiple runs of the same sample
The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate different runs FASTQ files of the same sample before performing profiling, when `--perform_runmerging` is supplied. Below is an example for the same sample sequenced across 3 lanes:
@ -312,9 +308,6 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
- `test`
- A profile with a complete configuration for automated testing
- Includes links to test data so needs no other parameters
- `test_pep`
- A profile with a complete configuration for running a pipeline with PEP as input
- Includes links to test data so needs no other parameters
- `docker`
- A generic configuration profile to be used with [Docker](https://docker.com/)
- `singularity`

View file

@ -81,7 +81,7 @@ class WorkflowMain {
// Check input has been provided
if (!params.input) {
log.error "Please provide an input samplesheet or PEP to the pipeline e.g. '--input samplesheet.csv'"
log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'"
System.exit(1)
}
}

View file

@ -30,6 +30,11 @@
"git_sha": "8cab56516076b23c6f8eb1ac20ba4ce9692c85e1",
"installed_by": ["modules"]
},
"bracken/combinebrackenoutputs": {
"branch": "master",
"git_sha": "9c87d5fdad182590a370ea43a4ecebd200a6f6fb",
"installed_by": ["modules"]
},
"cat/fastq": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
@ -55,20 +60,11 @@
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"installed_by": ["modules"]
},
"eido/convert": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"installed_by": ["modules"]
},
"eido/validate": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"installed_by": ["modules"]
},
"falco": {
"branch": "master",
"git_sha": "fc959214036403ad83efe7a41d43d0606c445cda",
"installed_by": ["modules"]
"installed_by": ["modules"],
"patch": "modules/nf-core/falco/falco.diff"
},
"fastp": {
"branch": "master",
@ -167,12 +163,12 @@
},
"motus/merge": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "3fce766123e71e82fb384db7d07b59180baa9ee9",
"installed_by": ["modules"]
},
"motus/profile": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "3fce766123e71e82fb384db7d07b59180baa9ee9",
"installed_by": ["modules"]
},
"multiqc": {

View file

@ -1,6 +1,5 @@
process DATABASE_CHECK {
tag "$databasesheet"
label 'process_single'
process SAMPLESHEET_CHECK {
tag "$samplesheet"
conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@ -8,18 +7,17 @@ process DATABASE_CHECK {
'quay.io/biocontainers/python:3.8.3' }"
input:
path databasesheet
path samplesheet
output:
path '*.csv' , emit: csv
path "versions.yml", emit: versions
when:
task.ext.when == null || task.ext.when
script: // This script is bundled with the pipeline, in nf-core/taxprofiler/bin/
"""
cat $databasesheet >> database_sheet.valid.csv
check_samplesheet.py \\
$samplesheet \\
samplesheet.valid.csv
cat <<-END_VERSIONS > versions.yml
"${task.process}":

View file

@ -0,0 +1,37 @@
process BRACKEN_COMBINEBRACKENOUTPUTS {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::bracken=2.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0':
'quay.io/biocontainers/bracken:2.7--py39hc16433a_0' }"
input:
tuple val(meta), path(input)
output:
tuple val(meta), path("*.txt"), emit: txt
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}"
// WARN: Version information not provided by tool on CLI.
// Please update version string below when bumping container versions.
def VERSION = '2.7'
"""
combine_bracken_outputs.py \\
$args \\
--files ${input} \\
-o ${prefix}.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
combine_bracken_output: ${VERSION}
END_VERSIONS
"""
}

View file

@ -0,0 +1,41 @@
name: "bracken_combinebrackenoutputs"
description: Combine output of metagenomic samples analyzed by bracken.
keywords:
- sort
tools:
- "bracken":
description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
homepage: https://ccb.jhu.edu/software/bracken/
documentation: https://ccb.jhu.edu/software/bracken/index.shtml?t=manual
tool_dev_url: https://github.com/jenniferlu717/Bracken
doi: "10.7717/peerj-cs.104"
licence: ["GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input:
type: file
description: List of output files from bracken
pattern: "*"
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: Combined output in table format
pattern: "*.txt"
authors:
- "@jfy133"

View file

@ -1,38 +0,0 @@
process EIDO_CONVERT {
tag "$samplesheet"
label 'process_single'
conda (params.enable_conda ? "conda-forge::eido=0.1.9" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/eido/0.1.9_cv1/eido_0.1.9_cv1.sif' :
'biocontainers/eido:0.1.9_cv1' }"
input:
path samplesheet
val format
path pep_input_base_dir
output:
path "versions.yml" , emit: versions
path "${prefix}.${format}" , emit: samplesheet_converted
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "samplesheet_converted"
"""
eido \\
convert \\
-f $format \\
$samplesheet \\
$args \\
-p samples=${prefix}.${format}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
eido: \$(echo \$(eido --version 2>&1) | sed 's/^.*eido //;s/ .*//' ))
END_VERSIONS
"""
}

View file

@ -1,39 +0,0 @@
name: "eido_convert"
description: Convert any PEP project or Nextflow samplesheet to any format
keywords:
- eido
- convert
- PEP
- format
- samplesheet
tools:
- "eido":
description: "Convert any PEP project or Nextflow samplesheet to any format"
homepage: "http://eido.databio.org/en/latest/"
documentation: "http://eido.databio.org/en/latest/"
doi: "10.1093/gigascience/giab077"
licence: "BSD-2-Clause"
input:
- samplesheet:
type: file
description: Nextflow samplesheet or PEP project
pattern: "*.{yaml,yml,csv}"
- format:
type: value
description: Extension of an output file
- pep_input_base_dir:
type: file
description: Optional path to the directory where files specified in a PEP config file are stored. Any paths specified in the config will need to be relative to this base directory.
output:
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- samplesheet_converted:
type: file
description: PEP project or samplesheet converted to csv file
authors:
- "@rafalstepien"

View file

@ -1,33 +0,0 @@
process EIDO_VALIDATE {
tag "$samplesheet"
label 'process_single'
conda (params.enable_conda ? "conda-forge::eido=0.1.9" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/eido/0.1.9_cv2/eido_0.1.9_cv2.sif' :
'biocontainers/eido:0.1.9_cv2' }"
input:
path samplesheet
path schema
path pep_input_base_dir
output:
path "versions.yml" , emit: versions
path "*.log" , emit: log
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "validation"
"""
eido validate $args $samplesheet -s $schema -e > ${prefix}.log
cat <<-END_VERSIONS > versions.yml
"${task.process}":
eido: \$(echo \$(eido --version 2>&1) | sed 's/^.*eido //;s/ .*//' ))
END_VERSIONS
"""
}

View file

@ -1,41 +0,0 @@
name: "eido_validate"
description: Validate samplesheet or PEP config against a schema
keywords:
- eido
- validate
- schema
- format
- pep
tools:
- "validate":
description: "Validate samplesheet or PEP config against a schema."
homepage: "http://eido.databio.org/en/latest/"
documentation: "http://eido.databio.org/en/latest/"
doi: "10.1093/gigascience/giab077"
licence: "BSD-2-Clause"
input:
- samplesheet:
type: file
description: Samplesheet or PEP file to be validated
pattern: "*.{yaml,yml,csv}"
- schema:
type: file
description: Schema that the samplesheet will be validated against
pattern: "*.{yaml,yml}"
- pep_input_base_dir:
type: file
description: Optional path to the directory where files specified in a PEP config file are stored. Any paths specified in the config will need to be relative to this base directory.
output:
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- log:
type: file
description: File containing validation log.
pattern: "*.log"
authors:
- "@rafalstepien"

16
modules/nf-core/falco/falco.diff generated Normal file
View file

@ -0,0 +1,16 @@
Changes in module 'nf-core/falco'
--- modules/nf-core/falco/main.nf
+++ modules/nf-core/falco/main.nf
@@ -33,7 +33,9 @@
"""
} else {
"""
- falco $args --threads $task.cpus ${reads}
+ [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
+ [ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
+ falco $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
************************************************************

View file

@ -33,7 +33,9 @@ process FALCO {
"""
} else {
"""
falco $args --threads $task.cpus ${reads}
[ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
[ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
falco $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":

View file

@ -1,13 +1,11 @@
VERSION = '3.0.1'
process MOTUS_MERGE {
tag "$meta.id"
label 'process_single'
conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
conda (params.enable_conda ? "bioconda::motus=3.0.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0':
'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/motus:3.0.3--pyhdfd78af_0':
'quay.io/biocontainers/motus:3.0.3--pyhdfd78af_0' }"
input:
tuple val(meta), path(input)

View file

@ -14,7 +14,7 @@ tools:
homepage: "https://motu-tool.org/"
documentation: "https://github.com/motu-tool/mOTUs/wiki"
tool_dev_url: "https://github.com/motu-tool/mOTUs"
doi: "10.1038/s41467-019-08844-4"
doi: "10.1186/s40168-022-01410-z"
licence: "['GPL v3']"
input:

View file

@ -2,10 +2,10 @@ process MOTUS_PROFILE {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
conda (params.enable_conda ? "bioconda::motus=3.0.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0':
'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/motus:3.0.3--pyhdfd78af_0':
'quay.io/biocontainers/motus:3.0.3--pyhdfd78af_0' }"
input:
tuple val(meta), path(reads)

View file

@ -11,7 +11,7 @@ tools:
homepage: "https://motu-tool.org/"
documentation: "https://github.com/motu-tool/mOTUs/wiki"
tool_dev_url: "https://github.com/motu-tool/mOTUs"
doi: "10.1038/s41467-019-08844-4"
doi: "10.1186/s40168-022-01410-z"
licence: "['GPL v3']"
input:

View file

@ -252,7 +252,6 @@ profiles {
test_nothing { includeConfig 'conf/test_nothing.config' }
test_motus { includeConfig 'conf/test_motus.config' }
test_krakenuniq { includeConfig 'conf/test_krakenuniq.config' }
test_pep { includeConfig 'conf/test_pep.config' }
}

View file

@ -2,7 +2,6 @@
// Check input samplesheet and get read channels
//
include { DATABASE_CHECK } from '../../modules/local/database_check'
include { UNTAR } from '../../modules/nf-core/untar/main'
workflow DB_CHECK {
@ -10,15 +9,27 @@ workflow DB_CHECK {
dbsheet // file: /path/to/dbsheet.csv
main:
ch_versions = Channel.empty()
// TODO: make database sheet check
// Checks:
// 1) no duplicates,
// 2) args do not have quotes, e.g. just `,,` and NOT `,"",`
parsed_samplesheet = DATABASE_CHECK ( dbsheet )
.csv
// special check to check _between_ rows, for which we must group rows together
// note: this will run in parallel to within-row validity, but we can assume this will run faster thus will fail first
Channel.fromPath(dbsheet)
.splitCsv ( header:true, sep:',' )
.map {[it.tool, it.db_name] }
.groupTuple()
.map {
tool, db_name ->
def unique_names = db_name.unique(false)
if ( unique_names.size() < db_name.size() ) exit 1, "[nf-core/taxprofiler] ERROR: Each database for a tool must have a unique name, duplicated detected. Tool: ${tool}, Database name: ${unique_names}"
}
// normal checks for within-row validity, so can be moved to separate functions
parsed_samplesheet = Channel.fromPath(dbsheet)
.splitCsv ( header:true, sep:',' )
.map { create_db_channels(it) }
.map {
validate_db_rows(it)
create_db_channels(it)
}
ch_dbs_for_untar = parsed_samplesheet
.branch {
@ -29,12 +40,32 @@ workflow DB_CHECK {
// TODO Filter to only run UNTAR on DBs of tools actually using?
// TODO make optional whether to save
UNTAR ( ch_dbs_for_untar.untar )
ch_versions = ch_versions.mix(UNTAR.out.versions.first())
ch_final_dbs = ch_dbs_for_untar.skip.mix( UNTAR.out.untar )
emit:
dbs = ch_final_dbs // channel: [ val(meta), [ db ] ]
versions = DATABASE_CHECK.out.versions.mix(UNTAR.out.versions.first()) // channel: [ versions.yml ]
versions = ch_versions // channel: [ versions.yml ]
}
def validate_db_rows(LinkedHashMap row){
// check minimum number of columns
if (row.size() < 4) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database input sheet - malformed row (e.g. missing column). See documentation for more information. Error in: ${row}"
// all columns there
def expected_headers = ['tool', 'db_name', 'db_params', 'db_path']
if ( !row.keySet().containsAll(expected_headers) ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database input sheet - malformed column names. Please check input TSV. Column names should be: ${expected_keys.join(", ")}"
// valid tools specified// TIFNISIH LIST
def expected_tools = [ "bracken", "centrifuge", "diamond", "kaiju", "kraken2", "krakenuniq", "malt", "metaphlan3", "motus" ]
if ( !expected_tools.contains(row.tool) ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid tool name. Please see documentation for all supported profilers. Error in: ${row}"
// detect quotes in params
if ( row.db_params.contains('"') ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database db_params entry. No quotes allowed. Error in: ${row}"
if ( row.db_params.contains("'") ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database db_params entry. No quotes allowed. Error in: ${row}"
}
def create_db_channels(LinkedHashMap row) {
@ -45,9 +76,11 @@ def create_db_channels(LinkedHashMap row) {
def array = []
if (!file(row.db_path, type: 'dir').exists()) {
exit 1, "ERROR: Please check input samplesheet -> database could not be found!\n${row.db_path}"
exit 1, "ERROR: Please check input samplesheet -> database path could not be found!\n${row.db_path}"
}
array = [ meta, file(row.db_path) ]
return array
}

View file

@ -2,62 +2,36 @@
// Check input samplesheet and get read channels
//
include { EIDO_VALIDATE } from '../../modules/nf-core/eido/validate/main'
include { EIDO_CONVERT } from '../../modules/nf-core/eido/convert/main'
include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check'
workflow INPUT_CHECK {
take:
samplesheet_or_pep_config // file: /path/to/samplesheet.csv or /path/to/pep/config.yaml
pep_input_base_dir
samplesheet // file: /path/to/samplesheet.csv
main:
ch_versions = Channel.empty()
EIDO_VALIDATE ( samplesheet_or_pep_config, file("$projectDir/assets/samplesheet_schema.yaml"), pep_input_base_dir )
ch_versions = ch_versions.mix(EIDO_VALIDATE.out.versions)
EIDO_CONVERT ( samplesheet_or_pep_config, "csv", pep_input_base_dir )
ch_versions = ch_versions.mix(EIDO_CONVERT.out.versions)
ch_parsed_samplesheet = EIDO_CONVERT.out.samplesheet_converted
parsed_samplesheet = SAMPLESHEET_CHECK ( samplesheet )
.csv
.splitCsv ( header:true, sep:',' )
.map { check_missing_and_singleend_autodetect(it) }
.branch {
fasta: it['fasta'] != ''
nanopore: it['instrument_platform'] == 'OXFORD_NANOPORE'
fastq: true
}
ch_parsed_samplesheet.fastq
fastq = parsed_samplesheet.fastq
.map { create_fastq_channel(it) }
.set { fastq }
ch_parsed_samplesheet.nanopore
nanopore = parsed_samplesheet.nanopore
.map { create_fastq_channel(it) }
.set { nanopore }
ch_parsed_samplesheet.fasta
fasta = parsed_samplesheet.fasta
.map { create_fasta_channel(it) }
.set { fasta }
emit:
fastq = fastq ?: [] // channel: [ val(meta), [ reads ] ]
nanopore = nanopore ?: [] // channel: [ val(meta), [ reads ] ]
fasta = fasta ?: [] // channel: [ val(meta), fasta ]
versions = ch_versions // channel: [ versions.yml ]
}
// Function to validate input sheet and auto-detect R1/R2
def check_missing_and_singleend_autodetect(LinkedHashMap row) {
// Checks not supported by EIDO(?)
if ( ( row['fastq_1'] != "" || row['fastq_2'] != "" ) && row['fasta'] != "" ) { exit 1, "[nf-core/taxprofiler] ERROR: FastQ and FastA files cannot be specified together in the same library. Check input samplesheet! Check sample: ${row['sample']}" }
if ( row['fastq_1'] == "" && row['fastq_2'] != "" ) { exit 1, "[nf-core/taxprofiler] ERROR: Input samplesheet has a missing fastq_1 when fastq_2 is specified. Check sample: ${row['sample']}" }
single_end = row['fastq_2'] == "" ? true : false
row['single_end'] = single_end
return row
versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ]
}
// Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
@ -87,12 +61,11 @@ def create_fastq_channel(LinkedHashMap row) {
if (!file(row.fastq_2).exists()) {
exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
}
fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
}
}
return fastq_meta
}// Function to get list of [ meta, fasta ]
def create_fasta_channel(LinkedHashMap row) {
def meta = [:]

View file

@ -41,14 +41,14 @@ workflow PROFILING {
}
.combine(databases)
.branch {
malt: it[2]['tool'] == 'malt'
kraken2: it[2]['tool'] == 'kraken2' || it[2]['tool'] == 'bracken' // to reuse the kraken module to produce the input data for bracken
metaphlan3: it[2]['tool'] == 'metaphlan3'
centrifuge: it[2]['tool'] == 'centrifuge'
kaiju: it[2]['tool'] == 'kaiju'
diamond: it[2]['tool'] == 'diamond'
motus: it[2]['tool'] == 'motus'
kaiju: it[2]['tool'] == 'kaiju'
kraken2: it[2]['tool'] == 'kraken2' || it[2]['tool'] == 'bracken' // to reuse the kraken module to produce the input data for bracken
krakenuniq: it[2]['tool'] == 'krakenuniq'
malt: it[2]['tool'] == 'malt'
metaphlan3: it[2]['tool'] == 'metaphlan3'
motus: it[2]['tool'] == 'motus'
unknown: true
}

View file

@ -2,6 +2,7 @@
// Standardise output files e.g. aggregation
//
include { BRACKEN_COMBINEBRACKENOUTPUTS } from '../../modules/nf-core/bracken/combinebrackenoutputs/main'
include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/kaiju/kaiju2table/main'
include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_KRAKEN } from '../../modules/nf-core/krakentools/combinekreports/main'
include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE } from '../../modules/nf-core/krakentools/combinekreports/main'
@ -25,10 +26,11 @@ workflow STANDARDISATION_PROFILES {
*/
ch_input_profiles = profiles
.branch {
motus: it[0]['tool'] == 'motus'
kraken2: it[0]['tool'] == 'kraken2'
bracken: it[0]['tool'] == 'bracken'
centrifuge: it[0]['tool'] == 'centrifuge'
kraken2: it[0]['tool'] == 'kraken2'
metaphlan3: it[0]['tool'] == 'metaphlan3'
motus: it[0]['tool'] == 'motus'
unknown: true
}
@ -49,7 +51,18 @@ workflow STANDARDISATION_PROFILES {
Standardise and aggregate
*/
// CENTRIFUGE
// Bracken
ch_profiles_for_bracken = ch_input_profiles.bracken
.map { [it[0]['db_name'], it[1]] }
.groupTuple()
.map {
[[id:it[0]], it[1]]
}
BRACKEN_COMBINEBRACKENOUTPUTS ( ch_profiles_for_bracken )
// CENTRIFUGE
// Collect and replace id for db_name for prefix
// Have to sort by size to ensure first file actually has hits otherwise

View file

@ -20,12 +20,11 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
// Check mandatory parameters
if ( params.input ) {
ch_input = file(params.input, checkIfExists: true)
pep_input_base_dir = file(params.input).extension.matches("yaml|yml") ? file(file(params.input).getParent(), checkIfExists: true) : []
} else {
exit 1, "Input samplesheet, or PEP config and base directory not specified"
exit 1, "Input samplesheet not specified"
}
if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
if (params.databases) { ch_databases = file(params.databases, checkIfExists: true) } else { exit 1, 'Input database sheet not specified!' }
if (params.shortread_qc_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
if (params.shortread_qc_includeunmerged && !params.shortread_qc_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging is not turned on. Please specify --shortread_qc_mergepairs"
@ -115,7 +114,7 @@ workflow TAXPROFILER {
SUBWORKFLOW: Read in samplesheet, validate and stage input files
*/
INPUT_CHECK (
ch_input, pep_input_base_dir
ch_input
)
ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)