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Revert PEP validation back to python samplesheet check

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This commit is contained in:
James Fellows Yates 2022-12-12 08:49:13 +01:00
parent 13c4f44ca6
commit 4b68e95770
18 changed files with 275 additions and 328 deletions
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2
README.md
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).

55
assets/samplesheet_schema.yaml
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@ -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

236
bin/check_samplesheet.py Executable file
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@ -0,0 +1,236 @@
#!/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",
".fa.gz",
".fasta",
".fasta.gz",
".fna",
".fna.gz",
".fas",
".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(",")]
lspl = [line_parsed[i] for i in header_locs.values()]
# Check valid number of columns per row
if len(lspl) < len(HEADER):
print_error(
"Invalid number of columns (minimum = {})!".format(len(HEADER)),
"Line",
line,
)
num_cols = len([x for x in lspl if x])
if num_cols < MIN_COLS:
print_error(
"Invalid number of populated columns (minimum = {})!".format(MIN_COLS),
"Line",
line,
)
## 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())

8
conf/modules.config
View file

@ -495,12 +495,4 @@ 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'
}
}

6
conf/test.config
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'
}
}

6
conf/test_krakenuniq.config
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'
}
}

45
conf/test_pep.config
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@ -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
}
}

7
docs/usage.md
View file

@ -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`

2
lib/WorkflowMain.groovy
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)
}
}

10
modules.json
View file

@ -55,16 +55,6 @@
"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",

27
modules/local/samplesheet_check.nf Normal file
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@ -0,0 +1,27 @@
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 ?
'https://depot.galaxyproject.org/singularity/python:3.8.3' :
'quay.io/biocontainers/python:3.8.3' }"
input:
path samplesheet
output:
path '*.csv' , emit: csv
path "versions.yml", emit: versions
script: // This script is bundled with the pipeline, in nf-core/taxprofiler/bin/
"""
check_samplesheet.py \\
$samplesheet \\
samplesheet.valid.csv
cat <<-END_VERSIONS > versions.yml
"${task.process}":
python: \$(python --version | sed 's/Python //g')
END_VERSIONS
"""
}

38
modules/nf-core/eido/convert/main.nf generated
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
"""
}

39
modules/nf-core/eido/convert/meta.yml generated
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"

33
modules/nf-core/eido/validate/main.nf generated
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
"""
}

41
modules/nf-core/eido/validate/meta.yml generated
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"

1
nextflow.config
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' }
}

42
subworkflows/local/input_check.nf
View file

@ -2,41 +2,31 @@
// 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
parsed_samplesheet.fastq
.map { create_fastq_channel(it) }
.set { fastq }
ch_parsed_samplesheet.nanopore
parsed_samplesheet.nanopore
.map { create_fastq_channel(it) }
.set { nanopore }
ch_parsed_samplesheet.fasta
parsed_samplesheet.fasta
.map { create_fasta_channel(it) }
.set { fasta }
@ -44,20 +34,7 @@ workflow INPUT_CHECK {
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: ${row['sample']}" }
single_end = row['fastq_2'] == "" ? true : false
row['single_end'] = single_end
return row
versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ]
}
// Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
@ -87,12 +64,11 @@ def create_fastq_channel(LinkedHashMap row) {
if (!file(row.fastq_2).exists()) {
exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${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 = [:]

5
workflows/taxprofiler.nf
View file

@ -20,9 +20,8 @@ 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!' }
@ -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)