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Merged
merged 4 commits into from
Nov 5, 2024
Merged

Expect input of prefixes to KrakenUniq #6912

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da8fa10
refactor!: expect input of prefixes
Midnighter Oct 30, 2024
e02d2c6
fix: always use list of files
Midnighter Nov 4, 2024
2b2ce42
refactor: change separator from space to tab
Midnighter Nov 5, 2024
6ef7b39
docs: add descriptive comments to commands
Midnighter Nov 5, 2024
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117 changes: 61 additions & 56 deletions modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,8 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
'biocontainers/krakenuniq:1.0.4--pl5321h6dccd9a_2' }"

input:
tuple val(meta), path(sequences)
// We stage sequencing files in a sub-directory so we don't accidentally gzip them later.
tuple val(meta), path(sequences, name: 'sequences/*'), val(prefixes)
val sequence_type
path db
val ram_chunk_size
Expand All @@ -28,6 +29,7 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {

script:
assert sequence_type in ['fasta', 'fastq']
sequences = sequences instanceof List ? sequences : [sequences]

def args = task.ext.args ?: ''
def args2 = task.ext.args ?: ''
Expand All @@ -38,25 +40,29 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
unclassified_option = save_output_reads ? "--unclassified-out \"${unclassified}\"" : ''
def output_option = save_output ? '--output "\${PREFIX}.krakenuniq.classified.txt"' : ''
def report = report_file ? '--report-file "\${PREFIX}.krakenuniq.report.txt"' : ''
compress_reads_command = save_output_reads ? "find . -name '*.${sequence_type}' -print0 | xargs -0 -t -P ${task.cpus} -I % gzip --no-name %" : ''
compress_reads_command = save_output_reads ? "find . -maxdepth 0 -name '*.${sequence_type}' -print0 | xargs -0 -t -P ${task.cpus} -I % gzip --no-name %" : ''
def command_inputs_file = '.inputs.txt'

if (meta.single_end) {
assert sequences.size() == prefixes.size()
command_inputs = [sequences, prefixes].transpose().collect { seq, prefix -> "${seq}\t${prefix}" }

"""
# Store the batch of samples for later command input.
cat <<-END_INPUTS > ${command_inputs_file}
${command_inputs.join('\n ')}
END_INPUTS

# Preload the KrakenUniq database into memory.
krakenuniq \\
$args \\
--db $db \\
--preload \\
--preload-size $ram_chunk_size \\
--threads $task.cpus

strip_suffix() {
local result=\$1
# Strip any file extensions.
echo "\${result%%.*}"
}

printf "%s\\n" ${sequences} | while read FASTQ; do \\
PREFIX="\$(strip_suffix "\${FASTQ}")"

# Run the KrakenUniq classification on each sample in the batch.
while IFS='\t' read -r SEQ PREFIX; do
krakenuniq \\
--db $db \\
--threads $task.cpus \\
Expand All @@ -65,8 +71,8 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
$unclassified_option \\
$classified_option \\
$args2 \\
"\${FASTQ}"
done
"\${SEQ}"
done < ${command_inputs_file}

$compress_reads_command

Expand All @@ -76,26 +82,25 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
END_VERSIONS
"""
} else {
assert sequences.size() / 2 == prefixes.size()
command_inputs = [sequences.collate(2), prefixes].transpose().collect { pair, prefix -> "${pair[0]}\t${pair[1]}\t${prefix}" }

"""
# Store the batch of samples for later command input.
cat <<-END_INPUTS > ${command_inputs_file}
${command_inputs.join('\n ')}
END_INPUTS

# Preload the KrakenUniq database into memory.
krakenuniq \\
$args \\
--db $db \\
--preload \\
--preload-size $ram_chunk_size \\
--threads $task.cpus

strip_suffix() {
local result
read result
# Strip any trailing dot or underscore.
result="\${result%_}"
echo "\${result%.}"
}

printf "%s %s\\n" ${sequences} | while read FASTQ; do \\
read -r -a FASTQ <<< "\${FASTQ}"
PREFIX="\$(printf "%s\\n" "\${FASTQ[@]}" | sed -e 'N;s/^\\(.*\\).*\\n\\1.*\$/\\1\\n\\1/;D' | strip_suffix)"

# Run the KrakenUniq classification on each sample in the batch.
while IFS='\t' read -r FIRST_SEQ SECOND_SEQ PREFIX; do
krakenuniq \\
--db $db \\
--threads $task.cpus \\
Expand All @@ -105,8 +110,8 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
$classified_option \\
--paired \\
$args2 \\
"\${FASTQ[@]}"
done
"\${FIRST_SEQ}" "\${SECOND_SEQ}"
done < ${command_inputs_file}

$compress_reads_command

Expand All @@ -119,6 +124,7 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {

stub:
assert sequence_type in ['fasta', 'fastq']
sequences = sequences instanceof List ? sequences : [sequences]

def args = task.ext.args ?: ''
def args2 = task.ext.args ?: ''
Expand All @@ -130,21 +136,26 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
def output_option = save_output ? '--output "\${PREFIX}.krakenuniq.classified.txt"' : ''
def report = report_file ? '--report-file "\${PREFIX}.krakenuniq.report.txt"' : ''
compress_reads_command = save_output_reads ? "find . -name '*.${sequence_type}' -print0 | xargs -0 -t -P ${task.cpus} -I % gzip --no-name %" : ''
def command_inputs_file = '.inputs.txt'

if (meta.single_end) {
assert sequences.size() == prefixes.size()
command_inputs = [sequences, prefixes].transpose().collect { seq, prefix -> "${seq}\t${prefix}" }

"""
# Store the batch of samples for later command input.
cat <<-END_INPUTS > ${command_inputs_file}
${command_inputs.join('\n ')}
END_INPUTS

# Preload the KrakenUniq database into memory.
echo krakenuniq \\
$args \\
--db $db \\
--preload \\
--preload-size $ram_chunk_size \\
--threads $task.cpus

strip_suffix() {
local result=\$1
# Strip any file extensions.
echo "\${result%%.*}"
}

create_file() {
echo '<3 nf-core' > "\$1"
}
Expand All @@ -153,11 +164,8 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
echo '<3 nf-core' | gzip -n > "\$1"
}

printf "%s\\n" ${sequences} | while read FASTQ; do \\
echo "\${FASTQ}"
PREFIX="\$(strip_suffix "\${FASTQ}")"
echo "\${PREFIX}"

# Run the KrakenUniq classification on each sample in the batch.
while IFS='\t' read -r SEQ PREFIX; do
echo krakenuniq \\
--db $db \\
--threads $task.cpus \\
Expand All @@ -166,13 +174,13 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
$unclassified_option \\
$classified_option \\
$args2 \\
"\${FASTQ}"
"\${SEQ}"

create_file "\${PREFIX}.krakenuniq.classified.txt"
create_file "\${PREFIX}.krakenuniq.report.txt"
create_gzip_file "\${PREFIX}.classified.${sequence_type}.gz"
create_gzip_file "\${PREFIX}.unclassified.${sequence_type}.gz"
done
done < ${command_inputs_file}

echo "$compress_reads_command"

Expand All @@ -182,22 +190,23 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
END_VERSIONS
"""
} else {
assert sequences.size() / 2 == prefixes.size()
command_inputs = [sequences.collate(2), prefixes].transpose().collect { pair, prefix -> "${pair[0]}\t${pair[1]}\t${prefix}" }

"""
# Store the batch of samples for later command input.
cat <<-END_INPUTS > ${command_inputs_file}
${command_inputs.join('\n ')}
END_INPUTS

# Preload the KrakenUniq database into memory.
echo krakenuniq \\
$args \\
--db $db \\
--preload \\
--preload-size $ram_chunk_size \\
--threads $task.cpus

strip_suffix() {
local result
read result
# Strip any trailing dot or underscore.
result="\${result%_}"
echo "\${result%.}"
}

create_file() {
echo '<3 nf-core' > "\$1"
}
Expand All @@ -206,12 +215,8 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
echo '<3 nf-core' | gzip -n > "\$1"
}

printf "%s %s\\n" ${sequences} | while read FASTQ; do \\
read -r -a FASTQ <<< "\${FASTQ}"
echo "\${FASTQ[@]}"
PREFIX="\$(printf "%s\\n" "\${FASTQ[@]}" | sed -e 'N;s/^\\(.*\\).*\\n\\1.*\$/\\1\\n\\1/;D' | strip_suffix)"
echo "\${PREFIX}"

# Run the KrakenUniq classification on each sample in the batch.
while IFS='\t' read -r FIRST_SEQ SECOND_SEQ PREFIX; do
echo krakenuniq \\
--db $db \\
--threads $task.cpus \\
Expand All @@ -221,13 +226,13 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
$classified_option \\
--paired \\
$args2 \\
"\${FASTQ[@]}"
"\${FIRST_SEQ}" "\${SECOND_SEQ}"

create_file "\${PREFIX}.krakenuniq.classified.txt"
create_file "\${PREFIX}.krakenuniq.report.txt"
create_gzip_file "\${PREFIX}.merged.classified.${sequence_type}.gz"
create_gzip_file "\${PREFIX}.merged.unclassified.${sequence_type}.gz"
done
done < ${command_inputs_file}

echo "$compress_reads_command"

Expand Down
5 changes: 5 additions & 0 deletions modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,11 @@ input:
type: file
description: List of input files containing sequences. All of them must be either
in FASTA or FASTQ format.
- prefixes:
type: string
description: >
List of sample identifiers or filename prefixes. Must correspond in order and
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Maybe give a suggestio how to fix the order (maybe with .sort? Although I can imagine in some very rare cases someone might be weird and not name things such as pairs properly)

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I think that in the normal case, prefixes will be constructed from samples as they come out of a channel and thus they will be in the same order. I do not want to suggest something here that potentially makes the use more complicated than necessary and potentially leads to user errors.

I am in favor of creating a batching function and having that properly tested, but I don't know where we would provide that from?

length to the 'sequences', or to the number of sequencing pairs.
- - sequence_type:
type: string
description: Format of all given sequencing files as literal string, either
Expand Down
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