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Fix strict syntax errors #1171

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Fix strict syntax errors #1171

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12 changes: 6 additions & 6 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -1012,7 +1012,7 @@ process {
}

withName: MALTEXTRACT {
ext.args = [
ext.args = { [
"-f ${params.metagenomics_maltextract_filter}",
"-a ${params.metagenomics_maltextract_toppercent}",
"--minPI ${params.metagenomics_maltextract_minpercentidentity}",
Expand All @@ -1022,8 +1022,8 @@ process {
params.metagenomics_maltextract_matches ? "--matches" : "",
params.metagenomics_maltextract_megansummary ? "--meganSummary" : "",
params.metagenomics_maltextract_usetopalignment ? "--useTopAlignment" : "",
{ meta.strandedness } == "single" ? '--singleStranded' : '',
].join(' ').trim()
meta.strandedness == "single" ? '--singleStranded' : '',
].join(' ').trim() }
publishDir = [
path: { "${params.outdir}/metagenomics/postprocessing/maltextract/" },
mode: params.publish_dir_mode,
Expand Down Expand Up @@ -1391,7 +1391,7 @@ process {
}

withName: MALTEXTRACT {
ext.args = [
ext.args = { [
"-f ${params.metagenomics_maltextract_filter}",
"-a ${params.metagenomics_maltextract_toppercent}",
"--minPI ${params.metagenomics_maltextract_minpercentidentity}",
Expand All @@ -1401,8 +1401,8 @@ process {
params.metagenomics_maltextract_matches ? "--matches" : "",
params.metagenomics_maltextract_megansummary ? "--meganSummary" : "",
params.metagenomics_maltextract_usetopalignment ? "--useTopAlignment" : "",
{ meta.strandedness } == "single" ? '--singleStranded' : '',
].join(' ').trim()
meta.strandedness == "single" ? '--singleStranded' : '',
].join(' ').trim() }
publishDir = [
[
path: { "${params.outdir}/metagenomics/maltextract/stats/" },
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/bwa/index/main.nf
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4 changes: 2 additions & 2 deletions modules/nf-core/samtools/mpileup/main.nf
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4 changes: 2 additions & 2 deletions modules/nf-core/samtools/view/main.nf
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6 changes: 3 additions & 3 deletions subworkflows/local/calculate_damage.nf
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Expand Up @@ -34,10 +34,10 @@ workflow CALCULATE_DAMAGE {
ch_refs
)
.multiMap{
ignore_me, meta, bam, bai, meta2, fasta, fasta_fai ->
ignore_me, meta, bam, bai, meta2, fasta_, fasta_fai_ ->
bam: [ meta, bam ]
fasta: fasta
fasta_fai: fasta_fai
fasta: fasta_
fasta_fai: fasta_fai_
}
// Calculate damage
if ( params.damagecalculation_tool == 'damageprofiler' ) {
Expand Down
2 changes: 1 addition & 1 deletion subworkflows/local/circularmapper.nf
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Expand Up @@ -41,7 +41,7 @@ workflow CIRCULARMAPPER {
.map{
// create meta consistent with rest of MAP workflow
meta, bam ->
new_meta = meta + [ reference: meta.id_index ]
def new_meta = meta + [ reference: meta.id_index ]
[ new_meta, bam ]
}
.map {
Expand Down
14 changes: 7 additions & 7 deletions subworkflows/local/deduplicate.nf
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Expand Up @@ -71,10 +71,10 @@ workflow DEDUPLICATE {
ch_refs
)
.multiMap{
ignore_me, meta, bam, bai, meta2, fasta, fasta_fai ->
ignore_me, meta, bam, bai, meta2, fasta_, fasta_fai_ ->
bam: [ meta, bam ]
fasta: [ meta2, fasta ]
fasta_fai: [ meta2, fasta_fai ]
fasta: [ meta2, fasta_ ]
fasta_fai: [ meta2, fasta_fai_ ]
}

// Dedup each bam
Expand Down Expand Up @@ -103,7 +103,7 @@ workflow DEDUPLICATE {
ch_input_for_samtools_merge = ch_dedupped_region_bam
.map {
meta, bam ->
meta2 = meta.clone().findAll{ it.key != 'genomic_region' }
def meta2 = meta.clone().findAll{ it.key != 'genomic_region' }
[ meta2, bam ]
}
.groupTuple()
Expand All @@ -117,10 +117,10 @@ workflow DEDUPLICATE {
)
.multiMap{
// bam here is a list of bams
ignore_me, meta, bam, meta2, fasta, fasta_fai ->
ignore_me, meta, bam, meta2, fasta_, fasta_fai_ ->
bam: [ meta, bam ]
fasta: [ meta2, fasta ]
fasta_fai: [ meta2, fasta_fai ]
fasta: [ meta2, fasta_ ]
fasta_fai: [ meta2, fasta_fai_ ]
}

// Merge the bams for each region into one bam
Expand Down
2 changes: 1 addition & 1 deletion subworkflows/local/genotype.nf
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Expand Up @@ -372,7 +372,7 @@ workflow GENOTYPE {
def strandedness = metas.collect { meta -> meta.strandedness }
def single_ends = metas.collect { meta -> meta.single_end }
def reference = combo_meta.reference
new_meta = [ sample_id: ids, strandedness: strandedness, single_end: single_ends, reference: reference ]
def new_meta = [ sample_id: ids, strandedness: strandedness, single_end: single_ends, reference: reference ]

[ combo_meta, new_meta, bams, bais ] // Drop bais
} // Collect all IDs into a list in meta.sample_id.
Expand Down
4 changes: 2 additions & 2 deletions subworkflows/local/manipulate_damage.nf
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Expand Up @@ -154,8 +154,8 @@ workflow MANIPULATE_DAMAGE {
ch_trimbam_input = ch_to_trim
.map {
meta, bam ->
trim_left = meta.strandedness == 'single' ? ( meta.damage_treatment == 'none' ? params.damage_manipulation_bamutils_trim_single_stranded_none_udg_left : meta.damage_treatment == 'half' ? params.damage_manipulation_bamutils_trim_single_stranded_half_udg_left : 0 ) : ( meta.damage_treatment == 'none' ? params.damage_manipulation_bamutils_trim_double_stranded_none_udg_left : meta.damage_treatment == 'half' ? params.damage_manipulation_bamutils_trim_double_stranded_half_udg_left : 0 )
trim_right = meta.strandedness == 'single' ? ( meta.damage_treatment == 'none' ? params.damage_manipulation_bamutils_trim_single_stranded_none_udg_right : meta.damage_treatment == 'half' ? params.damage_manipulation_bamutils_trim_single_stranded_half_udg_right : 0 ) : ( meta.damage_treatment == 'none' ? params.damage_manipulation_bamutils_trim_double_stranded_none_udg_right : meta.damage_treatment == 'half' ? params.damage_manipulation_bamutils_trim_double_stranded_half_udg_right : 0 )
def trim_left = meta.strandedness == 'single' ? ( meta.damage_treatment == 'none' ? params.damage_manipulation_bamutils_trim_single_stranded_none_udg_left : meta.damage_treatment == 'half' ? params.damage_manipulation_bamutils_trim_single_stranded_half_udg_left : 0 ) : ( meta.damage_treatment == 'none' ? params.damage_manipulation_bamutils_trim_double_stranded_none_udg_left : meta.damage_treatment == 'half' ? params.damage_manipulation_bamutils_trim_double_stranded_half_udg_left : 0 )
def trim_right = meta.strandedness == 'single' ? ( meta.damage_treatment == 'none' ? params.damage_manipulation_bamutils_trim_single_stranded_none_udg_right : meta.damage_treatment == 'half' ? params.damage_manipulation_bamutils_trim_single_stranded_half_udg_right : 0 ) : ( meta.damage_treatment == 'none' ? params.damage_manipulation_bamutils_trim_double_stranded_none_udg_right : meta.damage_treatment == 'half' ? params.damage_manipulation_bamutils_trim_double_stranded_half_udg_right : 0 )
[ meta, bam, trim_left, trim_right ]
}

Expand Down
42 changes: 21 additions & 21 deletions subworkflows/local/map.nf
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Expand Up @@ -38,10 +38,10 @@ workflow MAP {
sharded_reads = SEQKIT_SPLIT2.out.reads
.transpose()
.map {
meta, reads ->
new_meta = meta.clone()
new_meta.shard_number = reads.getName().replaceAll(/.*(part_\d+).(?:fastq|fq).gz/, '$1')
[ new_meta, reads ]
meta, reads_ ->
def new_meta = meta.clone()
new_meta.shard_number = reads_.getName().replaceAll(/.*(part_\d+).(?:fastq|fq).gz/, '$1')
[ new_meta, reads_ ]
}
.groupTuple()

Expand All @@ -52,7 +52,7 @@ workflow MAP {
}

if ( params.mapping_tool == 'bwaaln' ) {
ch_index_for_mapping = index.map{ meta, index, fasta -> [ meta, index ] }
ch_index_for_mapping = index.map{ meta, index_, fasta -> [ meta, index_ ] }
ch_reads_for_mapping = ch_input_for_mapping

FASTQ_ALIGN_BWAALN ( ch_reads_for_mapping, ch_index_for_mapping )
Expand All @@ -61,7 +61,7 @@ workflow MAP {
.map{
// create meta consistent with rest of workflow
meta, bam ->
new_meta = meta + [ reference: meta.id_index ]
def new_meta = meta + [ reference: meta.id_index ]
[ new_meta, bam ]
}

Expand All @@ -71,10 +71,10 @@ workflow MAP {
ch_input_for_mapping = ch_input_for_mapping
.combine( index )
.multiMap {
meta, reads, meta2, index, fasta ->
new_meta = meta + [ reference: meta2.id ]
reads: [ new_meta, reads ]
index: [ meta2, index ]
meta, reads_, meta2, index_, fasta ->
def new_meta = meta + [ reference: meta2.id ]
reads: [ new_meta, reads_ ]
index: [ meta2, index_ ]
fasta: [ meta2, fasta ]
}

Expand All @@ -88,12 +88,12 @@ workflow MAP {

} else if ( params.mapping_tool == 'bowtie2' ) {
ch_input_for_mapping = ch_input_for_mapping
.combine( index.map{ meta, index, fasta -> [ meta, index ] } )
.combine( index.map{ meta, index_, fasta -> [ meta, index_ ] } )
.multiMap {
meta, reads, meta2, index ->
new_meta = meta + [ reference: meta2.id ]
reads: [ new_meta, reads ]
index: [ meta2, index ]
meta, reads_, meta2, index_ ->
def new_meta = meta + [ reference: meta2.id ]
reads: [ new_meta, reads_ ]
index: [ meta2, index_ ]
}

BOWTIE2_ALIGN ( ch_input_for_mapping.reads, ch_input_for_mapping.index, false, true )
Expand All @@ -117,12 +117,12 @@ workflow MAP {
ch_mapped_lane_bai = CIRCULARMAPPER.out.bai // [ [ meta ], bai/csi ]
} else if ( params.mapping_tool == 'mapad' ) {
ch_input_for_mapping = ch_input_for_mapping
.combine( index.map{ meta, index, fasta -> [ meta, index ] } )
.combine( index.map{ meta, index_, fasta -> [ meta, index_ ] } )
.multiMap {
meta, reads, meta2, index ->
new_meta = meta + [ reference: meta2.id ]
reads: [ new_meta, reads ]
index: [ meta2, index ]
meta, reads_, meta2, index_ ->
def new_meta = meta + [ reference: meta2.id ]
reads: [ new_meta, reads_ ]
index: [ meta2, index_ ]
strandedness: meta.strandedness=="double"
}

Expand Down Expand Up @@ -159,7 +159,7 @@ workflow MAP {
.flatMap()
.map {
meta, bam ->
new_meta = meta.clone().findAll{ it.key !in ['lane', 'colour_chemistry', 'shard_number'] }
def new_meta = meta.clone().findAll{ it.key !in ['lane', 'colour_chemistry', 'shard_number'] }
[ new_meta, bam ]
}
.groupTuple()
Expand Down
7 changes: 4 additions & 3 deletions subworkflows/local/metagenomics_postprocessing.nf
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Expand Up @@ -6,9 +6,10 @@ include { MEGAN_RMA2INFO } from '../../modules/nf-core/megan/rma2info/main

workflow METAGENOMICS_POSTPROCESSING {

take: ch_postprocessing_input // different between each profiling --> postprocessing tool, defined in metagenomics profiling subworkflow
take: ch_tax_list
take: ch_ncbi_dir
take:
ch_postprocessing_input // different between each profiling --> postprocessing tool, defined in metagenomics profiling subworkflow
ch_tax_list
ch_ncbi_dir

main:
ch_versions = Channel.empty()
Expand Down
6 changes: 4 additions & 2 deletions subworkflows/local/metagenomics_profiling.nf
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Expand Up @@ -78,14 +78,16 @@ workflow METAGENOMICS_PROFILING {
// could be prevented by branching early and running the lower part twice for ss and ds individually
// but this is an edge-case and might never be relevant...
ch_input_for_malt = ch_reads.combine(ch_tmp_groups).map{ meta, reads, n_groups ->
[
def result = [
[
label: label,
strandedness:meta.strandedness,
id:"${meta.strandedness}stranded_${groups_counter++%n_groups}"
id:"${meta.strandedness}stranded_${groups_counter % n_groups}"
],
reads
]
groups_counter += 1
return result
}
.groupTuple(by:0)

Expand Down
8 changes: 4 additions & 4 deletions subworkflows/local/preprocessing_adapterremoval.nf
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Expand Up @@ -45,10 +45,10 @@ workflow PREPROCESSING_ADAPTERREMOVAL {
ADAPTERREMOVAL_PAIRED.out.singles_truncated,
ADAPTERREMOVAL_PAIRED.out.paired_truncated
)
.map { meta, reads ->
.map { meta, reads_ ->
def meta_new = meta.clone()
meta_new.single_end = true
[meta_new, reads]
[meta_new, reads_]
}
.groupTuple()
// Paired-end reads cause a nested tuple during grouping.
Expand All @@ -69,10 +69,10 @@ workflow PREPROCESSING_ADAPTERREMOVAL {
ADAPTERREMOVAL_PAIRED.out.collapsed,
ADAPTERREMOVAL_PAIRED.out.collapsed_truncated
)
.map { meta, reads ->
.map { meta, reads_ ->
def meta_new = meta.clone()
meta_new.single_end = true
[meta_new, reads]
[meta_new, reads_]
}
.groupTuple()
.map { meta, fastq -> [meta, fastq.flatten()] }
Expand Down
4 changes: 2 additions & 2 deletions subworkflows/local/preprocessing_fastp.nf
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Expand Up @@ -32,10 +32,10 @@ workflow PREPROCESSING_FASTP {
if ( !params.preprocessing_skippairmerging ) {
ch_fastp_reads_prepped_pe = FASTP_PAIRED.out.reads_merged
.map {
meta, reads ->
meta, reads_ ->
def meta_new = meta.clone()
meta_new['single_end'] = true
[ meta_new, [ reads ].flatten() ]
[ meta_new, [ reads_ ].flatten() ]
}

ch_fastp_reads_prepped = ch_fastp_reads_prepped_pe.mix( FASTP_SINGLE.out.reads )
Expand Down
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