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bentshermanbentsherman
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Fix strict syntax errors
1 parent 2d477bb commit 5b1c505

18 files changed

Lines changed: 78 additions & 68 deletions

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‎conf/modules.config‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1012,7 +1012,7 @@ process {
10121012
}
10131013

10141014
withName: MALTEXTRACT {
1015-
ext.args = [
1015+
ext.args = { [
10161016
"-f ${params.metagenomics_maltextract_filter}",
10171017
"-a ${params.metagenomics_maltextract_toppercent}",
10181018
"--minPI ${params.metagenomics_maltextract_minpercentidentity}",
@@ -1022,8 +1022,8 @@ process {
10221022
params.metagenomics_maltextract_matches ? "--matches" : "",
10231023
params.metagenomics_maltextract_megansummary ? "--meganSummary" : "",
10241024
params.metagenomics_maltextract_usetopalignment ? "--useTopAlignment" : "",
1025-
{ meta.strandedness } == "single" ? '--singleStranded' : '',
1026-
].join(' ').trim()
1025+
meta.strandedness == "single" ? '--singleStranded' : '',
1026+
].join(' ').trim() }
10271027
publishDir = [
10281028
path: { "${params.outdir}/metagenomics/postprocessing/maltextract/" },
10291029
mode: params.publish_dir_mode,
@@ -1391,7 +1391,7 @@ process {
13911391
}
13921392

13931393
withName: MALTEXTRACT {
1394-
ext.args = [
1394+
ext.args = { [
13951395
"-f ${params.metagenomics_maltextract_filter}",
13961396
"-a ${params.metagenomics_maltextract_toppercent}",
13971397
"--minPI ${params.metagenomics_maltextract_minpercentidentity}",
@@ -1401,8 +1401,8 @@ process {
14011401
params.metagenomics_maltextract_matches ? "--matches" : "",
14021402
params.metagenomics_maltextract_megansummary ? "--meganSummary" : "",
14031403
params.metagenomics_maltextract_usetopalignment ? "--useTopAlignment" : "",
1404-
{ meta.strandedness } == "single" ? '--singleStranded' : '',
1405-
].join(' ').trim()
1404+
meta.strandedness == "single" ? '--singleStranded' : '',
1405+
].join(' ').trim() }
14061406
publishDir = [
14071407
[
14081408
path: { "${params.outdir}/metagenomics/maltextract/stats/" },

‎modules/nf-core/bwa/index/main.nf‎

Lines changed: 1 addition & 1 deletion
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‎modules/nf-core/samtools/mpileup/main.nf‎

Lines changed: 2 additions & 2 deletions
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‎modules/nf-core/samtools/view/main.nf‎

Lines changed: 2 additions & 2 deletions
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‎subworkflows/local/calculate_damage.nf‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -34,10 +34,10 @@ workflow CALCULATE_DAMAGE {
3434
ch_refs
3535
)
3636
.multiMap{
37-
ignore_me, meta, bam, bai, meta2, fasta, fasta_fai ->
37+
ignore_me, meta, bam, bai, meta2, fasta_, fasta_fai_ ->
3838
bam: [ meta, bam ]
39-
fasta: fasta
40-
fasta_fai: fasta_fai
39+
fasta: fasta_
40+
fasta_fai: fasta_fai_
4141
}
4242
// Calculate damage
4343
if ( params.damagecalculation_tool == 'damageprofiler' ) {

‎subworkflows/local/circularmapper.nf‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -41,7 +41,7 @@ workflow CIRCULARMAPPER {
4141
.map{
4242
// create meta consistent with rest of MAP workflow
4343
meta, bam ->
44-
new_meta = meta + [ reference: meta.id_index ]
44+
def new_meta = meta + [ reference: meta.id_index ]
4545
[ new_meta, bam ]
4646
}
4747
.map {

‎subworkflows/local/deduplicate.nf‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -71,10 +71,10 @@ workflow DEDUPLICATE {
7171
ch_refs
7272
)
7373
.multiMap{
74-
ignore_me, meta, bam, bai, meta2, fasta, fasta_fai ->
74+
ignore_me, meta, bam, bai, meta2, fasta_, fasta_fai_ ->
7575
bam: [ meta, bam ]
76-
fasta: [ meta2, fasta ]
77-
fasta_fai: [ meta2, fasta_fai ]
76+
fasta: [ meta2, fasta_ ]
77+
fasta_fai: [ meta2, fasta_fai_ ]
7878
}
7979

8080
// Dedup each bam
@@ -103,7 +103,7 @@ workflow DEDUPLICATE {
103103
ch_input_for_samtools_merge = ch_dedupped_region_bam
104104
.map {
105105
meta, bam ->
106-
meta2 = meta.clone().findAll{ it.key != 'genomic_region' }
106+
def meta2 = meta.clone().findAll{ it.key != 'genomic_region' }
107107
[ meta2, bam ]
108108
}
109109
.groupTuple()
@@ -117,10 +117,10 @@ workflow DEDUPLICATE {
117117
)
118118
.multiMap{
119119
// bam here is a list of bams
120-
ignore_me, meta, bam, meta2, fasta, fasta_fai ->
120+
ignore_me, meta, bam, meta2, fasta_, fasta_fai_ ->
121121
bam: [ meta, bam ]
122-
fasta: [ meta2, fasta ]
123-
fasta_fai: [ meta2, fasta_fai ]
122+
fasta: [ meta2, fasta_ ]
123+
fasta_fai: [ meta2, fasta_fai_ ]
124124
}
125125

126126
// Merge the bams for each region into one bam

‎subworkflows/local/genotype.nf‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -372,7 +372,7 @@ workflow GENOTYPE {
372372
def strandedness = metas.collect { meta -> meta.strandedness }
373373
def single_ends = metas.collect { meta -> meta.single_end }
374374
def reference = combo_meta.reference
375-
new_meta = [ sample_id: ids, strandedness: strandedness, single_end: single_ends, reference: reference ]
375+
def new_meta = [ sample_id: ids, strandedness: strandedness, single_end: single_ends, reference: reference ]
376376

377377
[ combo_meta, new_meta, bams, bais ] // Drop bais
378378
} // Collect all IDs into a list in meta.sample_id.

‎subworkflows/local/manipulate_damage.nf‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -154,8 +154,8 @@ workflow MANIPULATE_DAMAGE {
154154
ch_trimbam_input = ch_to_trim
155155
.map {
156156
meta, bam ->
157-
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 )
158-
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 )
157+
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 )
158+
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 )
159159
[ meta, bam, trim_left, trim_right ]
160160
}
161161

‎subworkflows/local/map.nf‎

Lines changed: 21 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -38,10 +38,10 @@ workflow MAP {
3838
sharded_reads = SEQKIT_SPLIT2.out.reads
3939
.transpose()
4040
.map {
41-
meta, reads ->
42-
new_meta = meta.clone()
43-
new_meta.shard_number = reads.getName().replaceAll(/.*(part_\d+).(?:fastq|fq).gz/, '$1')
44-
[ new_meta, reads ]
41+
meta, reads_ ->
42+
def new_meta = meta.clone()
43+
new_meta.shard_number = reads_.getName().replaceAll(/.*(part_\d+).(?:fastq|fq).gz/, '$1')
44+
[ new_meta, reads_ ]
4545
}
4646
.groupTuple()
4747

@@ -52,7 +52,7 @@ workflow MAP {
5252
}
5353

5454
if ( params.mapping_tool == 'bwaaln' ) {
55-
ch_index_for_mapping = index.map{ meta, index, fasta -> [ meta, index ] }
55+
ch_index_for_mapping = index.map{ meta, index_, fasta -> [ meta, index_ ] }
5656
ch_reads_for_mapping = ch_input_for_mapping
5757

5858
FASTQ_ALIGN_BWAALN ( ch_reads_for_mapping, ch_index_for_mapping )
@@ -61,7 +61,7 @@ workflow MAP {
6161
.map{
6262
// create meta consistent with rest of workflow
6363
meta, bam ->
64-
new_meta = meta + [ reference: meta.id_index ]
64+
def new_meta = meta + [ reference: meta.id_index ]
6565
[ new_meta, bam ]
6666
}
6767

@@ -71,10 +71,10 @@ workflow MAP {
7171
ch_input_for_mapping = ch_input_for_mapping
7272
.combine( index )
7373
.multiMap {
74-
meta, reads, meta2, index, fasta ->
75-
new_meta = meta + [ reference: meta2.id ]
76-
reads: [ new_meta, reads ]
77-
index: [ meta2, index ]
74+
meta, reads_, meta2, index_, fasta ->
75+
def new_meta = meta + [ reference: meta2.id ]
76+
reads: [ new_meta, reads_ ]
77+
index: [ meta2, index_ ]
7878
fasta: [ meta2, fasta ]
7979
}
8080

@@ -88,12 +88,12 @@ workflow MAP {
8888

8989
} else if ( params.mapping_tool == 'bowtie2' ) {
9090
ch_input_for_mapping = ch_input_for_mapping
91-
.combine( index.map{ meta, index, fasta -> [ meta, index ] } )
91+
.combine( index.map{ meta, index_, fasta -> [ meta, index_ ] } )
9292
.multiMap {
93-
meta, reads, meta2, index ->
94-
new_meta = meta + [ reference: meta2.id ]
95-
reads: [ new_meta, reads ]
96-
index: [ meta2, index ]
93+
meta, reads_, meta2, index_ ->
94+
def new_meta = meta + [ reference: meta2.id ]
95+
reads: [ new_meta, reads_ ]
96+
index: [ meta2, index_ ]
9797
}
9898

9999
BOWTIE2_ALIGN ( ch_input_for_mapping.reads, ch_input_for_mapping.index, false, true )
@@ -117,12 +117,12 @@ workflow MAP {
117117
ch_mapped_lane_bai = CIRCULARMAPPER.out.bai // [ [ meta ], bai/csi ]
118118
} else if ( params.mapping_tool == 'mapad' ) {
119119
ch_input_for_mapping = ch_input_for_mapping
120-
.combine( index.map{ meta, index, fasta -> [ meta, index ] } )
120+
.combine( index.map{ meta, index_, fasta -> [ meta, index_ ] } )
121121
.multiMap {
122-
meta, reads, meta2, index ->
123-
new_meta = meta + [ reference: meta2.id ]
124-
reads: [ new_meta, reads ]
125-
index: [ meta2, index ]
122+
meta, reads_, meta2, index_ ->
123+
def new_meta = meta + [ reference: meta2.id ]
124+
reads: [ new_meta, reads_ ]
125+
index: [ meta2, index_ ]
126126
strandedness: meta.strandedness=="double"
127127
}
128128

@@ -159,7 +159,7 @@ workflow MAP {
159159
.flatMap()
160160
.map {
161161
meta, bam ->
162-
new_meta = meta.clone().findAll{ it.key !in ['lane', 'colour_chemistry', 'shard_number'] }
162+
def new_meta = meta.clone().findAll{ it.key !in ['lane', 'colour_chemistry', 'shard_number'] }
163163
[ new_meta, bam ]
164164
}
165165
.groupTuple()

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