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maxulyssemaxulysse
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cannot exclude with glob patterns
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+34
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+34
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‎conf/modules.config‎

Lines changed: 34 additions & 46 deletions
Original file line numberDiff line numberDiff line change
@@ -41,8 +41,7 @@ process {
4141
publishDir = [
4242
path: { "${params.outdir}/genome" },
4343
mode: params.publish_dir_mode,
44-
pattern: "{!versions.yml}",
45-
saveAs: { params.save_reference ? it : null }
44+
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
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]
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}
4847

@@ -54,8 +53,7 @@ process {
5453
publishDir = [
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path: { "${params.outdir}/genome/index" },
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mode: params.publish_dir_mode,
57-
pattern: "{!versions.yml}",
58-
saveAs: { params.save_reference ? it : null }
56+
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
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]
6058
}
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@@ -64,17 +62,15 @@ process {
6462
publishDir = [
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path: { "${params.outdir}/genome" },
6664
mode: params.publish_dir_mode,
67-
pattern: "{!versions.yml}",
68-
saveAs: { params.save_reference ? it : null }
65+
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
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]
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}
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7269
withName: 'HISAT2_EXTRACTSPLICESITES' {
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publishDir = [
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path: { "${params.outdir}/genome/index" },
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mode: params.publish_dir_mode,
76-
pattern: "{!versions.yml}",
77-
saveAs: { params.save_reference ? it : null }
73+
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
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]
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}
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@@ -83,8 +79,7 @@ process {
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publishDir = [
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path: { "${params.outdir}/genome/index" },
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mode: params.publish_dir_mode,
86-
pattern: "{!versions.yml}",
87-
saveAs: { params.save_reference ? it : null }
82+
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
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]
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}
9085

@@ -93,53 +88,47 @@ process {
9388
publishDir = [
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path: { "${params.outdir}/genome/index" },
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mode: params.publish_dir_mode,
96-
pattern: "{!versions.yml}",
97-
saveAs: { params.save_reference ? it : null }
91+
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
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]
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}
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10195
withName: 'GTF2BED' {
10296
publishDir = [
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path: { "${params.outdir}/genome" },
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mode: params.publish_dir_mode,
105-
pattern: "{!versions.yml}",
106-
saveAs: { params.save_reference ? it : null }
99+
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
107100
]
108101
}
109102

110103
withName: 'CAT_ADDITIONAL_FASTA|PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' {
111104
publishDir = [
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path: { "${params.outdir}/genome" },
113106
mode: params.publish_dir_mode,
114-
pattern: "{!versions.yml}",
115-
saveAs: { params.save_reference ? it : null }
107+
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
116108
]
117109
}
118110

119111
withName: 'GTF_GENE_FILTER' {
120112
publishDir = [
121113
path: { "${params.outdir}/genome" },
122114
mode: params.publish_dir_mode,
123-
pattern: "{!versions.yml}",
124-
saveAs: { params.save_reference ? it : null }
115+
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
125116
]
126117
}
127118

128119
withName: 'CUSTOM_GETCHROMSIZES' {
129120
publishDir = [
130121
path: { "${params.outdir}/genome" },
131122
mode: params.publish_dir_mode,
132-
pattern: "{!versions.yml}",
133-
saveAs: { params.save_reference ? it : null }
123+
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
134124
]
135125
}
136126

137127
withName: 'CAT_FASTQ' {
138128
publishDir = [
139129
path: { "${params.outdir}/fastq" },
140130
mode: params.publish_dir_mode,
141-
pattern: "{!versions.yml}",
142-
saveAs: { params.save_merged_fastq ? it : null }
131+
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_merged_fastq ? filename : null }
143132
]
144133
}
145134
}
@@ -151,8 +140,7 @@ if (!params.skip_bbsplit && params.bbsplit_fasta_list) {
151140
publishDir = [
152141
path: { "${params.outdir}/genome/index" },
153142
mode: params.publish_dir_mode,
154-
pattern: "{!versions.yml}",
155-
saveAs: { params.save_reference ? it : null }
143+
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
156144
]
157145
}
158146
}
@@ -203,7 +191,7 @@ if (!(params.skip_fastqc || params.skip_qc)) {
203191
publishDir = [
204192
path: { "${params.outdir}/${params.trimmer}/fastqc" },
205193
mode: params.publish_dir_mode,
206-
pattern: "{!versions.yml}"
194+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
207195
]
208196
}
209197
}
@@ -488,7 +476,7 @@ if (!params.skip_alignment) {
488476
publishDir = [
489477
path: { "${params.outdir}/${params.aligner}/bigwig" },
490478
mode: params.publish_dir_mode,
491-
pattern: "{!versions.yml}"
479+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
492480
]
493481
}
494482

@@ -504,7 +492,7 @@ if (!params.skip_alignment) {
504492
publishDir = [
505493
path: { "${params.outdir}/${params.aligner}/bigwig" },
506494
mode: params.publish_dir_mode,
507-
pattern: "{!versions.yml}"
495+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
508496
]
509497
}
510498
}
@@ -520,7 +508,7 @@ if (!params.skip_alignment) {
520508
publishDir = [
521509
path: { "${params.outdir}/${params.aligner}/stringtie" },
522510
mode: params.publish_dir_mode,
523-
pattern: "{!versions.yml}"
511+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
524512
]
525513
}
526514
}
@@ -574,31 +562,31 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
574562
publishDir = [
575563
path: { "${params.outdir}/${params.aligner}" },
576564
mode: params.publish_dir_mode,
577-
pattern: "{!versions.yml,!*_meta_info.json}"
565+
saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('_meta_info.json') ? null : filename }
578566
]
579567
}
580568

581569
withName: '.*:QUANTIFY_STAR_SALMON:SALMON_TX2GENE' {
582570
publishDir = [
583571
path: { "${params.outdir}/${params.aligner}" },
584572
mode: params.publish_dir_mode,
585-
pattern: "{!versions.yml}"
573+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
586574
]
587575
}
588576

589577
withName: '.*:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT' {
590578
publishDir = [
591579
path: { "${params.outdir}/${params.aligner}" },
592580
mode: params.publish_dir_mode,
593-
pattern: "{!versions.yml}"
581+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
594582
]
595583
}
596584

597585
withName: '.*:QUANTIFY_STAR_SALMON:SALMON_SE_.*' {
598586
publishDir = [
599587
path: { "${params.outdir}/${params.aligner}" },
600588
mode: params.publish_dir_mode,
601-
pattern: "{!versions.yml}"
589+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
602590
]
603591
}
604592
}
@@ -763,7 +751,7 @@ if (!params.skip_alignment && params.aligner == 'star_rsem') {
763751
publishDir = [
764752
path: { "${params.outdir}/${params.aligner}" },
765753
mode: params.publish_dir_mode,
766-
pattern: "{!versions.yml}"
754+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
767755
]
768756
}
769757
}
@@ -851,7 +839,7 @@ if (!params.skip_alignment && !params.skip_qc) {
851839
publishDir = [
852840
path: { "${params.outdir}/${params.aligner}/qualimap" },
853841
mode: params.publish_dir_mode,
854-
pattern: "{!versions.yml}"
842+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
855843
]
856844
}
857845
}
@@ -902,15 +890,15 @@ if (!params.skip_alignment && !params.skip_qc) {
902890
publishDir = [
903891
path: { "${params.outdir}/${params.aligner}/featurecounts" },
904892
mode: params.publish_dir_mode,
905-
pattern: "{!versions.yml}"
893+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
906894
]
907895
}
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909897
withName: 'MULTIQC_CUSTOM_BIOTYPE' {
910898
publishDir = [
911899
path: { "${params.outdir}/${params.aligner}/featurecounts" },
912900
mode: params.publish_dir_mode,
913-
pattern: "{!versions.yml}"
901+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
914902
]
915903
}
916904
}
@@ -922,7 +910,7 @@ if (!params.skip_alignment && !params.skip_qc) {
922910
publishDir = [
923911
path: { "${params.outdir}/${params.aligner}/rseqc/bam_stat" },
924912
mode: params.publish_dir_mode,
925-
pattern: "{!versions.yml}"
913+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
926914
]
927915
}
928916
}
@@ -934,7 +922,7 @@ if (!params.skip_alignment && !params.skip_qc) {
934922
publishDir = [
935923
path: { "${params.outdir}/${params.aligner}/rseqc/infer_experiment" },
936924
mode: params.publish_dir_mode,
937-
pattern: "{!versions.yml}"
925+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
938926
]
939927
}
940928
}
@@ -1023,7 +1011,7 @@ if (!params.skip_alignment && !params.skip_qc) {
10231011
publishDir = [
10241012
path: { "${params.outdir}/${params.aligner}/rseqc/read_distribution" },
10251013
mode: params.publish_dir_mode,
1026-
pattern: "{!versions.yml}"
1014+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
10271015
]
10281016
}
10291017
}
@@ -1037,7 +1025,7 @@ if (!params.skip_alignment && !params.skip_qc) {
10371025
path: { "${params.outdir}/${params.aligner}/rseqc/inner_distance/txt" },
10381026
mode: params.publish_dir_mode,
10391027
pattern: '*.txt',
1040-
pattern: "{!versions.yml}"
1028+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
10411029
],
10421030
[
10431031
path: { "${params.outdir}/${params.aligner}/rseqc/inner_distance/pdf" },
@@ -1060,7 +1048,7 @@ if (!params.skip_alignment && !params.skip_qc) {
10601048
publishDir = [
10611049
path: { "${params.outdir}/${params.aligner}/rseqc/tin" },
10621050
mode: params.publish_dir_mode,
1063-
pattern: "{!versions.yml}"
1051+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
10641052
]
10651053
}
10661054
}
@@ -1077,7 +1065,7 @@ if (!params.skip_multiqc) {
10771065
params.skip_alignment? '' : "/${params.aligner}"
10781066
].join('') },
10791067
mode: params.publish_dir_mode,
1080-
pattern: "{!versions.yml}"
1068+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
10811069
]
10821070
}
10831071
}
@@ -1094,31 +1082,31 @@ if (!params.skip_pseudo_alignment && params.pseudo_aligner == 'salmon') {
10941082
publishDir = [
10951083
path: { "${params.outdir}/${params.pseudo_aligner}" },
10961084
mode: params.publish_dir_mode,
1097-
pattern: "{!versions.yml,!*_meta_info.json}"
1085+
saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('_meta_info.json') ? null : filename }
10981086
]
10991087
}
11001088

11011089
withName: '.*:QUANTIFY_SALMON:SALMON_TX2GENE' {
11021090
publishDir = [
11031091
path: { "${params.outdir}/${params.pseudo_aligner}" },
11041092
mode: params.publish_dir_mode,
1105-
pattern: "{!versions.yml}"
1093+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
11061094
]
11071095
}
11081096

11091097
withName: '.*:QUANTIFY_SALMON:SALMON_TXIMPORT' {
11101098
publishDir = [
11111099
path: { "${params.outdir}/${params.pseudo_aligner}" },
11121100
mode: params.publish_dir_mode,
1113-
pattern: "{!versions.yml}"
1101+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
11141102
]
11151103
}
11161104

11171105
withName: '.*:QUANTIFY_SALMON:SALMON_SE_.*' {
11181106
publishDir = [
11191107
path: { "${params.outdir}/${params.pseudo_aligner}" },
11201108
mode: params.publish_dir_mode,
1121-
pattern: "{!versions.yml}"
1109+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
11221110
]
11231111
}
11241112
}

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