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maxulyssemaxulysse
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better usage of pattern
1 parent 04f8beb commit 47e219a

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+46
-34
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+46
-34
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‎conf/modules.config‎

Lines changed: 46 additions & 34 deletions
Original file line numberDiff line numberDiff line change
@@ -41,7 +41,8 @@ process {
4141
publishDir = [
4242
path: { "${params.outdir}/genome" },
4343
mode: params.publish_dir_mode,
44-
saveAs: { filename -> params.save_reference ? filename.equals('versions.yml') ? null : filename : null }
44+
pattern: "{!versions.yml}",
45+
saveAs: { params.save_reference ? it : null }
4546
]
4647
}
4748

@@ -53,7 +54,8 @@ process {
5354
publishDir = [
5455
path: { "${params.outdir}/genome/index" },
5556
mode: params.publish_dir_mode,
56-
saveAs: { filename -> params.save_reference ? filename.equals('versions.yml') ? null : filename : null }
57+
pattern: "{!versions.yml}",
58+
saveAs: { params.save_reference ? it : null }
5759
]
5860
}
5961

@@ -62,15 +64,17 @@ process {
6264
publishDir = [
6365
path: { "${params.outdir}/genome" },
6466
mode: params.publish_dir_mode,
65-
saveAs: { filename -> params.save_reference ? filename.equals('versions.yml') ? null : filename : null }
67+
pattern: "{!versions.yml}",
68+
saveAs: { params.save_reference ? it : null }
6669
]
6770
}
6871

6972
withName: 'HISAT2_EXTRACTSPLICESITES' {
7073
publishDir = [
7174
path: { "${params.outdir}/genome/index" },
7275
mode: params.publish_dir_mode,
73-
saveAs: { filename -> params.save_reference ? filename.equals('versions.yml') ? null : filename : null }
76+
pattern: "{!versions.yml}",
77+
saveAs: { params.save_reference ? it : null }
7478
]
7579
}
7680

@@ -79,7 +83,8 @@ process {
7983
publishDir = [
8084
path: { "${params.outdir}/genome/index" },
8185
mode: params.publish_dir_mode,
82-
saveAs: { filename -> params.save_reference ? filename.equals('versions.yml') ? null : filename : null }
86+
pattern: "{!versions.yml}",
87+
saveAs: { params.save_reference ? it : null }
8388
]
8489
}
8590

@@ -88,47 +93,53 @@ process {
8893
publishDir = [
8994
path: { "${params.outdir}/genome/index" },
9095
mode: params.publish_dir_mode,
91-
saveAs: { filename -> params.save_reference ? filename.equals('versions.yml') ? null : filename : null }
96+
pattern: "{!versions.yml}",
97+
saveAs: { params.save_reference ? it : null }
9298
]
9399
}
94100

95101
withName: 'GTF2BED' {
96102
publishDir = [
97103
path: { "${params.outdir}/genome" },
98104
mode: params.publish_dir_mode,
99-
saveAs: { filename -> params.save_reference ? filename.equals('versions.yml') ? null : filename : null }
105+
pattern: "{!versions.yml}",
106+
saveAs: { params.save_reference ? it : null }
100107
]
101108
}
102109

103110
withName: 'CAT_ADDITIONAL_FASTA|PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' {
104111
publishDir = [
105112
path: { "${params.outdir}/genome" },
106113
mode: params.publish_dir_mode,
107-
saveAs: { filename -> params.save_reference ? filename.equals('versions.yml') ? null : filename : null }
114+
pattern: "{!versions.yml}",
115+
saveAs: { params.save_reference ? it : null }
108116
]
109117
}
110118

111119
withName: 'GTF_GENE_FILTER' {
112120
publishDir = [
113121
path: { "${params.outdir}/genome" },
114122
mode: params.publish_dir_mode,
115-
saveAs: { filename -> params.save_reference ? filename.equals('versions.yml') ? null : filename : null }
123+
pattern: "{!versions.yml}",
124+
saveAs: { params.save_reference ? it : null }
116125
]
117126
}
118127

119128
withName: 'CUSTOM_GETCHROMSIZES' {
120129
publishDir = [
121130
path: { "${params.outdir}/genome" },
122131
mode: params.publish_dir_mode,
123-
saveAs: { filename -> params.save_reference ? filename.equals('versions.yml') ? null : filename : null }
132+
pattern: "{!versions.yml}",
133+
saveAs: { params.save_reference ? it : null }
124134
]
125135
}
126136

127137
withName: 'CAT_FASTQ' {
128138
publishDir = [
129139
path: { "${params.outdir}/fastq" },
130140
mode: params.publish_dir_mode,
131-
saveAs: { filename -> params.save_merged_fastq ? filename.equals('versions.yml') ? null : filename : null }
141+
pattern: "{!versions.yml}",
142+
saveAs: { params.save_merged_fastq ? it : null }
132143
]
133144
}
134145
}
@@ -140,7 +151,8 @@ if (!params.skip_bbsplit && params.bbsplit_fasta_list) {
140151
publishDir = [
141152
path: { "${params.outdir}/genome/index" },
142153
mode: params.publish_dir_mode,
143-
saveAs: { filename -> params.save_reference ? filename.equals('versions.yml') ? null : filename : null }
154+
pattern: "{!versions.yml}",
155+
saveAs: { params.save_reference ? it : null }
144156
]
145157
}
146158
}
@@ -191,7 +203,7 @@ if (!(params.skip_fastqc || params.skip_qc)) {
191203
publishDir = [
192204
path: { "${params.outdir}/${params.trimmer}/fastqc" },
193205
mode: params.publish_dir_mode,
194-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
206+
pattern: "{!versions.yml}"
195207
]
196208
}
197209
}
@@ -476,7 +488,7 @@ if (!params.skip_alignment) {
476488
publishDir = [
477489
path: { "${params.outdir}/${params.aligner}/bigwig" },
478490
mode: params.publish_dir_mode,
479-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
491+
pattern: "{!versions.yml}"
480492
]
481493
}
482494

@@ -492,7 +504,7 @@ if (!params.skip_alignment) {
492504
publishDir = [
493505
path: { "${params.outdir}/${params.aligner}/bigwig" },
494506
mode: params.publish_dir_mode,
495-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
507+
pattern: "{!versions.yml}"
496508
]
497509
}
498510
}
@@ -508,7 +520,7 @@ if (!params.skip_alignment) {
508520
publishDir = [
509521
path: { "${params.outdir}/${params.aligner}/stringtie" },
510522
mode: params.publish_dir_mode,
511-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
523+
pattern: "{!versions.yml}"
512524
]
513525
}
514526
}
@@ -562,31 +574,31 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
562574
publishDir = [
563575
path: { "${params.outdir}/${params.aligner}" },
564576
mode: params.publish_dir_mode,
565-
saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('_meta_info.json') ? null : filename }
577+
pattern: "{!versions.yml,!*_meta_info.json}"
566578
]
567579
}
568580

569581
withName: '.*:QUANTIFY_STAR_SALMON:SALMON_TX2GENE' {
570582
publishDir = [
571583
path: { "${params.outdir}/${params.aligner}" },
572584
mode: params.publish_dir_mode,
573-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
585+
pattern: "{!versions.yml}"
574586
]
575587
}
576588

577589
withName: '.*:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT' {
578590
publishDir = [
579591
path: { "${params.outdir}/${params.aligner}" },
580592
mode: params.publish_dir_mode,
581-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
593+
pattern: "{!versions.yml}"
582594
]
583595
}
584596

585597
withName: '.*:QUANTIFY_STAR_SALMON:SALMON_SE_.*' {
586598
publishDir = [
587599
path: { "${params.outdir}/${params.aligner}" },
588600
mode: params.publish_dir_mode,
589-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
601+
pattern: "{!versions.yml}"
590602
]
591603
}
592604
}
@@ -751,7 +763,7 @@ if (!params.skip_alignment && params.aligner == 'star_rsem') {
751763
publishDir = [
752764
path: { "${params.outdir}/${params.aligner}" },
753765
mode: params.publish_dir_mode,
754-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
766+
pattern: "{!versions.yml}"
755767
]
756768
}
757769
}
@@ -839,7 +851,7 @@ if (!params.skip_alignment && !params.skip_qc) {
839851
publishDir = [
840852
path: { "${params.outdir}/${params.aligner}/qualimap" },
841853
mode: params.publish_dir_mode,
842-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
854+
pattern: "{!versions.yml}"
843855
]
844856
}
845857
}
@@ -890,15 +902,15 @@ if (!params.skip_alignment && !params.skip_qc) {
890902
publishDir = [
891903
path: { "${params.outdir}/${params.aligner}/featurecounts" },
892904
mode: params.publish_dir_mode,
893-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
905+
pattern: "{!versions.yml}"
894906
]
895907
}
896908

897909
withName: 'MULTIQC_CUSTOM_BIOTYPE' {
898910
publishDir = [
899911
path: { "${params.outdir}/${params.aligner}/featurecounts" },
900912
mode: params.publish_dir_mode,
901-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
913+
pattern: "{!versions.yml}"
902914
]
903915
}
904916
}
@@ -910,7 +922,7 @@ if (!params.skip_alignment && !params.skip_qc) {
910922
publishDir = [
911923
path: { "${params.outdir}/${params.aligner}/rseqc/bam_stat" },
912924
mode: params.publish_dir_mode,
913-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
925+
pattern: "{!versions.yml}"
914926
]
915927
}
916928
}
@@ -922,7 +934,7 @@ if (!params.skip_alignment && !params.skip_qc) {
922934
publishDir = [
923935
path: { "${params.outdir}/${params.aligner}/rseqc/infer_experiment" },
924936
mode: params.publish_dir_mode,
925-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
937+
pattern: "{!versions.yml}"
926938
]
927939
}
928940
}
@@ -1011,7 +1023,7 @@ if (!params.skip_alignment && !params.skip_qc) {
10111023
publishDir = [
10121024
path: { "${params.outdir}/${params.aligner}/rseqc/read_distribution" },
10131025
mode: params.publish_dir_mode,
1014-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
1026+
pattern: "{!versions.yml}"
10151027
]
10161028
}
10171029
}
@@ -1025,7 +1037,7 @@ if (!params.skip_alignment && !params.skip_qc) {
10251037
path: { "${params.outdir}/${params.aligner}/rseqc/inner_distance/txt" },
10261038
mode: params.publish_dir_mode,
10271039
pattern: '*.txt',
1028-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
1040+
pattern: "{!versions.yml}"
10291041
],
10301042
[
10311043
path: { "${params.outdir}/${params.aligner}/rseqc/inner_distance/pdf" },
@@ -1048,7 +1060,7 @@ if (!params.skip_alignment && !params.skip_qc) {
10481060
publishDir = [
10491061
path: { "${params.outdir}/${params.aligner}/rseqc/tin" },
10501062
mode: params.publish_dir_mode,
1051-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
1063+
pattern: "{!versions.yml}"
10521064
]
10531065
}
10541066
}
@@ -1065,7 +1077,7 @@ if (!params.skip_multiqc) {
10651077
params.skip_alignment? '' : "/${params.aligner}"
10661078
].join('') },
10671079
mode: params.publish_dir_mode,
1068-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
1080+
pattern: "{!versions.yml}"
10691081
]
10701082
}
10711083
}
@@ -1082,31 +1094,31 @@ if (!params.skip_pseudo_alignment && params.pseudo_aligner == 'salmon') {
10821094
publishDir = [
10831095
path: { "${params.outdir}/${params.pseudo_aligner}" },
10841096
mode: params.publish_dir_mode,
1085-
saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('_meta_info.json') ? null : filename }
1097+
pattern: "{!versions.yml,!*_meta_info.json}"
10861098
]
10871099
}
10881100

10891101
withName: '.*:QUANTIFY_SALMON:SALMON_TX2GENE' {
10901102
publishDir = [
10911103
path: { "${params.outdir}/${params.pseudo_aligner}" },
10921104
mode: params.publish_dir_mode,
1093-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
1105+
pattern: "{!versions.yml}"
10941106
]
10951107
}
10961108

10971109
withName: '.*:QUANTIFY_SALMON:SALMON_TXIMPORT' {
10981110
publishDir = [
10991111
path: { "${params.outdir}/${params.pseudo_aligner}" },
11001112
mode: params.publish_dir_mode,
1101-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
1113+
pattern: "{!versions.yml}"
11021114
]
11031115
}
11041116

11051117
withName: '.*:QUANTIFY_SALMON:SALMON_SE_.*' {
11061118
publishDir = [
11071119
path: { "${params.outdir}/${params.pseudo_aligner}" },
11081120
mode: params.publish_dir_mode,
1109-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
1121+
pattern: "{!versions.yml}"
11101122
]
11111123
}
11121124
}

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