@@ -18,7 +18,7 @@ process {
1818 // BBSPLIT
1919 withName: '.*:PREPARE_GENOME:BBMAP_BBSPLIT' {
2020 ext.args = 'build=1'
21- publishDir = [
21+ publishDir = [
2222 mode: params.publish_dir_mode,
2323 path: { "${params.outdir}/reference" },
2424 pattern: "bbmap",
@@ -27,8 +27,9 @@ process {
2727 }
2828
2929 withName: 'BWAMEM1_INDEX' {
30- ext.when = { !params.bwa && params.step == "mapping" && (params.aligner == "bwa-mem" || params.aligner == "sentieon-bwamem" || params.aligner == "parabricks")}
31- publishDir = [
30+ ext.when = { !params.bwa && params.step == "mapping" && (params.aligner == "bwa-mem" || params.aligner == "sentieon-bwamem" || params.aligner == "parabricks")}
31+ ext.prefix = { params.aligner == "parabricks" ? "${fasta.name}" : "${fasta.baseName}" }
32+ publishDir = [
3233 mode: params.publish_dir_mode,
3334 path: { "${params.outdir}/reference" },
3435 pattern: "bwa",
@@ -37,8 +38,8 @@ process {
3738 }
3839
3940 withName: 'BWAMEM2_INDEX' {
40- ext.when = { !params.bwamem2 && params.step == "mapping" && params.aligner == "bwa-mem2" }
41- publishDir = [
41+ ext.when = { !params.bwamem2 && params.step == "mapping" && params.aligner == "bwa-mem2" }
42+ publishDir = [
4243 mode: params.publish_dir_mode,
4344 path: { "${params.outdir}/reference" },
4445 pattern: "bwamem2",
@@ -47,8 +48,8 @@ process {
4748 }
4849
4950 withName: 'CNVKIT_ANTITARGET' {
50- ext.when = { params.tools && params.tools.split(',').contains('cnvkit') }
51- publishDir = [
51+ ext.when = { params.tools && params.tools.split(',').contains('cnvkit') }
52+ publishDir = [
5253 mode: params.publish_dir_mode,
5354 path: { "${params.outdir}/reference" },
5455 pattern: "*{bed}",
@@ -57,9 +58,9 @@ process {
5758 }
5859
5960 withName: 'CNVKIT_REFERENCE' {
60- ext.prefix = { 'cnvkit' }
61- ext.when = { params.tools && params.tools.split(',').contains('cnvkit') && !params.cnvkit_reference }
62- publishDir = [
61+ ext.prefix = { 'cnvkit' }
62+ ext.when = { params.tools && params.tools.split(',').contains('cnvkit') && !params.cnvkit_reference }
63+ publishDir = [
6364 mode: params.publish_dir_mode,
6465 path: { "${params.outdir}/reference" },
6566 pattern: "*{cnn}",
@@ -68,7 +69,7 @@ process {
6869 }
6970
7071 withName: 'DRAGMAP_HASHTABLE' {
71- ext.when = { !params.dragmap && params.step == "mapping" && params.aligner == "dragmap" }
72+ ext.when = { !params.dragmap && params.step == "mapping" && params.aligner == "dragmap" }
7273 publishDir = [
7374 mode: params.publish_dir_mode,
7475 path: { "${params.outdir}/reference" },
@@ -79,8 +80,8 @@ process {
7980
8081 withName: 'GATK4_CREATESEQUENCEDICTIONARY' {
8182 // Prevents dict creation, when step is annotate, controlfreec, or when msisensor2 (as the only tool) is run from variantcalling entrystep
82- ext.when = { !params.dict && params.step != "annotate" && params.step != "controlfreec" && !(params.step == "variantcalling" && params.tools.split(',').size() == 1 && params.tools.contains('msisensor2')) }
83- publishDir = [
83+ ext.when = { !params.dict && params.step != "annotate" && params.step != "controlfreec" && !(params.step == "variantcalling" && params.tools.split(',').size() == 1 && params.tools.contains('msisensor2')) }
84+ publishDir = [
8485 mode: params.publish_dir_mode,
8586 path: { "${params.outdir}/reference/dict" },
8687 pattern: "*dict",
@@ -89,7 +90,7 @@ process {
8990 }
9091
9192 withName: 'MSISENSOR2_SCAN' {
92- publishDir = [
93+ publishDir = [
9394 mode: params.publish_dir_mode,
9495 path: { "${params.outdir}/reference/msisensor2" },
9596 pattern: "*scan",
@@ -98,7 +99,7 @@ process {
9899 }
99100
100101 withName: 'MSISENSORPRO_SCAN' {
101- publishDir = [
102+ publishDir = [
102103 mode: params.publish_dir_mode,
103104 path: { "${params.outdir}/reference/msisensorpro" },
104105 pattern: "*list",
@@ -107,8 +108,8 @@ process {
107108 }
108109
109110 withName: 'SAMTOOLS_FAIDX' {
110- ext.when = { !params.fasta_fai && params.step != "annotate" }
111- publishDir = [
111+ ext.when = { !params.fasta_fai && params.step != "annotate" }
112+ publishDir = [
112113 mode: params.publish_dir_mode,
113114 path: { "${params.outdir}/reference/fai" },
114115 pattern: "*fai",
@@ -117,8 +118,8 @@ process {
117118 }
118119
119120 withName: 'TABIX_BCFTOOLS_ANNOTATIONS' {
120- ext.when = { !params.bcftools_annotations_tbi && params.bcftools_annotations && params.tools && params.tools.split(',').contains('bcfann') }
121- publishDir = [
121+ ext.when = { !params.bcftools_annotations_tbi && params.bcftools_annotations && params.tools && params.tools.split(',').contains('bcfann') }
122+ publishDir = [
122123 mode: params.publish_dir_mode,
123124 path: { "${params.outdir}/reference/bcfann" },
124125 pattern: "*vcf.gz.tbi",
@@ -127,8 +128,8 @@ process {
127128 }
128129
129130 withName: 'TABIX_DBSNP' {
130- ext.when = { !params.dbsnp_tbi && params.dbsnp && ((params.step == "mapping" || params.step == "markduplicates" || params.step == "prepare_recalibration") || params.tools && (params.tools.split(',').contains('controlfreec') || params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper') || params.tools.split(',').contains('sentieon_dnascope') || params.tools.split(',').contains('muse') || params.tools.split(',').contains('mutect2'))) }
131- publishDir = [
131+ ext.when = { !params.dbsnp_tbi && params.dbsnp && ((params.step == "mapping" || params.step == "markduplicates" || params.step == "prepare_recalibration") || params.tools && (params.tools.split(',').contains('controlfreec') || params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper') || params.tools.split(',').contains('sentieon_dnascope') || params.tools.split(',').contains('muse') || params.tools.split(',').contains('mutect2'))) }
132+ publishDir = [
132133 mode: params.publish_dir_mode,
133134 path: { "${params.outdir}/reference/dbsnp" },
134135 pattern: "*vcf.gz.tbi",
@@ -137,8 +138,8 @@ process {
137138 }
138139
139140 withName: 'TABIX_GERMLINE_RESOURCE' {
140- ext.when = { !params.germline_resource_tbi && params.germline_resource && params.tools && params.tools.split(',').contains('mutect2') }
141- publishDir = [
141+ ext.when = { !params.germline_resource_tbi && params.germline_resource && params.tools && params.tools.split(',').contains('mutect2') }
142+ publishDir = [
142143 mode: params.publish_dir_mode,
143144 path: { "${params.outdir}/reference/germline_resource" },
144145 pattern: "*vcf.gz.tbi",
@@ -147,8 +148,8 @@ process {
147148 }
148149
149150 withName: 'TABIX_KNOWN_INDELS' {
150- ext.when = { !params.known_indels_tbi && params.known_indels && (params.step == 'mapping' || params.step == "markduplicates" || params.step == 'prepare_recalibration' || (params.tools && (params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper') || params.tools.split(',').contains('sentieon_dnascope'))) ) }
151- publishDir = [
151+ ext.when = { !params.known_indels_tbi && params.known_indels && (params.step == 'mapping' || params.step == "markduplicates" || params.step == 'prepare_recalibration' || (params.tools && (params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper') || params.tools.split(',').contains('sentieon_dnascope'))) ) }
152+ publishDir = [
152153 mode: params.publish_dir_mode,
153154 path: { "${params.outdir}/reference/known_indels" },
154155 pattern: "*vcf.gz.tbi",
@@ -157,8 +158,8 @@ process {
157158 }
158159
159160 withName: 'TABIX_KNOWN_SNPS' {
160- ext.when = { !params.known_snps_tbi && params.known_snps && (params.step == 'mapping' || params.step == "markduplicates" || params.step == 'prepare_recalibration' || (params.tools && (params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper') )) ) }
161- publishDir = [
161+ ext.when = { !params.known_snps_tbi && params.known_snps && (params.step == 'mapping' || params.step == "markduplicates" || params.step == 'prepare_recalibration' || (params.tools && (params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper') )) ) }
162+ publishDir = [
162163 mode: params.publish_dir_mode,
163164 path: { "${params.outdir}/reference/known_snps" },
164165 pattern: "*vcf.gz.tbi",
@@ -167,8 +168,8 @@ process {
167168 }
168169
169170 withName: 'TABIX_PON' {
170- ext.when = { !params.pon_tbi && params.pon && params.tools && params.tools.split(',').contains('mutect2') }
171- publishDir = [
171+ ext.when = { !params.pon_tbi && params.pon && params.tools && params.tools.split(',').contains('mutect2') }
172+ publishDir = [
172173 mode: params.publish_dir_mode,
173174 path: { "${params.outdir}/reference/pon" },
174175 pattern: "*vcf.gz.tbi",
@@ -177,25 +178,25 @@ process {
177178 }
178179
179180 withName: 'UNZIP_ALLELES|UNZIP_LOCI|UNZIP_GC|UNZIP_RT' {
180- ext.when = { params.tools && params.tools.split(',').contains('ascat')}
181- publishDir = [
181+ ext.when = { params.tools && params.tools.split(',').contains('ascat')}
182+ publishDir = [
182183 enabled: false
183184 ]
184185 }
185186
186187 withName: 'UNTAR_CHR_DIR' {
187- ext.prefix = 'chr_dir'
188- ext.when = { params.tools && params.tools.split(',').contains('controlfreec')}
189- publishDir = [
188+ ext.prefix = 'chr_dir'
189+ ext.when = { params.tools && params.tools.split(',').contains('controlfreec')}
190+ publishDir = [
190191 mode: params.publish_dir_mode,
191192 path: { "${params.outdir}/reference/" },
192193 saveAs: { (params.save_reference || params.build_only_index) && !it.equals('versions.yml') ? it : null }
193194 ]
194195 }
195196
196197 withName: 'UNTAR_MSISENSOR2_MODELS' {
197- ext.prefix = 'models'
198- publishDir = [
198+ ext.prefix = 'models'
199+ publishDir = [
199200 enabled: true,
200201 mode: params.publish_dir_mode,
201202 path: { "${params.outdir}/reference/msisensor2" },
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