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Changed options.publish_files definition in functions.nf/initOptions

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Jeremy1805 2020-08-20 11:57:10 +01:00
parent 47b6dd70e4
commit 789dc4f09a
24 changed files with 24 additions and 24 deletions
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2
software/SOFTWARE/TOOL/functions.nf
View file

@ -20,7 +20,7 @@ def initOptions(Map args) {
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files ?: null options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }

2
software/bwa/index/functions.nf
View file

@ -20,7 +20,7 @@ def initOptions(Map args) {
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files ?: null options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }

2
software/bwa/mem/functions.nf
View file

@ -20,7 +20,7 @@ def initOptions(Map args) {
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files ?: null options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }

2
software/deeptools/computematrix/functions.nf
View file

@ -20,7 +20,7 @@ def initOptions(Map args) {
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files ?: null options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }

2
software/deeptools/plotfingerprint/functions.nf
View file

@ -20,7 +20,7 @@ def initOptions(Map args) {
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files ?: null options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }

2
software/deeptools/plotheatmap/functions.nf
View file

@ -20,7 +20,7 @@ def initOptions(Map args) {
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files ?: null options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }

2
software/deeptools/plotprofile/functions.nf
View file

@ -20,7 +20,7 @@ def initOptions(Map args) {
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files ?: null options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }

2
software/fastqc/functions.nf
View file

@ -20,7 +20,7 @@ def initOptions(Map args) {
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files ?: null options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }

2
software/homer/annotatepeaks/functions.nf
View file

@ -20,7 +20,7 @@ def initOptions(Map args) {
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files ?: null options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }

2
software/lib/functions.nf
View file

@ -20,7 +20,7 @@ def initOptions(Map args) {
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files ?: null options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }

2
software/macs2/callpeak/functions.nf
View file

@ -20,7 +20,7 @@ def initOptions(Map args) {
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files ?: null options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }

2
software/phantompeakqualtools/functions.nf
View file

@ -20,7 +20,7 @@ def initOptions(Map args) {
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files ?: null options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }

2
software/picard/collectmultiplemetrics/functions.nf
View file

@ -20,7 +20,7 @@ def initOptions(Map args) {
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files ?: null options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }

2
software/picard/markduplicates/functions.nf
View file

@ -20,7 +20,7 @@ def initOptions(Map args) {
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files ?: null options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }

2
software/picard/mergesamfiles/functions.nf
View file

@ -20,7 +20,7 @@ def initOptions(Map args) {
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files ?: null options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }

2
software/preseq/lcextrap/functions.nf
View file

@ -20,7 +20,7 @@ def initOptions(Map args) {
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files ?: null options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }

2
software/samtools/flagstat/functions.nf
View file

@ -20,7 +20,7 @@ def initOptions(Map args) {
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files ?: null options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }

2
software/samtools/idxstats/functions.nf
View file

@ -20,7 +20,7 @@ def initOptions(Map args) {
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files ?: null options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }

2
software/samtools/index/functions.nf
View file

@ -20,7 +20,7 @@ def initOptions(Map args) {
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files ?: null options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }

2
software/samtools/sort/functions.nf
View file

@ -20,7 +20,7 @@ def initOptions(Map args) {
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files ?: null options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }

2
software/samtools/stats/functions.nf
View file

@ -20,7 +20,7 @@ def initOptions(Map args) {
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files ?: null options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }

2
software/subread/featurecounts/functions.nf
View file

@ -20,7 +20,7 @@ def initOptions(Map args) {
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files ?: null options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }

2
software/trimgalore/functions.nf
View file

@ -20,7 +20,7 @@ def initOptions(Map args) {
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files ?: null options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }

2
software/ucsc/bedgraphtobigwig/functions.nf
View file

@ -20,7 +20,7 @@ def initOptions(Map args) {
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files ?: null options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }