From 789dc4f09a285185f448a39667285543f6efab80 Mon Sep 17 00:00:00 2001 From: Jeremy1805 Date: Thu, 20 Aug 2020 11:57:10 +0100 Subject: [PATCH] Changed options.publish_files definition in functions.nf/initOptions --- software/SOFTWARE/TOOL/functions.nf | 2 +- software/bwa/index/functions.nf | 2 +- software/bwa/mem/functions.nf | 2 +- software/deeptools/computematrix/functions.nf | 2 +- software/deeptools/plotfingerprint/functions.nf | 2 +- software/deeptools/plotheatmap/functions.nf | 2 +- software/deeptools/plotprofile/functions.nf | 2 +- software/fastqc/functions.nf | 2 +- software/homer/annotatepeaks/functions.nf | 2 +- software/lib/functions.nf | 2 +- software/macs2/callpeak/functions.nf | 2 +- software/phantompeakqualtools/functions.nf | 2 +- software/picard/collectmultiplemetrics/functions.nf | 2 +- software/picard/markduplicates/functions.nf | 2 +- software/picard/mergesamfiles/functions.nf | 2 +- software/preseq/lcextrap/functions.nf | 2 +- software/samtools/flagstat/functions.nf | 2 +- software/samtools/idxstats/functions.nf | 2 +- software/samtools/index/functions.nf | 2 +- software/samtools/sort/functions.nf | 2 +- software/samtools/stats/functions.nf | 2 +- software/subread/featurecounts/functions.nf | 2 +- software/trimgalore/functions.nf | 2 +- software/ucsc/bedgraphtobigwig/functions.nf | 2 +- 24 files changed, 24 insertions(+), 24 deletions(-) diff --git a/software/SOFTWARE/TOOL/functions.nf b/software/SOFTWARE/TOOL/functions.nf index 75553cdf..6fa66a28 100644 --- a/software/SOFTWARE/TOOL/functions.nf +++ b/software/SOFTWARE/TOOL/functions.nf @@ -20,7 +20,7 @@ def initOptions(Map args) { options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false 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 ?: '' return options } diff --git a/software/bwa/index/functions.nf b/software/bwa/index/functions.nf index 75553cdf..6fa66a28 100644 --- a/software/bwa/index/functions.nf +++ b/software/bwa/index/functions.nf @@ -20,7 +20,7 @@ def initOptions(Map args) { options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false 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 ?: '' return options } diff --git a/software/bwa/mem/functions.nf b/software/bwa/mem/functions.nf index 75553cdf..6fa66a28 100644 --- a/software/bwa/mem/functions.nf +++ b/software/bwa/mem/functions.nf @@ -20,7 +20,7 @@ def initOptions(Map args) { options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false 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 ?: '' return options } diff --git a/software/deeptools/computematrix/functions.nf b/software/deeptools/computematrix/functions.nf index 75553cdf..6fa66a28 100644 --- a/software/deeptools/computematrix/functions.nf +++ b/software/deeptools/computematrix/functions.nf @@ -20,7 +20,7 @@ def initOptions(Map args) { options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false 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 ?: '' return options } diff --git a/software/deeptools/plotfingerprint/functions.nf b/software/deeptools/plotfingerprint/functions.nf index 75553cdf..6fa66a28 100644 --- a/software/deeptools/plotfingerprint/functions.nf +++ b/software/deeptools/plotfingerprint/functions.nf @@ -20,7 +20,7 @@ def initOptions(Map args) { options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false 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 ?: '' return options } diff --git a/software/deeptools/plotheatmap/functions.nf b/software/deeptools/plotheatmap/functions.nf index 75553cdf..6fa66a28 100644 --- a/software/deeptools/plotheatmap/functions.nf +++ b/software/deeptools/plotheatmap/functions.nf @@ -20,7 +20,7 @@ def initOptions(Map args) { options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false 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 ?: '' return options } diff --git a/software/deeptools/plotprofile/functions.nf b/software/deeptools/plotprofile/functions.nf index 75553cdf..6fa66a28 100644 --- a/software/deeptools/plotprofile/functions.nf +++ b/software/deeptools/plotprofile/functions.nf @@ -20,7 +20,7 @@ def initOptions(Map args) { options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false 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 ?: '' return options } diff --git a/software/fastqc/functions.nf b/software/fastqc/functions.nf index 75553cdf..6fa66a28 100644 --- a/software/fastqc/functions.nf +++ b/software/fastqc/functions.nf @@ -20,7 +20,7 @@ def initOptions(Map args) { options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false 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 ?: '' return options } diff --git a/software/homer/annotatepeaks/functions.nf b/software/homer/annotatepeaks/functions.nf index 75553cdf..6fa66a28 100644 --- a/software/homer/annotatepeaks/functions.nf +++ b/software/homer/annotatepeaks/functions.nf @@ -20,7 +20,7 @@ def initOptions(Map args) { options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false 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 ?: '' return options } diff --git a/software/lib/functions.nf b/software/lib/functions.nf index 75553cdf..6fa66a28 100644 --- a/software/lib/functions.nf +++ b/software/lib/functions.nf @@ -20,7 +20,7 @@ def initOptions(Map args) { options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false 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 ?: '' return options } diff --git a/software/macs2/callpeak/functions.nf b/software/macs2/callpeak/functions.nf index 75553cdf..6fa66a28 100644 --- a/software/macs2/callpeak/functions.nf +++ b/software/macs2/callpeak/functions.nf @@ -20,7 +20,7 @@ def initOptions(Map args) { options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false 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 ?: '' return options } diff --git a/software/phantompeakqualtools/functions.nf b/software/phantompeakqualtools/functions.nf index 75553cdf..6fa66a28 100644 --- a/software/phantompeakqualtools/functions.nf +++ b/software/phantompeakqualtools/functions.nf @@ -20,7 +20,7 @@ def initOptions(Map args) { options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false 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 ?: '' return options } diff --git a/software/picard/collectmultiplemetrics/functions.nf b/software/picard/collectmultiplemetrics/functions.nf index 75553cdf..6fa66a28 100644 --- a/software/picard/collectmultiplemetrics/functions.nf +++ b/software/picard/collectmultiplemetrics/functions.nf @@ -20,7 +20,7 @@ def initOptions(Map args) { options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false 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 ?: '' return options } diff --git a/software/picard/markduplicates/functions.nf b/software/picard/markduplicates/functions.nf index 75553cdf..6fa66a28 100644 --- a/software/picard/markduplicates/functions.nf +++ b/software/picard/markduplicates/functions.nf @@ -20,7 +20,7 @@ def initOptions(Map args) { options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false 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 ?: '' return options } diff --git a/software/picard/mergesamfiles/functions.nf b/software/picard/mergesamfiles/functions.nf index 75553cdf..6fa66a28 100644 --- a/software/picard/mergesamfiles/functions.nf +++ b/software/picard/mergesamfiles/functions.nf @@ -20,7 +20,7 @@ def initOptions(Map args) { options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false 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 ?: '' return options } diff --git a/software/preseq/lcextrap/functions.nf b/software/preseq/lcextrap/functions.nf index 75553cdf..6fa66a28 100644 --- a/software/preseq/lcextrap/functions.nf +++ b/software/preseq/lcextrap/functions.nf @@ -20,7 +20,7 @@ def initOptions(Map args) { options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false 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 ?: '' return options } diff --git a/software/samtools/flagstat/functions.nf b/software/samtools/flagstat/functions.nf index 75553cdf..6fa66a28 100644 --- a/software/samtools/flagstat/functions.nf +++ b/software/samtools/flagstat/functions.nf @@ -20,7 +20,7 @@ def initOptions(Map args) { options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false 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 ?: '' return options } diff --git a/software/samtools/idxstats/functions.nf b/software/samtools/idxstats/functions.nf index 75553cdf..6fa66a28 100644 --- a/software/samtools/idxstats/functions.nf +++ b/software/samtools/idxstats/functions.nf @@ -20,7 +20,7 @@ def initOptions(Map args) { options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false 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 ?: '' return options } diff --git a/software/samtools/index/functions.nf b/software/samtools/index/functions.nf index 75553cdf..6fa66a28 100644 --- a/software/samtools/index/functions.nf +++ b/software/samtools/index/functions.nf @@ -20,7 +20,7 @@ def initOptions(Map args) { options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false 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 ?: '' return options } diff --git a/software/samtools/sort/functions.nf b/software/samtools/sort/functions.nf index 75553cdf..6fa66a28 100644 --- a/software/samtools/sort/functions.nf +++ b/software/samtools/sort/functions.nf @@ -20,7 +20,7 @@ def initOptions(Map args) { options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false 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 ?: '' return options } diff --git a/software/samtools/stats/functions.nf b/software/samtools/stats/functions.nf index 75553cdf..6fa66a28 100644 --- a/software/samtools/stats/functions.nf +++ b/software/samtools/stats/functions.nf @@ -20,7 +20,7 @@ def initOptions(Map args) { options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false 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 ?: '' return options } diff --git a/software/subread/featurecounts/functions.nf b/software/subread/featurecounts/functions.nf index 75553cdf..6fa66a28 100644 --- a/software/subread/featurecounts/functions.nf +++ b/software/subread/featurecounts/functions.nf @@ -20,7 +20,7 @@ def initOptions(Map args) { options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false 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 ?: '' return options } diff --git a/software/trimgalore/functions.nf b/software/trimgalore/functions.nf index 75553cdf..6fa66a28 100644 --- a/software/trimgalore/functions.nf +++ b/software/trimgalore/functions.nf @@ -20,7 +20,7 @@ def initOptions(Map args) { options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false 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 ?: '' return options } diff --git a/software/ucsc/bedgraphtobigwig/functions.nf b/software/ucsc/bedgraphtobigwig/functions.nf index 75553cdf..6fa66a28 100644 --- a/software/ucsc/bedgraphtobigwig/functions.nf +++ b/software/ucsc/bedgraphtobigwig/functions.nf @@ -20,7 +20,7 @@ def initOptions(Map args) { options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false 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 ?: '' return options }