diff --git a/modules/abacas/main.nf b/modules/abacas/main.nf index 7fe71e3a..49040214 100644 --- a/modules/abacas/main.nf +++ b/modules/abacas/main.nf @@ -17,7 +17,7 @@ process ABACAS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ abacas.pl \\ -r $fasta \\ diff --git a/modules/adapterremoval/main.nf b/modules/adapterremoval/main.nf index 33955ed2..0cf257ff 100644 --- a/modules/adapterremoval/main.nf +++ b/modules/adapterremoval/main.nf @@ -17,7 +17,7 @@ process ADAPTERREMOVAL { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" if (meta.single_end) { """ diff --git a/modules/agrvate/main.nf b/modules/agrvate/main.nf index 06392e16..aff72abc 100644 --- a/modules/agrvate/main.nf +++ b/modules/agrvate/main.nf @@ -17,7 +17,7 @@ process AGRVATE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ agrvate \\ $args \\ diff --git a/modules/allelecounter/main.nf b/modules/allelecounter/main.nf index 5cbc4cbd..850a018f 100644 --- a/modules/allelecounter/main.nf +++ b/modules/allelecounter/main.nf @@ -18,7 +18,7 @@ process ALLELECOUNTER { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def reference_options = fasta ? "-r $fasta": "" """ diff --git a/modules/arriba/main.nf b/modules/arriba/main.nf index 459ff100..0fcb6ba7 100644 --- a/modules/arriba/main.nf +++ b/modules/arriba/main.nf @@ -19,7 +19,7 @@ process ARRIBA { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def blacklist = (args.contains('-b')) ? '' : '-f blacklist' """ arriba \\ diff --git a/modules/artic/guppyplex/main.nf b/modules/artic/guppyplex/main.nf index a69e5381..780f5111 100644 --- a/modules/artic/guppyplex/main.nf +++ b/modules/artic/guppyplex/main.nf @@ -16,7 +16,7 @@ process ARTIC_GUPPYPLEX { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ artic \\ guppyplex \\ diff --git a/modules/assemblyscan/main.nf b/modules/assemblyscan/main.nf index 7b5b752b..56541222 100644 --- a/modules/assemblyscan/main.nf +++ b/modules/assemblyscan/main.nf @@ -16,7 +16,7 @@ process ASSEMBLYSCAN { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ assembly-scan $assembly > ${prefix}.json diff --git a/modules/ataqv/ataqv/main.nf b/modules/ataqv/ataqv/main.nf index 39602d30..20525e85 100644 --- a/modules/ataqv/ataqv/main.nf +++ b/modules/ataqv/ataqv/main.nf @@ -21,7 +21,7 @@ process ATAQV_ATAQV { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def peak = peak_file ? "--peak-file $peak_file" : '' def tss = tss_file ? "--tss-file $tss_file" : '' def excl_regs = excl_regs_file ? "--excluded-region-file $excl_regs_file" : '' diff --git a/modules/bamaligncleaner/main.nf b/modules/bamaligncleaner/main.nf index f1481c39..88fe21aa 100644 --- a/modules/bamaligncleaner/main.nf +++ b/modules/bamaligncleaner/main.nf @@ -16,7 +16,7 @@ process BAMALIGNCLEANER { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ bamAlignCleaner \\ diff --git a/modules/bamtools/split/main.nf b/modules/bamtools/split/main.nf index 676aab6f..8d5e5690 100644 --- a/modules/bamtools/split/main.nf +++ b/modules/bamtools/split/main.nf @@ -16,7 +16,7 @@ process BAMTOOLS_SPLIT { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ bamtools \\ split \\ diff --git a/modules/bamutil/trimbam/main.nf b/modules/bamutil/trimbam/main.nf index a210fe5f..9ceb2b65 100644 --- a/modules/bamutil/trimbam/main.nf +++ b/modules/bamutil/trimbam/main.nf @@ -16,7 +16,7 @@ process BAMUTIL_TRIMBAM { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ bam \\ trimBam \\ diff --git a/modules/bandage/image/main.nf b/modules/bandage/image/main.nf index e31566d1..bc2a9495 100644 --- a/modules/bandage/image/main.nf +++ b/modules/bandage/image/main.nf @@ -17,7 +17,7 @@ process BANDAGE_IMAGE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ Bandage image $gfa ${prefix}.png $args Bandage image $gfa ${prefix}.svg $args diff --git a/modules/bbmap/align/main.nf b/modules/bbmap/align/main.nf index ef23fada..ac839497 100644 --- a/modules/bbmap/align/main.nf +++ b/modules/bbmap/align/main.nf @@ -18,7 +18,7 @@ process BBMAP_ALIGN { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" input = meta.single_end ? "in=${fastq}" : "in=${fastq[0]} in2=${fastq[1]}" diff --git a/modules/bbmap/bbduk/main.nf b/modules/bbmap/bbduk/main.nf index 98a21eab..79c3c306 100644 --- a/modules/bbmap/bbduk/main.nf +++ b/modules/bbmap/bbduk/main.nf @@ -18,7 +18,7 @@ process BBMAP_BBDUK { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def raw = meta.single_end ? "in=${reads[0]}" : "in1=${reads[0]} in2=${reads[1]}" def trimmed = meta.single_end ? "out=${prefix}.fastq.gz" : "out1=${prefix}_1.fastq.gz out2=${prefix}_2.fastq.gz" def contaminants_fa = contaminants ? "ref=$contaminants" : '' diff --git a/modules/bbmap/bbsplit/main.nf b/modules/bbmap/bbsplit/main.nf index 53f6b1aa..0c916dfe 100644 --- a/modules/bbmap/bbsplit/main.nf +++ b/modules/bbmap/bbsplit/main.nf @@ -22,7 +22,7 @@ process BBMAP_BBSPLIT { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def avail_mem = 3 if (!task.memory) { diff --git a/modules/bcftools/consensus/main.nf b/modules/bcftools/consensus/main.nf index 9b9384a6..4633790e 100644 --- a/modules/bcftools/consensus/main.nf +++ b/modules/bcftools/consensus/main.nf @@ -16,7 +16,7 @@ process BCFTOOLS_CONSENSUS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ cat $fasta | bcftools consensus $vcf $args > ${prefix}.fa header=\$(head -n 1 ${prefix}.fa | sed 's/>//g') diff --git a/modules/bcftools/filter/main.nf b/modules/bcftools/filter/main.nf index 87ad3183..95e0249a 100644 --- a/modules/bcftools/filter/main.nf +++ b/modules/bcftools/filter/main.nf @@ -16,7 +16,7 @@ process BCFTOOLS_FILTER { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ bcftools filter \\ --output ${prefix}.vcf.gz \\ diff --git a/modules/bcftools/index/main.nf b/modules/bcftools/index/main.nf index 8f40c683..0cdebf31 100644 --- a/modules/bcftools/index/main.nf +++ b/modules/bcftools/index/main.nf @@ -17,7 +17,7 @@ process BCFTOOLS_INDEX { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ bcftools \\ diff --git a/modules/bcftools/mpileup/main.nf b/modules/bcftools/mpileup/main.nf index 9d91193c..8a209a66 100644 --- a/modules/bcftools/mpileup/main.nf +++ b/modules/bcftools/mpileup/main.nf @@ -21,7 +21,7 @@ process BCFTOOLS_MPILEUP { def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def args3 = task.ext.args3 ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ echo "${meta.id}" > sample_name.list diff --git a/modules/bcftools/norm/main.nf b/modules/bcftools/norm/main.nf index 79ab36e0..95da56db 100644 --- a/modules/bcftools/norm/main.nf +++ b/modules/bcftools/norm/main.nf @@ -17,7 +17,7 @@ process BCFTOOLS_NORM { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ bcftools norm \\ --fasta-ref ${fasta} \\ diff --git a/modules/bcftools/query/main.nf b/modules/bcftools/query/main.nf index 1919fa76..d1098f99 100644 --- a/modules/bcftools/query/main.nf +++ b/modules/bcftools/query/main.nf @@ -19,7 +19,7 @@ process BCFTOOLS_QUERY { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def regions_file = regions ? "--regions-file ${regions}" : "" def targets_file = targets ? "--targets-file ${targets}" : "" def samples_file = samples ? "--samples-file ${samples}" : "" diff --git a/modules/bcftools/reheader/main.nf b/modules/bcftools/reheader/main.nf index 3cbe2d8f..018431a9 100644 --- a/modules/bcftools/reheader/main.nf +++ b/modules/bcftools/reheader/main.nf @@ -18,7 +18,7 @@ process BCFTOOLS_REHEADER { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def update_sequences = fai ? "-f $fai" : "" def new_header = header ? "-h $header" : "" """ diff --git a/modules/bcftools/stats/main.nf b/modules/bcftools/stats/main.nf index c66f4453..67e8dca7 100644 --- a/modules/bcftools/stats/main.nf +++ b/modules/bcftools/stats/main.nf @@ -16,7 +16,7 @@ process BCFTOOLS_STATS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ bcftools stats $args $vcf > ${prefix}.bcftools_stats.txt cat <<-END_VERSIONS > versions.yml diff --git a/modules/bcftools/view/main.nf b/modules/bcftools/view/main.nf index b2cbb580..f37c1ab9 100644 --- a/modules/bcftools/view/main.nf +++ b/modules/bcftools/view/main.nf @@ -19,7 +19,7 @@ process BCFTOOLS_VIEW { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def regions_file = regions ? "--regions-file ${regions}" : "" def targets_file = targets ? "--targets-file ${targets}" : "" def samples_file = samples ? "--samples-file ${samples}" : "" diff --git a/modules/bedtools/bamtobed/main.nf b/modules/bedtools/bamtobed/main.nf index aebf7339..98d9ea2f 100644 --- a/modules/bedtools/bamtobed/main.nf +++ b/modules/bedtools/bamtobed/main.nf @@ -16,7 +16,7 @@ process BEDTOOLS_BAMTOBED { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ bedtools \\ bamtobed \\ diff --git a/modules/bedtools/complement/main.nf b/modules/bedtools/complement/main.nf index df44b5bc..3146827c 100644 --- a/modules/bedtools/complement/main.nf +++ b/modules/bedtools/complement/main.nf @@ -17,7 +17,7 @@ process BEDTOOLS_COMPLEMENT { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ bedtools \\ complement \\ diff --git a/modules/bedtools/genomecov/main.nf b/modules/bedtools/genomecov/main.nf index e2a74ed3..ca491e75 100644 --- a/modules/bedtools/genomecov/main.nf +++ b/modules/bedtools/genomecov/main.nf @@ -24,7 +24,7 @@ process BEDTOOLS_GENOMECOV { args += " -bg" } - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" if (intervals.name =~ /\.bam/) { """ bedtools \\ diff --git a/modules/bedtools/intersect/main.nf b/modules/bedtools/intersect/main.nf index e01c78ac..afb0d056 100644 --- a/modules/bedtools/intersect/main.nf +++ b/modules/bedtools/intersect/main.nf @@ -17,7 +17,7 @@ process BEDTOOLS_INTERSECT { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ bedtools \\ intersect \\ diff --git a/modules/bedtools/makewindows/main.nf b/modules/bedtools/makewindows/main.nf index cb7d6561..2414393c 100644 --- a/modules/bedtools/makewindows/main.nf +++ b/modules/bedtools/makewindows/main.nf @@ -17,7 +17,7 @@ process BEDTOOLS_MAKEWINDOWS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def arg_input = use_bed ? "-b $regions" : "-g $regions" """ bedtools \\ diff --git a/modules/bedtools/maskfasta/main.nf b/modules/bedtools/maskfasta/main.nf index 77be060c..7eeb4c7d 100644 --- a/modules/bedtools/maskfasta/main.nf +++ b/modules/bedtools/maskfasta/main.nf @@ -17,7 +17,7 @@ process BEDTOOLS_MASKFASTA { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ bedtools \\ maskfasta \\ diff --git a/modules/bedtools/merge/main.nf b/modules/bedtools/merge/main.nf index 907f1c9b..5f1da95b 100644 --- a/modules/bedtools/merge/main.nf +++ b/modules/bedtools/merge/main.nf @@ -16,7 +16,7 @@ process BEDTOOLS_MERGE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ bedtools \\ merge \\ diff --git a/modules/bedtools/slop/main.nf b/modules/bedtools/slop/main.nf index e5d92850..9d8633ec 100644 --- a/modules/bedtools/slop/main.nf +++ b/modules/bedtools/slop/main.nf @@ -17,7 +17,7 @@ process BEDTOOLS_SLOP { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ bedtools \\ slop \\ diff --git a/modules/bedtools/sort/main.nf b/modules/bedtools/sort/main.nf index 15e69036..1ed95a57 100644 --- a/modules/bedtools/sort/main.nf +++ b/modules/bedtools/sort/main.nf @@ -17,7 +17,7 @@ process BEDTOOLS_SORT { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ bedtools \\ sort \\ diff --git a/modules/bedtools/subtract/main.nf b/modules/bedtools/subtract/main.nf index e645109d..b2efefe5 100644 --- a/modules/bedtools/subtract/main.nf +++ b/modules/bedtools/subtract/main.nf @@ -16,7 +16,7 @@ process BEDTOOLS_SUBTRACT { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ bedtools \\ subtract \\ diff --git a/modules/bismark/align/main.nf b/modules/bismark/align/main.nf index 95e7cdfc..e490b48c 100644 --- a/modules/bismark/align/main.nf +++ b/modules/bismark/align/main.nf @@ -19,7 +19,7 @@ process BISMARK_ALIGN { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def fastq = meta.single_end ? reads : "-1 ${reads[0]} -2 ${reads[1]}" """ bismark \\ diff --git a/modules/bismark/deduplicate/main.nf b/modules/bismark/deduplicate/main.nf index c95c54d1..16c624f1 100644 --- a/modules/bismark/deduplicate/main.nf +++ b/modules/bismark/deduplicate/main.nf @@ -17,7 +17,7 @@ process BISMARK_DEDUPLICATE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def seqtype = meta.single_end ? '-s' : '-p' """ deduplicate_bismark \\ diff --git a/modules/blast/blastn/main.nf b/modules/blast/blastn/main.nf index d1bdcf77..3a0bafe0 100644 --- a/modules/blast/blastn/main.nf +++ b/modules/blast/blastn/main.nf @@ -17,7 +17,7 @@ process BLAST_BLASTN { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ DB=`find -L ./ -name "*.ndb" | sed 's/.ndb//'` blastn \\ diff --git a/modules/bowtie/align/main.nf b/modules/bowtie/align/main.nf index 12188269..b25b5e21 100644 --- a/modules/bowtie/align/main.nf +++ b/modules/bowtie/align/main.nf @@ -20,7 +20,7 @@ process BOWTIE_ALIGN { script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def unaligned = params.save_unaligned ? "--un ${prefix}.unmapped.fastq" : '' def endedness = meta.single_end ? "$reads" : "-1 ${reads[0]} -2 ${reads[1]}" """ diff --git a/modules/bowtie2/align/main.nf b/modules/bowtie2/align/main.nf index 11c9c20a..41c8a6bf 100644 --- a/modules/bowtie2/align/main.nf +++ b/modules/bowtie2/align/main.nf @@ -20,7 +20,7 @@ process BOWTIE2_ALIGN { script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" if (meta.single_end) { def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : '' """ diff --git a/modules/bwa/aln/main.nf b/modules/bwa/aln/main.nf index f6cdaefa..992e25de 100644 --- a/modules/bwa/aln/main.nf +++ b/modules/bwa/aln/main.nf @@ -17,7 +17,7 @@ process BWA_ALN { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" if (meta.single_end) { """ diff --git a/modules/bwa/mem/main.nf b/modules/bwa/mem/main.nf index 9a04ed63..801293a8 100644 --- a/modules/bwa/mem/main.nf +++ b/modules/bwa/mem/main.nf @@ -18,7 +18,7 @@ process BWA_MEM { script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def read_group = meta.read_group ? "-R ${meta.read_group}" : "" """ INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'` diff --git a/modules/bwa/sampe/main.nf b/modules/bwa/sampe/main.nf index 2abd9335..0b5ec255 100644 --- a/modules/bwa/sampe/main.nf +++ b/modules/bwa/sampe/main.nf @@ -17,7 +17,7 @@ process BWA_SAMPE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def read_group = meta.read_group ? "-r ${meta.read_group}" : "" """ diff --git a/modules/bwa/samse/main.nf b/modules/bwa/samse/main.nf index 56e9127f..bee06bc8 100644 --- a/modules/bwa/samse/main.nf +++ b/modules/bwa/samse/main.nf @@ -17,7 +17,7 @@ process BWA_SAMSE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def read_group = meta.read_group ? "-r ${meta.read_group}" : "" """ diff --git a/modules/bwamem2/mem/main.nf b/modules/bwamem2/mem/main.nf index 7c238741..81b4b8ab 100644 --- a/modules/bwamem2/mem/main.nf +++ b/modules/bwamem2/mem/main.nf @@ -18,7 +18,7 @@ process BWAMEM2_MEM { script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def read_group = meta.read_group ? "-R ${meta.read_group}" : "" """ INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'` diff --git a/modules/bwameth/align/main.nf b/modules/bwameth/align/main.nf index 06e9da44..0bcd9bac 100644 --- a/modules/bwameth/align/main.nf +++ b/modules/bwameth/align/main.nf @@ -18,7 +18,7 @@ process BWAMETH_ALIGN { script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def read_group = meta.read_group ? "-R ${meta.read_group}" : "" """ INDEX=`find -L ${index} -name "*.bwameth.c2t" | sed 's/.bwameth.c2t//'` diff --git a/modules/cat/fastq/main.nf b/modules/cat/fastq/main.nf index b6be93b0..c5ece83a 100644 --- a/modules/cat/fastq/main.nf +++ b/modules/cat/fastq/main.nf @@ -16,7 +16,7 @@ process CAT_FASTQ { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def readList = reads.collect{ it.toString() } if (meta.single_end) { if (readList.size > 1) { diff --git a/modules/chromap/chromap/main.nf b/modules/chromap/chromap/main.nf index f6686cf2..4a7f0097 100644 --- a/modules/chromap/chromap/main.nf +++ b/modules/chromap/chromap/main.nf @@ -28,7 +28,7 @@ process CHROMAP_CHROMAP { script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def args_list = args.tokenize() def file_extension = args.contains("--SAM") ? 'sam' : args.contains("--TagAlign")? 'tagAlign' : args.contains("--pairs")? 'pairs' : 'bed' diff --git a/modules/clonalframeml/main.nf b/modules/clonalframeml/main.nf index 60eaad12..db647a38 100644 --- a/modules/clonalframeml/main.nf +++ b/modules/clonalframeml/main.nf @@ -21,7 +21,7 @@ process CLONALFRAMEML { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ ClonalFrameML \\ $newick \\ diff --git a/modules/cmseq/polymut/main.nf b/modules/cmseq/polymut/main.nf index 18bb8c59..47e86f0c 100644 --- a/modules/cmseq/polymut/main.nf +++ b/modules/cmseq/polymut/main.nf @@ -18,7 +18,7 @@ process CMSEQ_POLYMUT { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def fasta_refid = fasta ? "-c $fasta" : "" def sortindex = bai ? "" : "--sortindex" """ diff --git a/modules/cooler/cload/main.nf b/modules/cooler/cload/main.nf index ed7a41a1..d8bdc031 100644 --- a/modules/cooler/cload/main.nf +++ b/modules/cooler/cload/main.nf @@ -18,7 +18,7 @@ process COOLER_CLOAD { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def nproc = args.contains('pairix') || args.contains('tabix')? "--nproc $task.cpus" : '' """ diff --git a/modules/cooler/dump/main.nf b/modules/cooler/dump/main.nf index 0836640e..a438acc8 100644 --- a/modules/cooler/dump/main.nf +++ b/modules/cooler/dump/main.nf @@ -17,7 +17,7 @@ process COOLER_DUMP { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def suffix = resolution ? "::$resolution" : "" """ cooler dump \\ diff --git a/modules/cooler/merge/main.nf b/modules/cooler/merge/main.nf index 0fed76c9..b1814b68 100644 --- a/modules/cooler/merge/main.nf +++ b/modules/cooler/merge/main.nf @@ -16,7 +16,7 @@ process COOLER_MERGE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ cooler merge \\ $args \\ diff --git a/modules/cooler/zoomify/main.nf b/modules/cooler/zoomify/main.nf index e61ca99d..226d4114 100644 --- a/modules/cooler/zoomify/main.nf +++ b/modules/cooler/zoomify/main.nf @@ -16,7 +16,7 @@ process COOLER_ZOOMIFY { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ cooler zoomify \\ $args \\ diff --git a/modules/csvtk/split/main.nf b/modules/csvtk/split/main.nf index 89b44154..52ab7ec7 100644 --- a/modules/csvtk/split/main.nf +++ b/modules/csvtk/split/main.nf @@ -18,7 +18,7 @@ process CSVTK_SPLIT { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def delimiter = in_format == "tsv" ? "--tabs" : (in_format == "csv" ? "--delimiter ',' " : in_format) def out_delimiter = out_format == "tsv" ? "--out-tabs" : (out_format == "csv" ? "--out-delimiter ',' " : out_format) out_extension = out_format == "tsv" ? 'tsv' : 'csv' diff --git a/modules/cutadapt/main.nf b/modules/cutadapt/main.nf index f98113e8..89105715 100644 --- a/modules/cutadapt/main.nf +++ b/modules/cutadapt/main.nf @@ -17,7 +17,7 @@ process CUTADAPT { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def trimmed = meta.single_end ? "-o ${prefix}.trim.fastq.gz" : "-o ${prefix}_1.trim.fastq.gz -p ${prefix}_2.trim.fastq.gz" """ cutadapt \\ diff --git a/modules/dastool/dastool/main.nf b/modules/dastool/dastool/main.nf index b67ee993..722f6c55 100644 --- a/modules/dastool/dastool/main.nf +++ b/modules/dastool/dastool/main.nf @@ -28,7 +28,7 @@ process DASTOOL_DASTOOL { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def bin_list = bins instanceof List ? bins.join(",") : "$bins" def engine = search_engine ? "--search_engine $search_engine" : "--search_engine diamond" def db_dir = db_directory ? "--db_directory $db_directory" : "" diff --git a/modules/dastool/scaffolds2bin/main.nf b/modules/dastool/scaffolds2bin/main.nf index 78a06b6e..09f800bb 100644 --- a/modules/dastool/scaffolds2bin/main.nf +++ b/modules/dastool/scaffolds2bin/main.nf @@ -17,7 +17,7 @@ process DASTOOL_SCAFFOLDS2BIN { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def file_extension = extension ? extension : "fasta" """ diff --git a/modules/deeptools/computematrix/main.nf b/modules/deeptools/computematrix/main.nf index e39310f4..70be934b 100644 --- a/modules/deeptools/computematrix/main.nf +++ b/modules/deeptools/computematrix/main.nf @@ -18,7 +18,7 @@ process DEEPTOOLS_COMPUTEMATRIX { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ computeMatrix \\ $args \\ diff --git a/modules/deeptools/plotfingerprint/main.nf b/modules/deeptools/plotfingerprint/main.nf index aeb635ce..7925c9a9 100644 --- a/modules/deeptools/plotfingerprint/main.nf +++ b/modules/deeptools/plotfingerprint/main.nf @@ -18,7 +18,7 @@ process DEEPTOOLS_PLOTFINGERPRINT { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def extend = (meta.single_end && params.fragment_size > 0) ? "--extendReads ${params.fragment_size}" : '' """ plotFingerprint \\ diff --git a/modules/deeptools/plotheatmap/main.nf b/modules/deeptools/plotheatmap/main.nf index f981744e..992c9058 100644 --- a/modules/deeptools/plotheatmap/main.nf +++ b/modules/deeptools/plotheatmap/main.nf @@ -17,7 +17,7 @@ process DEEPTOOLS_PLOTHEATMAP { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ plotHeatmap \\ $args \\ diff --git a/modules/deeptools/plotprofile/main.nf b/modules/deeptools/plotprofile/main.nf index b32e04d3..60184fa6 100644 --- a/modules/deeptools/plotprofile/main.nf +++ b/modules/deeptools/plotprofile/main.nf @@ -17,7 +17,7 @@ process DEEPTOOLS_PLOTPROFILE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ plotProfile \\ $args \\ diff --git a/modules/delly/call/main.nf b/modules/delly/call/main.nf index d4aa1adb..fc04cda7 100644 --- a/modules/delly/call/main.nf +++ b/modules/delly/call/main.nf @@ -19,7 +19,7 @@ process DELLY_CALL { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ delly \\ call \\ diff --git a/modules/diamond/blastp/main.nf b/modules/diamond/blastp/main.nf index 015be864..c7342767 100644 --- a/modules/diamond/blastp/main.nf +++ b/modules/diamond/blastp/main.nf @@ -19,7 +19,7 @@ process DIAMOND_BLASTP { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'` diff --git a/modules/diamond/blastx/main.nf b/modules/diamond/blastx/main.nf index f4018aa9..bd7d1dd9 100644 --- a/modules/diamond/blastx/main.nf +++ b/modules/diamond/blastx/main.nf @@ -19,7 +19,7 @@ process DIAMOND_BLASTX { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'` diff --git a/modules/dshbio/exportsegments/main.nf b/modules/dshbio/exportsegments/main.nf index 7cc5da22..d506a4b6 100644 --- a/modules/dshbio/exportsegments/main.nf +++ b/modules/dshbio/exportsegments/main.nf @@ -16,7 +16,7 @@ process DSHBIO_EXPORTSEGMENTS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ dsh-bio \\ export-segments \\ diff --git a/modules/dshbio/filterbed/main.nf b/modules/dshbio/filterbed/main.nf index 065d8bec..6480f4a4 100644 --- a/modules/dshbio/filterbed/main.nf +++ b/modules/dshbio/filterbed/main.nf @@ -16,7 +16,7 @@ process DSHBIO_FILTERBED { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ dsh-bio \\ filter-bed \\ diff --git a/modules/dshbio/filtergff3/main.nf b/modules/dshbio/filtergff3/main.nf index c738c95a..a0bbf3af 100644 --- a/modules/dshbio/filtergff3/main.nf +++ b/modules/dshbio/filtergff3/main.nf @@ -16,7 +16,7 @@ process DSHBIO_FILTERGFF3 { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ dsh-bio \\ filter-gff3 \\ diff --git a/modules/dshbio/splitbed/main.nf b/modules/dshbio/splitbed/main.nf index 60b8b7a3..8dbf1104 100644 --- a/modules/dshbio/splitbed/main.nf +++ b/modules/dshbio/splitbed/main.nf @@ -16,7 +16,7 @@ process DSHBIO_SPLITBED { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ dsh-bio \\ split-bed \\ diff --git a/modules/dshbio/splitgff3/main.nf b/modules/dshbio/splitgff3/main.nf index 7ad2fd08..fc868a39 100644 --- a/modules/dshbio/splitgff3/main.nf +++ b/modules/dshbio/splitgff3/main.nf @@ -16,7 +16,7 @@ process DSHBIO_SPLITGFF3 { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ dsh-bio \\ split-gff3 \\ diff --git a/modules/ectyper/main.nf b/modules/ectyper/main.nf index 5f458eb9..0e040958 100644 --- a/modules/ectyper/main.nf +++ b/modules/ectyper/main.nf @@ -18,7 +18,7 @@ process ECTYPER { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def is_compressed = fasta.getName().endsWith(".gz") ? true : false def fasta_name = fasta.getName().replace(".gz", "") """ diff --git a/modules/emmtyper/main.nf b/modules/emmtyper/main.nf index 9cf98694..70dabfb7 100644 --- a/modules/emmtyper/main.nf +++ b/modules/emmtyper/main.nf @@ -16,7 +16,7 @@ process EMMTYPER { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ emmtyper \\ $args \\ diff --git a/modules/ensemblvep/main.nf b/modules/ensemblvep/main.nf index 76cd9235..3182feb2 100644 --- a/modules/ensemblvep/main.nf +++ b/modules/ensemblvep/main.nf @@ -24,7 +24,7 @@ process ENSEMBLVEP { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def dir_cache = task.ext.use_cache ? "\${PWD}/${cache}" : "/.vep" """ mkdir $prefix diff --git a/modules/expansionhunter/main.nf b/modules/expansionhunter/main.nf index 2ef00d17..4db78230 100644 --- a/modules/expansionhunter/main.nf +++ b/modules/expansionhunter/main.nf @@ -18,7 +18,7 @@ process EXPANSIONHUNTER { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def gender = (meta.gender == 'male' || meta.gender == 1 || meta.gender == 'XY') ? "male" : "female" """ ExpansionHunter \\ diff --git a/modules/fastani/main.nf b/modules/fastani/main.nf index 7e3721bd..cc1c4902 100644 --- a/modules/fastani/main.nf +++ b/modules/fastani/main.nf @@ -17,7 +17,7 @@ process FASTANI { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" if (meta.batch_input) { """ diff --git a/modules/fastp/main.nf b/modules/fastp/main.nf index 05eb1e98..33603842 100644 --- a/modules/fastp/main.nf +++ b/modules/fastp/main.nf @@ -24,7 +24,7 @@ process FASTP { script: def args = task.ext.args ?: '' // Added soft-links to original fastqs for consistent naming in MultiQC - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" if (meta.single_end) { def fail_fastq = save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : '' """ diff --git a/modules/fastqc/main.nf b/modules/fastqc/main.nf index 673a00b8..d250eca0 100644 --- a/modules/fastqc/main.nf +++ b/modules/fastqc/main.nf @@ -18,7 +18,7 @@ process FASTQC { script: def args = task.ext.args ?: '' // Add soft-links to original FastQs for consistent naming in pipeline - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" if (meta.single_end) { """ [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz diff --git a/modules/fastqscan/main.nf b/modules/fastqscan/main.nf index 768728f2..a0dcc46a 100644 --- a/modules/fastqscan/main.nf +++ b/modules/fastqscan/main.nf @@ -16,7 +16,7 @@ process FASTQSCAN { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ zcat $reads | \\ fastq-scan \\ diff --git a/modules/fgbio/callmolecularconsensusreads/main.nf b/modules/fgbio/callmolecularconsensusreads/main.nf index f514b69a..3aab935b 100644 --- a/modules/fgbio/callmolecularconsensusreads/main.nf +++ b/modules/fgbio/callmolecularconsensusreads/main.nf @@ -16,7 +16,7 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ fgbio \\ CallMolecularConsensusReads \\ diff --git a/modules/fgbio/fastqtobam/main.nf b/modules/fgbio/fastqtobam/main.nf index 40713d03..126c3dd8 100644 --- a/modules/fgbio/fastqtobam/main.nf +++ b/modules/fgbio/fastqtobam/main.nf @@ -17,7 +17,7 @@ process FGBIO_FASTQTOBAM { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ mkdir tmp diff --git a/modules/fgbio/groupreadsbyumi/main.nf b/modules/fgbio/groupreadsbyumi/main.nf index b35186a5..47f000a5 100644 --- a/modules/fgbio/groupreadsbyumi/main.nf +++ b/modules/fgbio/groupreadsbyumi/main.nf @@ -18,7 +18,7 @@ process FGBIO_GROUPREADSBYUMI { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ mkdir tmp diff --git a/modules/fgbio/sortbam/main.nf b/modules/fgbio/sortbam/main.nf index c2822548..c542f3df 100644 --- a/modules/fgbio/sortbam/main.nf +++ b/modules/fgbio/sortbam/main.nf @@ -16,7 +16,7 @@ process FGBIO_SORTBAM { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ fgbio \\ SortBam \\ diff --git a/modules/filtlong/main.nf b/modules/filtlong/main.nf index 10e147a6..bb1c1eb3 100644 --- a/modules/filtlong/main.nf +++ b/modules/filtlong/main.nf @@ -16,7 +16,7 @@ process FILTLONG { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def short_reads = meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}" """ filtlong \\ diff --git a/modules/flash/main.nf b/modules/flash/main.nf index 23bd1892..7bc38c97 100644 --- a/modules/flash/main.nf +++ b/modules/flash/main.nf @@ -15,7 +15,7 @@ process FLASH { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ flash \\ $args \\ diff --git a/modules/freebayes/main.nf b/modules/freebayes/main.nf index b9a63d02..1dd91fef 100644 --- a/modules/freebayes/main.nf +++ b/modules/freebayes/main.nf @@ -22,7 +22,7 @@ process FREEBAYES { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def input = input_2 ? "${input_1} ${input_2}" : "${input_1}" def targets_file = targets ? "--target ${targets}" : "" def samples_file = samples ? "--samples ${samples}" : "" diff --git a/modules/gatk4/applybqsr/main.nf b/modules/gatk4/applybqsr/main.nf index f93dd574..bd428d6c 100644 --- a/modules/gatk4/applybqsr/main.nf +++ b/modules/gatk4/applybqsr/main.nf @@ -20,7 +20,7 @@ process GATK4_APPLYBQSR { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def interval = intervals ? "-L ${intervals}" : "" if (!task.memory) { log.info '[GATK ApplyBQSR] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' diff --git a/modules/gatk4/baserecalibrator/main.nf b/modules/gatk4/baserecalibrator/main.nf index b422a798..9b0bf286 100644 --- a/modules/gatk4/baserecalibrator/main.nf +++ b/modules/gatk4/baserecalibrator/main.nf @@ -22,7 +22,7 @@ process GATK4_BASERECALIBRATOR { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def intervalsCommand = intervalsBed ? "-L ${intervalsBed}" : "" def sitesCommand = knownSites.collect{"--known-sites ${it}"}.join(' ') diff --git a/modules/gatk4/bedtointervallist/main.nf b/modules/gatk4/bedtointervallist/main.nf index 77819a0f..c4538034 100644 --- a/modules/gatk4/bedtointervallist/main.nf +++ b/modules/gatk4/bedtointervallist/main.nf @@ -17,7 +17,7 @@ process GATK4_BEDTOINTERVALLIST { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ gatk BedToIntervalList \\ -I $bed \\ diff --git a/modules/gatk4/calculatecontamination/main.nf b/modules/gatk4/calculatecontamination/main.nf index 93a2ee57..7c112c3c 100644 --- a/modules/gatk4/calculatecontamination/main.nf +++ b/modules/gatk4/calculatecontamination/main.nf @@ -18,7 +18,7 @@ process GATK4_CALCULATECONTAMINATION { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def matched_command = matched ? " -matched ${matched} " : '' def segment_command = segmentout ? " -segments ${prefix}.segmentation.table" : '' """ diff --git a/modules/gatk4/createsomaticpanelofnormals/main.nf b/modules/gatk4/createsomaticpanelofnormals/main.nf index 9bc8d1d0..2860e82e 100644 --- a/modules/gatk4/createsomaticpanelofnormals/main.nf +++ b/modules/gatk4/createsomaticpanelofnormals/main.nf @@ -20,7 +20,7 @@ process GATK4_CREATESOMATICPANELOFNORMALS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ gatk \\ CreateSomaticPanelOfNormals \\ diff --git a/modules/gatk4/estimatelibrarycomplexity/main.nf b/modules/gatk4/estimatelibrarycomplexity/main.nf index b0b35e42..f636dc46 100644 --- a/modules/gatk4/estimatelibrarycomplexity/main.nf +++ b/modules/gatk4/estimatelibrarycomplexity/main.nf @@ -19,7 +19,7 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def crams = cram.collect(){ x -> "-I ".concat(x.toString()) }.join(" ") def avail_mem = 3 diff --git a/modules/gatk4/fastqtosam/main.nf b/modules/gatk4/fastqtosam/main.nf index fc075735..915eb996 100644 --- a/modules/gatk4/fastqtosam/main.nf +++ b/modules/gatk4/fastqtosam/main.nf @@ -16,7 +16,7 @@ process GATK4_FASTQTOSAM { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def read_files = meta.single_end ? "-F1 $reads" : "-F1 ${reads[0]} -F2 ${reads[1]}" """ gatk FastqToSam \\ diff --git a/modules/gatk4/filtermutectcalls/main.nf b/modules/gatk4/filtermutectcalls/main.nf index 7111db37..02fa804f 100644 --- a/modules/gatk4/filtermutectcalls/main.nf +++ b/modules/gatk4/filtermutectcalls/main.nf @@ -21,7 +21,7 @@ process GATK4_FILTERMUTECTCALLS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def orientationbias_options = '' if (orientationbias) { diff --git a/modules/gatk4/genotypegvcfs/main.nf b/modules/gatk4/genotypegvcfs/main.nf index ddb4a922..f0b35447 100644 --- a/modules/gatk4/genotypegvcfs/main.nf +++ b/modules/gatk4/genotypegvcfs/main.nf @@ -22,7 +22,7 @@ process GATK4_GENOTYPEGVCFS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def dbsnp_options = dbsnp ? "-D ${dbsnp}" : "" def interval_options = intervals_bed ? "-L ${intervals_bed}" : "" def gvcf_options = gvcf.name.endsWith(".vcf") || gvcf.name.endsWith(".vcf.gz") ? "$gvcf" : "gendb://$gvcf" diff --git a/modules/gatk4/getpileupsummaries/main.nf b/modules/gatk4/getpileupsummaries/main.nf index 0894e17b..99be601f 100644 --- a/modules/gatk4/getpileupsummaries/main.nf +++ b/modules/gatk4/getpileupsummaries/main.nf @@ -19,7 +19,7 @@ process GATK4_GETPILEUPSUMMARIES { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def sitesCommand = '' sitesCommand = sites ? " -L ${sites} " : " -L ${variants} " diff --git a/modules/gatk4/haplotypecaller/main.nf b/modules/gatk4/haplotypecaller/main.nf index 418a2785..e00f1e58 100644 --- a/modules/gatk4/haplotypecaller/main.nf +++ b/modules/gatk4/haplotypecaller/main.nf @@ -23,7 +23,7 @@ process GATK4_HAPLOTYPECALLER { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def interval_option = interval ? "-L ${interval}" : "" def dbsnp_option = dbsnp ? "-D ${dbsnp}" : "" def avail_mem = 3 diff --git a/modules/gatk4/intervallisttools/main.nf b/modules/gatk4/intervallisttools/main.nf index 8e5b70e1..7e1a47f7 100644 --- a/modules/gatk4/intervallisttools/main.nf +++ b/modules/gatk4/intervallisttools/main.nf @@ -16,7 +16,7 @@ process GATK4_INTERVALLISTTOOLS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ mkdir ${prefix}_split diff --git a/modules/gatk4/learnreadorientationmodel/main.nf b/modules/gatk4/learnreadorientationmodel/main.nf index 5e9700e3..ac021afa 100644 --- a/modules/gatk4/learnreadorientationmodel/main.nf +++ b/modules/gatk4/learnreadorientationmodel/main.nf @@ -16,7 +16,7 @@ process GATK4_LEARNREADORIENTATIONMODEL { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def inputs_list = [] f1r2.each() { a -> inputs_list.add(" -I " + a) } """ diff --git a/modules/gatk4/markduplicates/main.nf b/modules/gatk4/markduplicates/main.nf index 9f0b46da..a109facc 100644 --- a/modules/gatk4/markduplicates/main.nf +++ b/modules/gatk4/markduplicates/main.nf @@ -18,7 +18,7 @@ process GATK4_MARKDUPLICATES { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def bam_list = bams.collect(){ bam -> "--INPUT ".concat(bam.toString()) }.join(" ") def avail_mem = 3 if (!task.memory) { diff --git a/modules/gatk4/mergebamalignment/main.nf b/modules/gatk4/mergebamalignment/main.nf index 01effb0f..5e552cb2 100644 --- a/modules/gatk4/mergebamalignment/main.nf +++ b/modules/gatk4/mergebamalignment/main.nf @@ -19,7 +19,7 @@ process GATK4_MERGEBAMALIGNMENT { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ gatk MergeBamAlignment \\ ALIGNED=$aligned \\ diff --git a/modules/gatk4/mergevcfs/main.nf b/modules/gatk4/mergevcfs/main.nf index cbfc2e9d..cd1840c3 100644 --- a/modules/gatk4/mergevcfs/main.nf +++ b/modules/gatk4/mergevcfs/main.nf @@ -18,7 +18,7 @@ process GATK4_MERGEVCFS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" // Make list of VCFs to merge def input = "" diff --git a/modules/gatk4/mutect2/main.nf b/modules/gatk4/mutect2/main.nf index 662b3f0c..2cf940de 100644 --- a/modules/gatk4/mutect2/main.nf +++ b/modules/gatk4/mutect2/main.nf @@ -30,7 +30,7 @@ process GATK4_MUTECT2 { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def panels_command = '' def normals_command = '' diff --git a/modules/gatk4/revertsam/main.nf b/modules/gatk4/revertsam/main.nf index bca31a29..638b7705 100644 --- a/modules/gatk4/revertsam/main.nf +++ b/modules/gatk4/revertsam/main.nf @@ -16,7 +16,7 @@ process GATK4_REVERTSAM { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ gatk RevertSam \\ I=$bam \\ diff --git a/modules/gatk4/samtofastq/main.nf b/modules/gatk4/samtofastq/main.nf index aa9a6b2d..a909f540 100644 --- a/modules/gatk4/samtofastq/main.nf +++ b/modules/gatk4/samtofastq/main.nf @@ -16,7 +16,7 @@ process GATK4_SAMTOFASTQ { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def output = meta.single_end ? "FASTQ=${prefix}.fastq.gz" : "FASTQ=${prefix}_1.fastq.gz SECOND_END_FASTQ=${prefix}_2.fastq.gz" """ gatk SamToFastq \\ diff --git a/modules/gatk4/splitncigarreads/main.nf b/modules/gatk4/splitncigarreads/main.nf index 32d36df9..65b82a35 100644 --- a/modules/gatk4/splitncigarreads/main.nf +++ b/modules/gatk4/splitncigarreads/main.nf @@ -19,7 +19,7 @@ process GATK4_SPLITNCIGARREADS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ gatk SplitNCigarReads \\ -R $fasta \\ diff --git a/modules/gatk4/variantfiltration/main.nf b/modules/gatk4/variantfiltration/main.nf index d5cc1eb3..00dc2588 100644 --- a/modules/gatk4/variantfiltration/main.nf +++ b/modules/gatk4/variantfiltration/main.nf @@ -20,7 +20,7 @@ process GATK4_VARIANTFILTRATION { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def avail_mem = 3 if (!task.memory) { log.info '[GATK HaplotypeCaller] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' diff --git a/modules/genrich/main.nf b/modules/genrich/main.nf index dfbebd3a..d9deea3c 100644 --- a/modules/genrich/main.nf +++ b/modules/genrich/main.nf @@ -26,7 +26,7 @@ process GENRICH { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def control = control_bam ? "-c $control_bam" : '' def blacklist = blacklist_bed ? "-E $blacklist_bed" : "" def pvalues = save_pvalues ? "-f ${prefix}.pvalues.bedGraph" : "" diff --git a/modules/glnexus/main.nf b/modules/glnexus/main.nf index e36729b2..b8afca22 100644 --- a/modules/glnexus/main.nf +++ b/modules/glnexus/main.nf @@ -16,7 +16,7 @@ process GLNEXUS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" // Make list of GVCFs to merge def input = gvcfs.collect { it.toString() } diff --git a/modules/graphmap2/align/main.nf b/modules/graphmap2/align/main.nf index e0f2d4cd..554e585b 100644 --- a/modules/graphmap2/align/main.nf +++ b/modules/graphmap2/align/main.nf @@ -19,7 +19,7 @@ process GRAPHMAP2_ALIGN { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ graphmap2 \\ align \\ diff --git a/modules/gstama/collapse/main.nf b/modules/gstama/collapse/main.nf index d8a64113..1c06692d 100644 --- a/modules/gstama/collapse/main.nf +++ b/modules/gstama/collapse/main.nf @@ -26,7 +26,7 @@ process GSTAMA_COLLAPSE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ tama_collapse.py \\ -s $bam \\ diff --git a/modules/gstama/merge/main.nf b/modules/gstama/merge/main.nf index 4a8e829c..53ff93e4 100644 --- a/modules/gstama/merge/main.nf +++ b/modules/gstama/merge/main.nf @@ -20,7 +20,7 @@ process GSTAMA_MERGE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ tama_merge.py \\ -f $filelist \\ diff --git a/modules/gunc/run/main.nf b/modules/gunc/run/main.nf index 6ac681ad..8508c9f0 100644 --- a/modules/gunc/run/main.nf +++ b/modules/gunc/run/main.nf @@ -18,7 +18,7 @@ process GUNC_RUN { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ gunc \\ run \\ diff --git a/modules/hicap/main.nf b/modules/hicap/main.nf index ed1d7797..a96343f6 100644 --- a/modules/hicap/main.nf +++ b/modules/hicap/main.nf @@ -20,7 +20,7 @@ process HICAP { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def database_args = database_dir ? "--database_dir ${database_dir}" : "" def model_args = model_fp ? "--model_fp ${model_fp}" : "" def is_compressed = fasta.getName().endsWith(".gz") ? true : false diff --git a/modules/hifiasm/main.nf b/modules/hifiasm/main.nf index 7fc857f1..208554d6 100644 --- a/modules/hifiasm/main.nf +++ b/modules/hifiasm/main.nf @@ -27,7 +27,7 @@ process HIFIASM { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" if (use_parental_kmers) { """ hifiasm \\ diff --git a/modules/hisat2/align/main.nf b/modules/hisat2/align/main.nf index 0c5f4134..ae888616 100644 --- a/modules/hisat2/align/main.nf +++ b/modules/hisat2/align/main.nf @@ -22,7 +22,7 @@ process HISAT2_ALIGN { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def strandedness = '' if (meta.strandedness == 'forward') { diff --git a/modules/hmmcopy/readcounter/main.nf b/modules/hmmcopy/readcounter/main.nf index 6cd776a1..6399b1a2 100644 --- a/modules/hmmcopy/readcounter/main.nf +++ b/modules/hmmcopy/readcounter/main.nf @@ -18,7 +18,7 @@ process HMMCOPY_READCOUNTER { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ readCounter \\ $args \\ diff --git a/modules/hmmer/hmmalign/main.nf b/modules/hmmer/hmmalign/main.nf index a25871e8..e6d04044 100644 --- a/modules/hmmer/hmmalign/main.nf +++ b/modules/hmmer/hmmalign/main.nf @@ -17,7 +17,7 @@ process HMMER_HMMALIGN { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def fastacmd = fasta.getExtension() == 'gz' ? "gunzip -c $fasta" : "cat $fasta" """ $fastacmd | \\ diff --git a/modules/homer/annotatepeaks/main.nf b/modules/homer/annotatepeaks/main.nf index 321dbc7c..84e0241a 100644 --- a/modules/homer/annotatepeaks/main.nf +++ b/modules/homer/annotatepeaks/main.nf @@ -20,7 +20,7 @@ process HOMER_ANNOTATEPEAKS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ annotatePeaks.pl \\ $peak \\ diff --git a/modules/homer/findpeaks/main.nf b/modules/homer/findpeaks/main.nf index a39fe753..66de06b6 100644 --- a/modules/homer/findpeaks/main.nf +++ b/modules/homer/findpeaks/main.nf @@ -18,7 +18,7 @@ process HOMER_FINDPEAKS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ findPeaks \\ diff --git a/modules/homer/maketagdirectory/main.nf b/modules/homer/maketagdirectory/main.nf index 44490d50..72e2091f 100644 --- a/modules/homer/maketagdirectory/main.nf +++ b/modules/homer/maketagdirectory/main.nf @@ -19,7 +19,7 @@ process HOMER_MAKETAGDIRECTORY { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ makeTagDirectory \\ tag_dir \\ diff --git a/modules/homer/makeucscfile/main.nf b/modules/homer/makeucscfile/main.nf index 8a0e3f37..17e86947 100644 --- a/modules/homer/makeucscfile/main.nf +++ b/modules/homer/makeucscfile/main.nf @@ -18,7 +18,7 @@ process HOMER_MAKEUCSCFILE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ makeUCSCfile \\ $tagDir \\ diff --git a/modules/imputeme/vcftoprs/main.nf b/modules/imputeme/vcftoprs/main.nf index 0c8c1952..5fee90c2 100644 --- a/modules/imputeme/vcftoprs/main.nf +++ b/modules/imputeme/vcftoprs/main.nf @@ -16,7 +16,7 @@ process IMPUTEME_VCFTOPRS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ #!/usr/bin/env Rscript diff --git a/modules/ismapper/main.nf b/modules/ismapper/main.nf index 4a33261b..a51cc01e 100644 --- a/modules/ismapper/main.nf +++ b/modules/ismapper/main.nf @@ -16,7 +16,7 @@ process ISMAPPER { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ ismap \\ $args \\ diff --git a/modules/isoseq3/cluster/main.nf b/modules/isoseq3/cluster/main.nf index 27d5c3d8..fdd47971 100644 --- a/modules/isoseq3/cluster/main.nf +++ b/modules/isoseq3/cluster/main.nf @@ -26,7 +26,7 @@ process ISOSEQ3_CLUSTER { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ isoseq3 \\ cluster \\ diff --git a/modules/isoseq3/refine/main.nf b/modules/isoseq3/refine/main.nf index 5bde2f8f..5044cba2 100644 --- a/modules/isoseq3/refine/main.nf +++ b/modules/isoseq3/refine/main.nf @@ -21,7 +21,7 @@ process ISOSEQ3_REFINE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ isoseq3 \\ refine \\ diff --git a/modules/ivar/consensus/main.nf b/modules/ivar/consensus/main.nf index 4a657756..58d97c8c 100644 --- a/modules/ivar/consensus/main.nf +++ b/modules/ivar/consensus/main.nf @@ -20,7 +20,7 @@ process IVAR_CONSENSUS { script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : "" """ samtools mpileup \\ diff --git a/modules/ivar/trim/main.nf b/modules/ivar/trim/main.nf index 35798123..4d0c70a2 100644 --- a/modules/ivar/trim/main.nf +++ b/modules/ivar/trim/main.nf @@ -18,7 +18,7 @@ process IVAR_TRIM { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ ivar trim \\ $args \\ diff --git a/modules/ivar/variants/main.nf b/modules/ivar/variants/main.nf index ba791307..ce4abd4d 100644 --- a/modules/ivar/variants/main.nf +++ b/modules/ivar/variants/main.nf @@ -20,7 +20,7 @@ process IVAR_VARIANTS { script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : "" def features = params.gff ? "-g $gff" : "" """ diff --git a/modules/jupyternotebook/main.nf b/modules/jupyternotebook/main.nf index 02f1947f..e4bdf98b 100644 --- a/modules/jupyternotebook/main.nf +++ b/modules/jupyternotebook/main.nf @@ -24,7 +24,7 @@ process JUPYTERNOTEBOOK { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def parametrize = (task.ext.parametrize == null) ? true : task.ext.parametrize def implicit_params = (task.ext.implicit_params == null) ? true : task.ext.implicit_params def meta_params = (task.ext.meta_params == null) ? true : task.ext.meta_params diff --git a/modules/kallistobustools/count/main.nf b/modules/kallistobustools/count/main.nf index 00ca8971..d67eba31 100644 --- a/modules/kallistobustools/count/main.nf +++ b/modules/kallistobustools/count/main.nf @@ -22,7 +22,7 @@ process KALLISTOBUSTOOLS_COUNT { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def cdna = t1c ? "-c1 $t1c" : '' def introns = t2c ? "-c2 $t2c" : '' """ diff --git a/modules/kleborate/main.nf b/modules/kleborate/main.nf index b64a0c45..998eced1 100644 --- a/modules/kleborate/main.nf +++ b/modules/kleborate/main.nf @@ -16,7 +16,7 @@ process KLEBORATE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ kleborate \\ $args \\ diff --git a/modules/kraken2/kraken2/main.nf b/modules/kraken2/kraken2/main.nf index e5fb4b80..3c4d1caf 100644 --- a/modules/kraken2/kraken2/main.nf +++ b/modules/kraken2/kraken2/main.nf @@ -19,7 +19,7 @@ process KRAKEN2_KRAKEN2 { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def paired = meta.single_end ? "" : "--paired" def classified = meta.single_end ? "${prefix}.classified.fastq" : "${prefix}.classified#.fastq" def unclassified = meta.single_end ? "${prefix}.unclassified.fastq" : "${prefix}.unclassified#.fastq" diff --git a/modules/last/dotplot/main.nf b/modules/last/dotplot/main.nf index 51667378..e8857403 100644 --- a/modules/last/dotplot/main.nf +++ b/modules/last/dotplot/main.nf @@ -18,7 +18,7 @@ process LAST_DOTPLOT { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ last-dotplot \\ $args \\ diff --git a/modules/last/lastal/main.nf b/modules/last/lastal/main.nf index 4b90a965..b5ac8bfe 100644 --- a/modules/last/lastal/main.nf +++ b/modules/last/lastal/main.nf @@ -17,7 +17,7 @@ process LAST_LASTAL { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def trained_params = param_file ? "-p ${param_file}" : '' """ INDEX_NAME=\$(basename \$(ls $index/*.des) .des) diff --git a/modules/last/lastdb/main.nf b/modules/last/lastdb/main.nf index ff6485dc..e9895c5c 100644 --- a/modules/last/lastdb/main.nf +++ b/modules/last/lastdb/main.nf @@ -16,7 +16,7 @@ process LAST_LASTDB { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ mkdir lastdb lastdb \\ diff --git a/modules/last/mafconvert/main.nf b/modules/last/mafconvert/main.nf index f1a7312e..ca60e7fe 100644 --- a/modules/last/mafconvert/main.nf +++ b/modules/last/mafconvert/main.nf @@ -25,7 +25,7 @@ process LAST_MAFCONVERT { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ maf-convert $args $format $maf | gzip --no-name \\ > ${prefix}.${format}.gz diff --git a/modules/last/mafswap/main.nf b/modules/last/mafswap/main.nf index c66e47d4..0a58b027 100644 --- a/modules/last/mafswap/main.nf +++ b/modules/last/mafswap/main.nf @@ -16,7 +16,7 @@ process LAST_MAFSWAP { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ maf-swap $args $maf | gzip --no-name > ${prefix}.swapped.maf.gz diff --git a/modules/last/postmask/main.nf b/modules/last/postmask/main.nf index e4f4390a..fb097a11 100644 --- a/modules/last/postmask/main.nf +++ b/modules/last/postmask/main.nf @@ -16,7 +16,7 @@ process LAST_POSTMASK { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" if( "$maf" == "${prefix}.maf.gz" ) error "Input and output names are the same, use the suffix option to disambiguate" """ last-postmask $args $maf | gzip --no-name > ${prefix}.maf.gz diff --git a/modules/last/split/main.nf b/modules/last/split/main.nf index ecc47e80..60ed135b 100644 --- a/modules/last/split/main.nf +++ b/modules/last/split/main.nf @@ -16,7 +16,7 @@ process LAST_SPLIT { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ zcat < $maf | last-split $args | gzip --no-name > ${prefix}.maf.gz diff --git a/modules/last/train/main.nf b/modules/last/train/main.nf index 0a949857..471db7c1 100644 --- a/modules/last/train/main.nf +++ b/modules/last/train/main.nf @@ -17,7 +17,7 @@ process LAST_TRAIN { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ INDEX_NAME=\$(basename \$(ls $index/*.des) .des) diff --git a/modules/lima/main.nf b/modules/lima/main.nf index 64f6d87d..a662a7bb 100644 --- a/modules/lima/main.nf +++ b/modules/lima/main.nf @@ -30,7 +30,7 @@ process LIMA { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ OUT_EXT="" diff --git a/modules/lissero/main.nf b/modules/lissero/main.nf index b5cd2b68..667697ef 100644 --- a/modules/lissero/main.nf +++ b/modules/lissero/main.nf @@ -16,7 +16,7 @@ process LISSERO { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ lissero \\ $args \\ diff --git a/modules/lofreq/call/main.nf b/modules/lofreq/call/main.nf index 74995152..d7fd078b 100644 --- a/modules/lofreq/call/main.nf +++ b/modules/lofreq/call/main.nf @@ -17,7 +17,7 @@ process LOFREQ_CALL { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ lofreq \\ call \\ diff --git a/modules/lofreq/callparallel/main.nf b/modules/lofreq/callparallel/main.nf index 63ae2886..764efcc5 100644 --- a/modules/lofreq/callparallel/main.nf +++ b/modules/lofreq/callparallel/main.nf @@ -18,7 +18,7 @@ process LOFREQ_CALLPARALLEL { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ lofreq \\ call-parallel \\ diff --git a/modules/lofreq/filter/main.nf b/modules/lofreq/filter/main.nf index 6f13ae44..34a5aef8 100644 --- a/modules/lofreq/filter/main.nf +++ b/modules/lofreq/filter/main.nf @@ -16,7 +16,7 @@ process LOFREQ_FILTER { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ lofreq \\ filter \\ diff --git a/modules/lofreq/indelqual/main.nf b/modules/lofreq/indelqual/main.nf index bf04c5d2..5e5b8f44 100644 --- a/modules/lofreq/indelqual/main.nf +++ b/modules/lofreq/indelqual/main.nf @@ -17,7 +17,7 @@ process LOFREQ_INDELQUAL { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ lofreq indelqual \\ $args \\ diff --git a/modules/macs2/callpeak/main.nf b/modules/macs2/callpeak/main.nf index e8bfcda0..c5c88f8e 100644 --- a/modules/macs2/callpeak/main.nf +++ b/modules/macs2/callpeak/main.nf @@ -22,7 +22,7 @@ process MACS2_CALLPEAK { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def args_list = args.tokenize() def format = meta.single_end ? 'BAM' : 'BAMPE' def control = controlbam ? "--control $controlbam" : '' diff --git a/modules/manta/germline/main.nf b/modules/manta/germline/main.nf index 553f0be9..2a8c0acc 100644 --- a/modules/manta/germline/main.nf +++ b/modules/manta/germline/main.nf @@ -25,7 +25,7 @@ process MANTA_GERMLINE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def options_manta = target_bed ? "--exome --callRegions $target_bed" : "" """ configManta.py \ diff --git a/modules/manta/somatic/main.nf b/modules/manta/somatic/main.nf index 38d73133..1d62635b 100644 --- a/modules/manta/somatic/main.nf +++ b/modules/manta/somatic/main.nf @@ -27,7 +27,7 @@ process MANTA_SOMATIC { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def options_manta = target_bed ? "--exome --callRegions $target_bed" : "" """ diff --git a/modules/manta/tumoronly/main.nf b/modules/manta/tumoronly/main.nf index dc72fcc4..63f7a840 100644 --- a/modules/manta/tumoronly/main.nf +++ b/modules/manta/tumoronly/main.nf @@ -25,7 +25,7 @@ process MANTA_TUMORONLY { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def options_manta = target_bed ? "--exome --callRegions $target_bed" : "" """ configManta.py \ diff --git a/modules/mapdamage2/main.nf b/modules/mapdamage2/main.nf index 3673970e..e3668fda 100644 --- a/modules/mapdamage2/main.nf +++ b/modules/mapdamage2/main.nf @@ -34,7 +34,7 @@ process MAPDAMAGE2 { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ mapDamage \\ $args \\ diff --git a/modules/mash/sketch/main.nf b/modules/mash/sketch/main.nf index 0c0b6e17..d93641f7 100644 --- a/modules/mash/sketch/main.nf +++ b/modules/mash/sketch/main.nf @@ -16,7 +16,7 @@ process MASH_SKETCH { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ mash \\ sketch \\ diff --git a/modules/mashtree/main.nf b/modules/mashtree/main.nf index 6728e3ce..5da2f805 100644 --- a/modules/mashtree/main.nf +++ b/modules/mashtree/main.nf @@ -17,7 +17,7 @@ process MASHTREE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ mashtree \\ $args \\ diff --git a/modules/maxbin2/main.nf b/modules/maxbin2/main.nf index e13af704..4d384391 100644 --- a/modules/maxbin2/main.nf +++ b/modules/maxbin2/main.nf @@ -23,7 +23,7 @@ process MAXBIN2 { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def associate_files = reads ? "-reads $reads" : "-abund $abund" """ run_MaxBin.pl \\ diff --git a/modules/medaka/main.nf b/modules/medaka/main.nf index e7a8b9cc..761b1c34 100644 --- a/modules/medaka/main.nf +++ b/modules/medaka/main.nf @@ -16,7 +16,7 @@ process MEDAKA { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ medaka_consensus \\ -t $task.cpus \\ diff --git a/modules/megahit/main.nf b/modules/megahit/main.nf index 011fa7d3..7b511883 100644 --- a/modules/megahit/main.nf +++ b/modules/megahit/main.nf @@ -21,7 +21,7 @@ process MEGAHIT { script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" if (meta.single_end) { """ megahit \\ diff --git a/modules/meningotype/main.nf b/modules/meningotype/main.nf index 5dde5633..c3b65b9d 100644 --- a/modules/meningotype/main.nf +++ b/modules/meningotype/main.nf @@ -16,7 +16,7 @@ process MENINGOTYPE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ meningotype \\ $args \\ diff --git a/modules/metabat2/jgisummarizebamcontigdepths/main.nf b/modules/metabat2/jgisummarizebamcontigdepths/main.nf index e35d6715..4a5869b6 100644 --- a/modules/metabat2/jgisummarizebamcontigdepths/main.nf +++ b/modules/metabat2/jgisummarizebamcontigdepths/main.nf @@ -16,7 +16,7 @@ process METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ export OMP_NUM_THREADS=$task.cpus diff --git a/modules/metabat2/metabat2/main.nf b/modules/metabat2/metabat2/main.nf index d158af91..2d01fdf6 100644 --- a/modules/metabat2/metabat2/main.nf +++ b/modules/metabat2/metabat2/main.nf @@ -17,7 +17,7 @@ process METABAT2_METABAT2 { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def decompress_depth = depth ? "gzip -d -f $depth" : "" def depth_file = depth ? "-a ${depth.baseName}" : "" """ diff --git a/modules/metaphlan3/main.nf b/modules/metaphlan3/main.nf index 9463da6f..64965af3 100644 --- a/modules/metaphlan3/main.nf +++ b/modules/metaphlan3/main.nf @@ -19,7 +19,7 @@ process METAPHLAN3 { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def input_type = ("$input".endsWith(".fastq.gz")) ? "--input_type fastq" : ("$input".contains(".fasta")) ? "--input_type fasta" : ("$input".endsWith(".bowtie2out.txt")) ? "--input_type bowtie2out" : "--input_type sam" def input_data = ("$input_type".contains("fastq")) && !meta.single_end ? "${input[0]},${input[1]}" : "$input" def bowtie2_out = "$input_type" == "--input_type bowtie2out" || "$input_type" == "--input_type sam" ? '' : "--bowtie2out ${prefix}.bowtie2out.txt" diff --git a/modules/methyldackel/mbias/main.nf b/modules/methyldackel/mbias/main.nf index 1b4b14c4..021f76f1 100644 --- a/modules/methyldackel/mbias/main.nf +++ b/modules/methyldackel/mbias/main.nf @@ -18,7 +18,7 @@ process METHYLDACKEL_MBIAS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ MethylDackel mbias \\ $args \\ diff --git a/modules/minia/main.nf b/modules/minia/main.nf index 8516ef6e..ceff67c5 100644 --- a/modules/minia/main.nf +++ b/modules/minia/main.nf @@ -18,7 +18,7 @@ process MINIA { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def read_list = reads.join(",") """ echo "${read_list}" | sed 's/,/\\n/g' > input_files.txt diff --git a/modules/miniasm/main.nf b/modules/miniasm/main.nf index 35c2e2c0..b0db6925 100644 --- a/modules/miniasm/main.nf +++ b/modules/miniasm/main.nf @@ -17,7 +17,7 @@ process MINIASM { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ miniasm \\ $args \\ diff --git a/modules/minimap2/align/main.nf b/modules/minimap2/align/main.nf index c6c0c316..500250e9 100644 --- a/modules/minimap2/align/main.nf +++ b/modules/minimap2/align/main.nf @@ -17,7 +17,7 @@ process MINIMAP2_ALIGN { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}" """ minimap2 \\ diff --git a/modules/mlst/main.nf b/modules/mlst/main.nf index aa338420..b2983b82 100644 --- a/modules/mlst/main.nf +++ b/modules/mlst/main.nf @@ -16,7 +16,7 @@ process MLST { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ mlst \\ --threads $task.cpus \\ diff --git a/modules/mosdepth/main.nf b/modules/mosdepth/main.nf index b25e6a3d..d2669b7e 100644 --- a/modules/mosdepth/main.nf +++ b/modules/mosdepth/main.nf @@ -24,7 +24,7 @@ process MOSDEPTH { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def interval = window_size ? "--by ${window_size}" : "--by ${bed}" """ mosdepth \\ diff --git a/modules/msisensor/scan/main.nf b/modules/msisensor/scan/main.nf index 2419a0a1..223b4f44 100644 --- a/modules/msisensor/scan/main.nf +++ b/modules/msisensor/scan/main.nf @@ -16,7 +16,7 @@ process MSISENSOR_SCAN { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ msisensor \\ scan \\ diff --git a/modules/mtnucratio/main.nf b/modules/mtnucratio/main.nf index b8663469..83d6ea2b 100644 --- a/modules/mtnucratio/main.nf +++ b/modules/mtnucratio/main.nf @@ -18,7 +18,7 @@ process MTNUCRATIO { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ mtnucratio \\ diff --git a/modules/mummer/main.nf b/modules/mummer/main.nf index f4f3bb18..39ad3e8b 100644 --- a/modules/mummer/main.nf +++ b/modules/mummer/main.nf @@ -18,7 +18,7 @@ process MUMMER { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def is_compressed_ref = ref.getName().endsWith(".gz") ? true : false def fasta_name_ref = ref.getName().replace(".gz", "") diff --git a/modules/muscle/main.nf b/modules/muscle/main.nf index a50f5cb3..6d549aaa 100644 --- a/modules/muscle/main.nf +++ b/modules/muscle/main.nf @@ -23,7 +23,7 @@ process MUSCLE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def fasta_out = args.contains('-fasta') ? "-fastaout ${prefix}_muscle_msa.afa" : '' def clw_out = args.contains('-clw') ? "-clwout ${prefix}_muscle_msa.clw" : '' def msf_out = args.contains('-msf') ? "-msfout ${prefix}_muscle_msa.msf" : '' diff --git a/modules/nanolyse/main.nf b/modules/nanolyse/main.nf index f29eeb77..0ad0f799 100644 --- a/modules/nanolyse/main.nf +++ b/modules/nanolyse/main.nf @@ -18,7 +18,7 @@ process NANOLYSE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ gunzip -c $fastq | NanoLyse -r $fasta | gzip > ${prefix}.fastq.gz mv NanoLyse.log ${prefix}.nanolyse.log diff --git a/modules/ncbigenomedownload/main.nf b/modules/ncbigenomedownload/main.nf index 466c8d09..9897c861 100644 --- a/modules/ncbigenomedownload/main.nf +++ b/modules/ncbigenomedownload/main.nf @@ -29,7 +29,7 @@ process NCBIGENOMEDOWNLOAD { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def accessions_opt = accessions ? "-A ${accessions}" : "" """ ncbi-genome-download \\ diff --git a/modules/ngmaster/main.nf b/modules/ngmaster/main.nf index 0884b55c..7d04031c 100644 --- a/modules/ngmaster/main.nf +++ b/modules/ngmaster/main.nf @@ -16,7 +16,7 @@ process NGMASTER { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ ngmaster \\ $args \\ diff --git a/modules/nucmer/main.nf b/modules/nucmer/main.nf index bb5dcb7d..4e296515 100644 --- a/modules/nucmer/main.nf +++ b/modules/nucmer/main.nf @@ -17,7 +17,7 @@ process NUCMER { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def is_compressed_ref = ref.getName().endsWith(".gz") ? true : false def is_compressed_query = query.getName().endsWith(".gz") ? true : false def fasta_name_ref = ref.getName().replace(".gz", "") diff --git a/modules/pairtools/dedup/main.nf b/modules/pairtools/dedup/main.nf index 5ee9dc43..fe59e155 100644 --- a/modules/pairtools/dedup/main.nf +++ b/modules/pairtools/dedup/main.nf @@ -17,7 +17,7 @@ process PAIRTOOLS_DEDUP { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ pairtools dedup \\ $args \\ diff --git a/modules/pairtools/flip/main.nf b/modules/pairtools/flip/main.nf index 452800cc..376191ce 100644 --- a/modules/pairtools/flip/main.nf +++ b/modules/pairtools/flip/main.nf @@ -17,7 +17,7 @@ process PAIRTOOLS_FLIP { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ pairtools \\ flip \\ diff --git a/modules/pairtools/parse/main.nf b/modules/pairtools/parse/main.nf index 1d34d42c..7bd778c9 100644 --- a/modules/pairtools/parse/main.nf +++ b/modules/pairtools/parse/main.nf @@ -18,7 +18,7 @@ process PAIRTOOLS_PARSE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ pairtools \\ parse \\ diff --git a/modules/pairtools/restrict/main.nf b/modules/pairtools/restrict/main.nf index 9fcc245c..8759f709 100644 --- a/modules/pairtools/restrict/main.nf +++ b/modules/pairtools/restrict/main.nf @@ -17,7 +17,7 @@ process PAIRTOOLS_RESTRICT { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ pairtools \\ restrict \\ diff --git a/modules/pairtools/select/main.nf b/modules/pairtools/select/main.nf index f699afa3..a6d62ba7 100644 --- a/modules/pairtools/select/main.nf +++ b/modules/pairtools/select/main.nf @@ -17,7 +17,7 @@ process PAIRTOOLS_SELECT { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ pairtools select \\ "$args" \\ diff --git a/modules/pairtools/sort/main.nf b/modules/pairtools/sort/main.nf index 5caa5b74..d5996dd0 100644 --- a/modules/pairtools/sort/main.nf +++ b/modules/pairtools/sort/main.nf @@ -16,7 +16,7 @@ process PAIRTOOLS_SORT { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def mem = task.memory.toString().replaceAll(/(\s|\.|B)+/, '') """ pairtools \\ diff --git a/modules/pangolin/main.nf b/modules/pangolin/main.nf index 99a68e09..5ee2b2e0 100644 --- a/modules/pangolin/main.nf +++ b/modules/pangolin/main.nf @@ -16,7 +16,7 @@ process PANGOLIN { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ pangolin \\ $fasta\\ diff --git a/modules/paraclu/main.nf b/modules/paraclu/main.nf index a2003834..1623ea89 100644 --- a/modules/paraclu/main.nf +++ b/modules/paraclu/main.nf @@ -19,7 +19,7 @@ process PARACLU { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ awk -F "\t" '{print\$1"\t"\$6"\t"\$2"\t"\$5}' < $bed > ${bed}_4P diff --git a/modules/pbbam/pbmerge/main.nf b/modules/pbbam/pbmerge/main.nf index 970128cb..e0525cb1 100644 --- a/modules/pbbam/pbmerge/main.nf +++ b/modules/pbbam/pbmerge/main.nf @@ -17,7 +17,7 @@ process PBBAM_PBMERGE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ pbmerge \\ -o ${prefix}.bam \\ diff --git a/modules/pbccs/main.nf b/modules/pbccs/main.nf index 83e56d96..440fbc72 100644 --- a/modules/pbccs/main.nf +++ b/modules/pbccs/main.nf @@ -22,7 +22,7 @@ process PBCCS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ ccs \\ $bam \\ diff --git a/modules/peddy/main.nf b/modules/peddy/main.nf index 0a6c3384..d64c3762 100644 --- a/modules/peddy/main.nf +++ b/modules/peddy/main.nf @@ -20,7 +20,7 @@ process PEDDY { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ peddy \\ $args \\ diff --git a/modules/phantompeakqualtools/main.nf b/modules/phantompeakqualtools/main.nf index f2edabc3..6fe34cc2 100644 --- a/modules/phantompeakqualtools/main.nf +++ b/modules/phantompeakqualtools/main.nf @@ -20,7 +20,7 @@ process PHANTOMPEAKQUALTOOLS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ RUN_SPP=`which run_spp.R` Rscript -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" -p=$task.cpus diff --git a/modules/phyloflash/main.nf b/modules/phyloflash/main.nf index c507dd14..9ebc40de 100644 --- a/modules/phyloflash/main.nf +++ b/modules/phyloflash/main.nf @@ -18,7 +18,7 @@ process PHYLOFLASH { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" if (meta.single_end) { """ phyloFlash.pl \\ @@ -58,7 +58,7 @@ process PHYLOFLASH { } stub: - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ mkdir ${prefix} touch ${prefix}/${prefix}.SSU.collection.fasta diff --git a/modules/picard/collecthsmetrics/main.nf b/modules/picard/collecthsmetrics/main.nf index adb82d8c..3705b8fb 100644 --- a/modules/picard/collecthsmetrics/main.nf +++ b/modules/picard/collecthsmetrics/main.nf @@ -20,7 +20,7 @@ process PICARD_COLLECTHSMETRICS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def reference = fasta ? "-R $fasta" : "" def avail_mem = 3 diff --git a/modules/picard/collectmultiplemetrics/main.nf b/modules/picard/collectmultiplemetrics/main.nf index f52f5885..6b292534 100644 --- a/modules/picard/collectmultiplemetrics/main.nf +++ b/modules/picard/collectmultiplemetrics/main.nf @@ -18,7 +18,7 @@ process PICARD_COLLECTMULTIPLEMETRICS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def avail_mem = 3 if (!task.memory) { log.info '[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' diff --git a/modules/picard/collectwgsmetrics/main.nf b/modules/picard/collectwgsmetrics/main.nf index 94745d2d..eddb4604 100644 --- a/modules/picard/collectwgsmetrics/main.nf +++ b/modules/picard/collectwgsmetrics/main.nf @@ -17,7 +17,7 @@ process PICARD_COLLECTWGSMETRICS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def avail_mem = 3 if (!task.memory) { log.info '[Picard CollectWgsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' diff --git a/modules/picard/filtersamreads/main.nf b/modules/picard/filtersamreads/main.nf index 8b1d2e6b..d8de137b 100644 --- a/modules/picard/filtersamreads/main.nf +++ b/modules/picard/filtersamreads/main.nf @@ -17,7 +17,7 @@ process PICARD_FILTERSAMREADS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def avail_mem = 3 if (!task.memory) { log.info '[Picard FilterSamReads] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' diff --git a/modules/picard/markduplicates/main.nf b/modules/picard/markduplicates/main.nf index d4c5886f..d3bf6938 100644 --- a/modules/picard/markduplicates/main.nf +++ b/modules/picard/markduplicates/main.nf @@ -18,7 +18,7 @@ process PICARD_MARKDUPLICATES { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def avail_mem = 3 if (!task.memory) { log.info '[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' diff --git a/modules/picard/mergesamfiles/main.nf b/modules/picard/mergesamfiles/main.nf index 3a2fc620..86796593 100644 --- a/modules/picard/mergesamfiles/main.nf +++ b/modules/picard/mergesamfiles/main.nf @@ -16,7 +16,7 @@ process PICARD_MERGESAMFILES { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def bam_files = bams.sort() def avail_mem = 3 if (!task.memory) { diff --git a/modules/picard/sortsam/main.nf b/modules/picard/sortsam/main.nf index b264b927..eb3caf40 100644 --- a/modules/picard/sortsam/main.nf +++ b/modules/picard/sortsam/main.nf @@ -17,7 +17,7 @@ process PICARD_SORTSAM { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def avail_mem = 3 if (!task.memory) { log.info '[Picard SortSam] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' diff --git a/modules/pirate/main.nf b/modules/pirate/main.nf index 3bbb1d64..70de52e6 100644 --- a/modules/pirate/main.nf +++ b/modules/pirate/main.nf @@ -17,7 +17,7 @@ process PIRATE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ PIRATE \\ $args \\ diff --git a/modules/plink/extract/main.nf b/modules/plink/extract/main.nf index 34b12fca..9b8a52f3 100644 --- a/modules/plink/extract/main.nf +++ b/modules/plink/extract/main.nf @@ -18,7 +18,7 @@ process PLINK_EXTRACT { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" if( "$bed" == "${prefix}.bed" ) error "Input and output names are the same, use the suffix option to disambiguate" """ plink \\ diff --git a/modules/plink/vcf/main.nf b/modules/plink/vcf/main.nf index b6fd03d7..719e90d2 100644 --- a/modules/plink/vcf/main.nf +++ b/modules/plink/vcf/main.nf @@ -19,7 +19,7 @@ process PLINK_VCF { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ plink \\ diff --git a/modules/plink2/vcf/main.nf b/modules/plink2/vcf/main.nf index 8101f7dd..078ece1e 100644 --- a/modules/plink2/vcf/main.nf +++ b/modules/plink2/vcf/main.nf @@ -18,7 +18,7 @@ process PLINK2_VCF { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ plink2 \\ $args \\ diff --git a/modules/pmdtools/filter/main.nf b/modules/pmdtools/filter/main.nf index 301f9206..0b3bcbc6 100644 --- a/modules/pmdtools/filter/main.nf +++ b/modules/pmdtools/filter/main.nf @@ -21,7 +21,7 @@ process PMDTOOLS_FILTER { def args2 = task.ext.args2 ?: '' def args3 = task.ext.args3 ?: '' def split_cpus = Math.floor(task.cpus/2) - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" if ("$bam" == "${prefix}.bam") error "[pmdtools/filter] Input and output names are the same, use the suffix option to disambiguate!" //threshold and header flags activate filtering function of pmdtools """ diff --git a/modules/porechop/main.nf b/modules/porechop/main.nf index 2edc5c78..249efad9 100644 --- a/modules/porechop/main.nf +++ b/modules/porechop/main.nf @@ -16,7 +16,7 @@ process PORECHOP { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ porechop \\ -i $reads \\ diff --git a/modules/preseq/lcextrap/main.nf b/modules/preseq/lcextrap/main.nf index 43f86cf8..b5bd0620 100644 --- a/modules/preseq/lcextrap/main.nf +++ b/modules/preseq/lcextrap/main.nf @@ -18,7 +18,7 @@ process PRESEQ_LCEXTRAP { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def paired_end = meta.single_end ? '' : '-pe' """ preseq \\ diff --git a/modules/pydamage/analyze/main.nf b/modules/pydamage/analyze/main.nf index c55616db..c06c592c 100644 --- a/modules/pydamage/analyze/main.nf +++ b/modules/pydamage/analyze/main.nf @@ -16,7 +16,7 @@ process PYDAMAGE_ANALYZE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ pydamage \\ analyze \\ diff --git a/modules/pydamage/filter/main.nf b/modules/pydamage/filter/main.nf index 2e0afac9..ab0b2115 100644 --- a/modules/pydamage/filter/main.nf +++ b/modules/pydamage/filter/main.nf @@ -16,7 +16,7 @@ process PYDAMAGE_FILTER { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ pydamage \\ diff --git a/modules/qcat/main.nf b/modules/qcat/main.nf index 9f53f0cb..7d81952d 100644 --- a/modules/qcat/main.nf +++ b/modules/qcat/main.nf @@ -17,7 +17,7 @@ process QCAT { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ ## Unzip fastq file ## qcat doesn't support zipped files yet diff --git a/modules/racon/main.nf b/modules/racon/main.nf index 5936fac0..9be5ce63 100644 --- a/modules/racon/main.nf +++ b/modules/racon/main.nf @@ -16,7 +16,7 @@ process RACON { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ racon -t "$task.cpus" \\ "${reads}" \\ diff --git a/modules/rasusa/main.nf b/modules/rasusa/main.nf index b43792ee..c2893d18 100644 --- a/modules/rasusa/main.nf +++ b/modules/rasusa/main.nf @@ -17,7 +17,7 @@ process RASUSA { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def output = meta.single_end ? "--output ${prefix}.fastq.gz" : "--output ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz" """ rasusa \\ diff --git a/modules/rmarkdownnotebook/main.nf b/modules/rmarkdownnotebook/main.nf index 9a7db505..f8183216 100644 --- a/modules/rmarkdownnotebook/main.nf +++ b/modules/rmarkdownnotebook/main.nf @@ -25,7 +25,7 @@ process RMARKDOWNNOTEBOOK { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def parametrize = (task.ext.parametrize == null) ? true : task.ext.parametrize def implicit_params = (task.ext.implicit_params == null) ? true : task.ext.implicit_params def meta_params = (task.ext.meta_params == null) ? true : task.ext.meta_params diff --git a/modules/roary/main.nf b/modules/roary/main.nf index a05973eb..edda3281 100644 --- a/modules/roary/main.nf +++ b/modules/roary/main.nf @@ -17,7 +17,7 @@ process ROARY { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ roary \\ $args \\ diff --git a/modules/rseqc/bamstat/main.nf b/modules/rseqc/bamstat/main.nf index d9d3fa36..1141a13f 100644 --- a/modules/rseqc/bamstat/main.nf +++ b/modules/rseqc/bamstat/main.nf @@ -16,7 +16,7 @@ process RSEQC_BAMSTAT { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ bam_stat.py \\ -i $bam \\ diff --git a/modules/rseqc/inferexperiment/main.nf b/modules/rseqc/inferexperiment/main.nf index 3b879cfb..2243c43e 100644 --- a/modules/rseqc/inferexperiment/main.nf +++ b/modules/rseqc/inferexperiment/main.nf @@ -17,7 +17,7 @@ process RSEQC_INFEREXPERIMENT { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ infer_experiment.py \\ -i $bam \\ diff --git a/modules/rseqc/innerdistance/main.nf b/modules/rseqc/innerdistance/main.nf index 88bec499..425737d6 100644 --- a/modules/rseqc/innerdistance/main.nf +++ b/modules/rseqc/innerdistance/main.nf @@ -21,7 +21,7 @@ process RSEQC_INNERDISTANCE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" if (!meta.single_end) { """ inner_distance.py \\ diff --git a/modules/rseqc/junctionannotation/main.nf b/modules/rseqc/junctionannotation/main.nf index b6949641..d2562e5c 100644 --- a/modules/rseqc/junctionannotation/main.nf +++ b/modules/rseqc/junctionannotation/main.nf @@ -23,7 +23,7 @@ process RSEQC_JUNCTIONANNOTATION { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ junction_annotation.py \\ -i $bam \\ diff --git a/modules/rseqc/junctionsaturation/main.nf b/modules/rseqc/junctionsaturation/main.nf index 58451d2e..695762b5 100644 --- a/modules/rseqc/junctionsaturation/main.nf +++ b/modules/rseqc/junctionsaturation/main.nf @@ -18,7 +18,7 @@ process RSEQC_JUNCTIONSATURATION { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ junction_saturation.py \\ -i $bam \\ diff --git a/modules/rseqc/readdistribution/main.nf b/modules/rseqc/readdistribution/main.nf index 74af618d..333193e3 100644 --- a/modules/rseqc/readdistribution/main.nf +++ b/modules/rseqc/readdistribution/main.nf @@ -17,7 +17,7 @@ process RSEQC_READDISTRIBUTION { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ read_distribution.py \\ -i $bam \\ diff --git a/modules/rseqc/readduplication/main.nf b/modules/rseqc/readduplication/main.nf index 80fcb150..134f2e8d 100644 --- a/modules/rseqc/readduplication/main.nf +++ b/modules/rseqc/readduplication/main.nf @@ -19,7 +19,7 @@ process RSEQC_READDUPLICATION { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ read_duplication.py \\ -i $bam \\ diff --git a/modules/samblaster/main.nf b/modules/samblaster/main.nf index 8445b0d0..c6573283 100644 --- a/modules/samblaster/main.nf +++ b/modules/samblaster/main.nf @@ -18,7 +18,7 @@ process SAMBLASTER { def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def args3 = task.ext.args3 ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" if( "$bam" == "${prefix}.bam" ) error "Input and output names are the same, use the suffix option to disambiguate" """ samtools view -h $args2 $bam | \\ diff --git a/modules/samtools/ampliconclip/main.nf b/modules/samtools/ampliconclip/main.nf index 87d6ff8b..55a2f736 100644 --- a/modules/samtools/ampliconclip/main.nf +++ b/modules/samtools/ampliconclip/main.nf @@ -21,7 +21,7 @@ process SAMTOOLS_AMPLICONCLIP { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def rejects = save_cliprejects ? "--rejects-file ${prefix}.cliprejects.bam" : "" def stats = save_clipstats ? "-f ${prefix}.clipstats.txt" : "" """ diff --git a/modules/samtools/bam2fq/main.nf b/modules/samtools/bam2fq/main.nf index 20e83a14..689eb960 100644 --- a/modules/samtools/bam2fq/main.nf +++ b/modules/samtools/bam2fq/main.nf @@ -17,7 +17,7 @@ process SAMTOOLS_BAM2FQ { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" if (split){ """ diff --git a/modules/samtools/depth/main.nf b/modules/samtools/depth/main.nf index f336547f..ebf029aa 100644 --- a/modules/samtools/depth/main.nf +++ b/modules/samtools/depth/main.nf @@ -16,7 +16,7 @@ process SAMTOOLS_DEPTH { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ samtools \\ diff --git a/modules/samtools/fastq/main.nf b/modules/samtools/fastq/main.nf index bdbf53e4..212e804e 100644 --- a/modules/samtools/fastq/main.nf +++ b/modules/samtools/fastq/main.nf @@ -16,7 +16,7 @@ process SAMTOOLS_FASTQ { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def endedness = meta.single_end ? "-0 ${prefix}.fastq.gz" : "-1 ${prefix}_1.fastq.gz -2 ${prefix}_2.fastq.gz" """ diff --git a/modules/samtools/fixmate/main.nf b/modules/samtools/fixmate/main.nf index 180833f4..8f86c1c4 100644 --- a/modules/samtools/fixmate/main.nf +++ b/modules/samtools/fixmate/main.nf @@ -16,7 +16,7 @@ process SAMTOOLS_FIXMATE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use the suffix option to disambiguate!" """ diff --git a/modules/samtools/mpileup/main.nf b/modules/samtools/mpileup/main.nf index 5f6e2d49..c40f46d1 100644 --- a/modules/samtools/mpileup/main.nf +++ b/modules/samtools/mpileup/main.nf @@ -17,7 +17,7 @@ process SAMTOOLS_MPILEUP { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ samtools mpileup \\ --fasta-ref $fasta \\ diff --git a/modules/samtools/sort/main.nf b/modules/samtools/sort/main.nf index 623f10b6..0c2cf25e 100644 --- a/modules/samtools/sort/main.nf +++ b/modules/samtools/sort/main.nf @@ -16,7 +16,7 @@ process SAMTOOLS_SORT { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ samtools sort $args -@ $task.cpus -o ${prefix}.bam -T $prefix $bam cat <<-END_VERSIONS > versions.yml diff --git a/modules/samtools/view/main.nf b/modules/samtools/view/main.nf index 464edd09..619b84dc 100644 --- a/modules/samtools/view/main.nf +++ b/modules/samtools/view/main.nf @@ -18,7 +18,7 @@ process SAMTOOLS_VIEW { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def reference = fasta ? "--reference ${fasta} -C" : "" def file_type = input.getExtension() """ diff --git a/modules/scoary/main.nf b/modules/scoary/main.nf index 8fed0119..ca33041d 100644 --- a/modules/scoary/main.nf +++ b/modules/scoary/main.nf @@ -17,7 +17,7 @@ process SCOARY { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def newick_tree = tree ? "-n ${tree}" : "" """ scoary \\ diff --git a/modules/seacr/callpeak/main.nf b/modules/seacr/callpeak/main.nf index 328e4e6c..12b9205f 100644 --- a/modules/seacr/callpeak/main.nf +++ b/modules/seacr/callpeak/main.nf @@ -19,7 +19,7 @@ process SEACR_CALLPEAK { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def function_switch = ctrlbedgraph ? "$ctrlbedgraph" : "$threshold" """ SEACR_1.3.sh \\ diff --git a/modules/seqsero2/main.nf b/modules/seqsero2/main.nf index a8dd731e..0a7aa6ad 100644 --- a/modules/seqsero2/main.nf +++ b/modules/seqsero2/main.nf @@ -18,7 +18,7 @@ process SEQSERO2 { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ SeqSero2_package.py \\ $args \\ diff --git a/modules/seqtk/mergepe/main.nf b/modules/seqtk/mergepe/main.nf index 954bed5c..299c9ea4 100644 --- a/modules/seqtk/mergepe/main.nf +++ b/modules/seqtk/mergepe/main.nf @@ -16,7 +16,7 @@ process SEQTK_MERGEPE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" if (meta.single_end) { """ ln -s ${reads} ${prefix}.fastq.gz diff --git a/modules/seqtk/sample/main.nf b/modules/seqtk/sample/main.nf index 83a107d0..96e08fd4 100644 --- a/modules/seqtk/sample/main.nf +++ b/modules/seqtk/sample/main.nf @@ -17,7 +17,7 @@ process SEQTK_SAMPLE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" if (meta.single_end) { """ seqtk \\ diff --git a/modules/sequenzautils/bam2seqz/main.nf b/modules/sequenzautils/bam2seqz/main.nf index 9082d426..ce9d1962 100644 --- a/modules/sequenzautils/bam2seqz/main.nf +++ b/modules/sequenzautils/bam2seqz/main.nf @@ -18,7 +18,7 @@ process SEQUENZAUTILS_BAM2SEQZ { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ sequenza-utils \\ bam2seqz \\ diff --git a/modules/sequenzautils/gcwiggle/main.nf b/modules/sequenzautils/gcwiggle/main.nf index 43358c43..a6fcb559 100644 --- a/modules/sequenzautils/gcwiggle/main.nf +++ b/modules/sequenzautils/gcwiggle/main.nf @@ -16,7 +16,7 @@ process SEQUENZAUTILS_GCWIGGLE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ sequenza-utils \\ gc_wiggle \\ diff --git a/modules/seqwish/induce/main.nf b/modules/seqwish/induce/main.nf index fb25a96e..089f3478 100644 --- a/modules/seqwish/induce/main.nf +++ b/modules/seqwish/induce/main.nf @@ -19,7 +19,7 @@ process SEQWISH_INDUCE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ seqwish \\ --threads $task.cpus \\ diff --git a/modules/snpdists/main.nf b/modules/snpdists/main.nf index de79e89b..c8d61161 100644 --- a/modules/snpdists/main.nf +++ b/modules/snpdists/main.nf @@ -16,7 +16,7 @@ process SNPDISTS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ snp-dists \\ $args \\ diff --git a/modules/snpeff/main.nf b/modules/snpeff/main.nf index 2cd023f6..d0ec993e 100644 --- a/modules/snpeff/main.nf +++ b/modules/snpeff/main.nf @@ -28,7 +28,7 @@ process SNPEFF { } else { avail_mem = task.memory.giga } - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def dir_cache = task.ext.use_cache ? "-dataDir \${PWD}/${cache}" : "" """ snpEff \\ diff --git a/modules/sortmerna/main.nf b/modules/sortmerna/main.nf index 83cd8092..5c0950d8 100644 --- a/modules/sortmerna/main.nf +++ b/modules/sortmerna/main.nf @@ -18,7 +18,7 @@ process SORTMERNA { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" if (meta.single_end) { """ sortmerna \\ diff --git a/modules/spades/main.nf b/modules/spades/main.nf index 4663ec55..ba690d35 100644 --- a/modules/spades/main.nf +++ b/modules/spades/main.nf @@ -22,7 +22,7 @@ process SPADES { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def maxmem = task.memory.toGiga() def illumina_reads = illumina ? ( meta.single_end ? "-s $illumina" : "-1 ${illumina[0]} -2 ${illumina[1]}" ) : "" def pacbio_reads = pacbio ? "--pacbio $pacbio" : "" diff --git a/modules/spatyper/main.nf b/modules/spatyper/main.nf index d7c75ba6..e0ba8d13 100644 --- a/modules/spatyper/main.nf +++ b/modules/spatyper/main.nf @@ -18,7 +18,7 @@ process SPATYPER { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def input_args = repeats && repeat_order ? "-r ${repeats} -o ${repeat_order}" : "" """ spaTyper \\ diff --git a/modules/staphopiasccmec/main.nf b/modules/staphopiasccmec/main.nf index f33634ae..dbb61a27 100644 --- a/modules/staphopiasccmec/main.nf +++ b/modules/staphopiasccmec/main.nf @@ -16,7 +16,7 @@ process STAPHOPIASCCMEC { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ staphopia-sccmec --assembly $fasta $args > ${prefix}.tsv diff --git a/modules/star/align/main.nf b/modules/star/align/main.nf index 46023d3e..9725496f 100644 --- a/modules/star/align/main.nf +++ b/modules/star/align/main.nf @@ -32,7 +32,7 @@ process STAR_ALIGN { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def ignore_gtf = star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf" def seq_platform = seq_platform ? "'PL:$seq_platform'" : "" def seq_center = seq_center ? "--outSAMattrRGline ID:$prefix 'CN:$seq_center' 'SM:$prefix' $seq_platform " : "--outSAMattrRGline ID:$prefix 'SM:$prefix' $seq_platform " diff --git a/modules/strelka/germline/main.nf b/modules/strelka/germline/main.nf index e991db67..324be6df 100644 --- a/modules/strelka/germline/main.nf +++ b/modules/strelka/germline/main.nf @@ -23,7 +23,7 @@ process STRELKA_GERMLINE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def regions = target_bed ? "--exome --callRegions ${target_bed}" : "" """ configureStrelkaGermlineWorkflow.py \\ diff --git a/modules/strelka/somatic/main.nf b/modules/strelka/somatic/main.nf index fa138633..a9766d01 100644 --- a/modules/strelka/somatic/main.nf +++ b/modules/strelka/somatic/main.nf @@ -23,7 +23,7 @@ process STRELKA_SOMATIC { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def options_target_bed = target_bed ? "--exome --callRegions ${target_bed}" : "" def options_manta = manta_candidate_small_indels ? "--indelCandidates ${manta_candidate_small_indels}" : "" """ diff --git a/modules/stringtie/stringtie/main.nf b/modules/stringtie/stringtie/main.nf index 4367a84d..9d62a966 100644 --- a/modules/stringtie/stringtie/main.nf +++ b/modules/stringtie/stringtie/main.nf @@ -20,7 +20,7 @@ process STRINGTIE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def strandedness = '' if (meta.strandedness == 'forward') { diff --git a/modules/subread/featurecounts/main.nf b/modules/subread/featurecounts/main.nf index 43a7f8cd..53eb279e 100644 --- a/modules/subread/featurecounts/main.nf +++ b/modules/subread/featurecounts/main.nf @@ -17,7 +17,7 @@ process SUBREAD_FEATURECOUNTS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def paired_end = meta.single_end ? '' : '-p' def strandedness = 0 diff --git a/modules/tabix/bgzip/main.nf b/modules/tabix/bgzip/main.nf index 13f9a942..ed9362b2 100644 --- a/modules/tabix/bgzip/main.nf +++ b/modules/tabix/bgzip/main.nf @@ -16,7 +16,7 @@ process TABIX_BGZIP { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ bgzip -c $args $input > ${prefix}.${input.getExtension()}.gz diff --git a/modules/tabix/bgziptabix/main.nf b/modules/tabix/bgziptabix/main.nf index 9a633d2e..20b47a9f 100644 --- a/modules/tabix/bgziptabix/main.nf +++ b/modules/tabix/bgziptabix/main.nf @@ -17,7 +17,7 @@ process TABIX_BGZIPTABIX { script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ bgzip -c $args $input > ${prefix}.gz tabix $args2 ${prefix}.gz diff --git a/modules/tiddit/cov/main.nf b/modules/tiddit/cov/main.nf index e9bb9b5d..c5a1ca0f 100644 --- a/modules/tiddit/cov/main.nf +++ b/modules/tiddit/cov/main.nf @@ -18,7 +18,7 @@ process TIDDIT_COV { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def reference = fasta ? "--ref $fasta" : "" """ tiddit \\ diff --git a/modules/tiddit/sv/main.nf b/modules/tiddit/sv/main.nf index 83a46f82..08eecc01 100644 --- a/modules/tiddit/sv/main.nf +++ b/modules/tiddit/sv/main.nf @@ -20,7 +20,7 @@ process TIDDIT_SV { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def reference = fasta == "dummy_file.txt" ? "--ref $fasta" : "" """ tiddit \\ diff --git a/modules/trimgalore/main.nf b/modules/trimgalore/main.nf index 86761ad8..ee40b780 100644 --- a/modules/trimgalore/main.nf +++ b/modules/trimgalore/main.nf @@ -38,7 +38,7 @@ process TRIMGALORE { def tpc_r2 = params.three_prime_clip_r2 > 0 ? "--three_prime_clip_r2 ${params.three_prime_clip_r2}" : '' // Added soft-links to original fastqs for consistent naming in MultiQC - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" if (meta.single_end) { """ [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz diff --git a/modules/ucsc/bed12tobigbed/main.nf b/modules/ucsc/bed12tobigbed/main.nf index 937eabd6..742798b3 100644 --- a/modules/ucsc/bed12tobigbed/main.nf +++ b/modules/ucsc/bed12tobigbed/main.nf @@ -19,7 +19,7 @@ process UCSC_BED12TOBIGBED { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ bedToBigBed \\ $bed \\ diff --git a/modules/ucsc/bedclip/main.nf b/modules/ucsc/bedclip/main.nf index 1d46342c..dacd7260 100755 --- a/modules/ucsc/bedclip/main.nf +++ b/modules/ucsc/bedclip/main.nf @@ -19,7 +19,7 @@ process UCSC_BEDCLIP { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ bedClip \\ $bedgraph \\ diff --git a/modules/ucsc/bedgraphtobigwig/main.nf b/modules/ucsc/bedgraphtobigwig/main.nf index e18b41bc..9ba306ab 100644 --- a/modules/ucsc/bedgraphtobigwig/main.nf +++ b/modules/ucsc/bedgraphtobigwig/main.nf @@ -19,7 +19,7 @@ process UCSC_BEDGRAPHTOBIGWIG { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ bedGraphToBigWig \\ $bedgraph \\ diff --git a/modules/ucsc/bigwigaverageoverbed/main.nf b/modules/ucsc/bigwigaverageoverbed/main.nf index 8c6f1178..1e97c83d 100644 --- a/modules/ucsc/bigwigaverageoverbed/main.nf +++ b/modules/ucsc/bigwigaverageoverbed/main.nf @@ -19,7 +19,7 @@ process UCSC_BIGWIGAVERAGEOVERBED { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" // BUG: bigWigAverageOverBed cannot handle ensembl seqlevels style """ bigWigAverageOverBed \\ diff --git a/modules/ucsc/liftover/main.nf b/modules/ucsc/liftover/main.nf index 1c667262..3dd9531e 100644 --- a/modules/ucsc/liftover/main.nf +++ b/modules/ucsc/liftover/main.nf @@ -20,7 +20,7 @@ process UCSC_LIFTOVER { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ liftOver \\ diff --git a/modules/ultra/pipeline/main.nf b/modules/ultra/pipeline/main.nf index 5df34121..f2dcb543 100644 --- a/modules/ultra/pipeline/main.nf +++ b/modules/ultra/pipeline/main.nf @@ -18,7 +18,7 @@ process ULTRA_PIPELINE { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ uLTRA \\ pipeline \\ diff --git a/modules/umitools/dedup/main.nf b/modules/umitools/dedup/main.nf index 287bb8c2..ce21437d 100644 --- a/modules/umitools/dedup/main.nf +++ b/modules/umitools/dedup/main.nf @@ -16,7 +16,7 @@ process UMITOOLS_DEDUP { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def paired = meta.single_end ? "" : "--paired" """ umi_tools dedup \\ diff --git a/modules/umitools/extract/main.nf b/modules/umitools/extract/main.nf index 3c2402e2..fba8f054 100644 --- a/modules/umitools/extract/main.nf +++ b/modules/umitools/extract/main.nf @@ -17,7 +17,7 @@ process UMITOOLS_EXTRACT { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" if (meta.single_end) { """ umi_tools \\ diff --git a/modules/unicycler/main.nf b/modules/unicycler/main.nf index 14319dc1..1ccc72a9 100644 --- a/modules/unicycler/main.nf +++ b/modules/unicycler/main.nf @@ -18,7 +18,7 @@ process UNICYCLER { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def short_reads = shortreads ? ( meta.single_end ? "-s $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}" ) : "" def long_reads = longreads ? "-l $longreads" : "" """ diff --git a/modules/variantbam/main.nf b/modules/variantbam/main.nf index 3d354016..11059a9a 100644 --- a/modules/variantbam/main.nf +++ b/modules/variantbam/main.nf @@ -18,7 +18,7 @@ process VARIANTBAM { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ variant \\ $bam \\ diff --git a/modules/vcftools/main.nf b/modules/vcftools/main.nf index 62fff0cf..fbe646ca 100644 --- a/modules/vcftools/main.nf +++ b/modules/vcftools/main.nf @@ -83,7 +83,7 @@ process VCFTOOLS { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def args_list = args.tokenize() def bed_arg = (args.contains('--bed')) ? "--bed ${bed}" : diff --git a/modules/yara/mapper/main.nf b/modules/yara/mapper/main.nf index 6e7f433b..4539033d 100644 --- a/modules/yara/mapper/main.nf +++ b/modules/yara/mapper/main.nf @@ -17,7 +17,7 @@ process YARA_MAPPER { script: def args = task.ext.args ?: '' - def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" if (meta.single_end) { """ yara_mapper \\ diff --git a/tests/modules/bbmap/bbduk/nextflow.config b/tests/modules/bbmap/bbduk/nextflow.config index 8940a9be..46fc33b4 100644 --- a/tests/modules/bbmap/bbduk/nextflow.config +++ b/tests/modules/bbmap/bbduk/nextflow.config @@ -4,7 +4,7 @@ process { withName: BBMAP_BBDUK { ext.args = 'trimq=10 qtrim=r' - ext.suffix = '.trim' + ext.prefix = { "${meta.id}.trim" } } } diff --git a/tests/modules/bcftools/reheader/nextflow.config b/tests/modules/bcftools/reheader/nextflow.config index a377b26d..55d2cff8 100644 --- a/tests/modules/bcftools/reheader/nextflow.config +++ b/tests/modules/bcftools/reheader/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: BCFTOOLS_REHEADER { - ext.suffix = '.updated' + ext.prefix = { "${meta.id}.updated" } } } diff --git a/tests/modules/bedtools/complement/nextflow.config b/tests/modules/bedtools/complement/nextflow.config index 561fdead..cb867120 100644 --- a/tests/modules/bedtools/complement/nextflow.config +++ b/tests/modules/bedtools/complement/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: BEDTOOLS_COMPLEMENT { - ext.suffix = '_out' + ext.prefix = { "${meta.id}_out" } } } diff --git a/tests/modules/bedtools/genomecov/nextflow.config b/tests/modules/bedtools/genomecov/nextflow.config index bc0e4aaf..6e1c03e2 100644 --- a/tests/modules/bedtools/genomecov/nextflow.config +++ b/tests/modules/bedtools/genomecov/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: BEDTOOLS_GENOMECOV { - ext.suffix = '_out' + ext.prefix = { "${meta.id}_out" } } } diff --git a/tests/modules/bedtools/intersect/nextflow.config b/tests/modules/bedtools/intersect/nextflow.config index c7d0c826..3aa2593f 100644 --- a/tests/modules/bedtools/intersect/nextflow.config +++ b/tests/modules/bedtools/intersect/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: BEDTOOLS_INTERSECT { - ext.suffix = '_out' + ext.prefix = { "${meta.id}_out" } } } diff --git a/tests/modules/bedtools/merge/nextflow.config b/tests/modules/bedtools/merge/nextflow.config index e7d635dd..545a523d 100644 --- a/tests/modules/bedtools/merge/nextflow.config +++ b/tests/modules/bedtools/merge/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: BEDTOOLS_MERGE { - ext.suffix = '_out' + ext.prefix = { "${meta.id}_out" } } } diff --git a/tests/modules/bedtools/slop/nextflow.config b/tests/modules/bedtools/slop/nextflow.config index 5dc03727..09abb51a 100644 --- a/tests/modules/bedtools/slop/nextflow.config +++ b/tests/modules/bedtools/slop/nextflow.config @@ -4,7 +4,7 @@ process { withName: BEDTOOLS_SLOP { ext.args = '-l 15 -r 30' - ext.suffix = '_out' + ext.prefix = { "${meta.id}_out" } } } diff --git a/tests/modules/bedtools/sort/nextflow.config b/tests/modules/bedtools/sort/nextflow.config index 6bb73232..2ecc295a 100644 --- a/tests/modules/bedtools/sort/nextflow.config +++ b/tests/modules/bedtools/sort/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: BEDTOOLS_SORT { - ext.suffix = '_out' + ext.prefix = { "${meta.id}_out" } } } diff --git a/tests/modules/diamond/blastp/nextflow.config b/tests/modules/diamond/blastp/nextflow.config index d1222d49..5a9aacad 100644 --- a/tests/modules/diamond/blastp/nextflow.config +++ b/tests/modules/diamond/blastp/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: DIAMOND_BLASTP { - ext.suffix = '.diamond_blastp' + ext.prefix = { "${meta.id}.diamond_blastp" } } } diff --git a/tests/modules/diamond/blastx/nextflow.config b/tests/modules/diamond/blastx/nextflow.config index 83169455..25320af3 100644 --- a/tests/modules/diamond/blastx/nextflow.config +++ b/tests/modules/diamond/blastx/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: DIAMOND_BLASTX { - ext.suffix = '.diamond_blastx' + ext.prefix = { "${meta.id}.diamond_blastx" } } } diff --git a/tests/modules/dshbio/filterbed/nextflow.config b/tests/modules/dshbio/filterbed/nextflow.config index 2f1e5ab9..3937a184 100644 --- a/tests/modules/dshbio/filterbed/nextflow.config +++ b/tests/modules/dshbio/filterbed/nextflow.config @@ -4,6 +4,6 @@ process { withName: DSHBIO_FILTERBED { ext.args = '--range chr1:0-1000' - ext.suffix = '.filtered' + ext.prefix = { "${meta.id}.filtered" } } } diff --git a/tests/modules/dshbio/filtergff3/nextflow.config b/tests/modules/dshbio/filtergff3/nextflow.config index c4b75eaf..80dcd28c 100644 --- a/tests/modules/dshbio/filtergff3/nextflow.config +++ b/tests/modules/dshbio/filtergff3/nextflow.config @@ -4,7 +4,7 @@ process { withName: DSHBIO_FILTERGFF3 { ext.args = '--range MT192765.1:0-1000' - ext.suffix = '.filtered' + ext.prefix = { "${meta.id}.filtered" } } } diff --git a/tests/modules/dshbio/splitbed/nextflow.config b/tests/modules/dshbio/splitbed/nextflow.config index 4369c509..ad9c045b 100644 --- a/tests/modules/dshbio/splitbed/nextflow.config +++ b/tests/modules/dshbio/splitbed/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: DSHBIO_SPLITBED { - ext.suffix = '.' + ext.prefix = { "${meta.id}." } ext.args = '--records 2' } diff --git a/tests/modules/dshbio/splitgff3/nextflow.config b/tests/modules/dshbio/splitgff3/nextflow.config index e31f8e13..f6a0b921 100644 --- a/tests/modules/dshbio/splitgff3/nextflow.config +++ b/tests/modules/dshbio/splitgff3/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: DSHBIO_SPLITGFF3 { - ext.suffix = '.' + ext.prefix = { "${meta.id}." } ext.args = '--records 15' } diff --git a/tests/modules/fgbio/callmolecularconsensusreads/nextflow.config b/tests/modules/fgbio/callmolecularconsensusreads/nextflow.config index 0a266da9..e6721ff6 100644 --- a/tests/modules/fgbio/callmolecularconsensusreads/nextflow.config +++ b/tests/modules/fgbio/callmolecularconsensusreads/nextflow.config @@ -4,12 +4,12 @@ process { withName: FGBIO_SORTBAM { ext.args = '-s TemplateCoordinate' - ext.suffix = '_out' + ext.prefix = { "${meta.id}_out" } } withName: FGBIO_CALLMOLECULARCONSENSUSREADS { ext.args = '-M 1' - ext.suffix = '_molreads' + ext.prefix = { "${meta.id}_molreads" } } } diff --git a/tests/modules/gatk4/createsomaticpanelofnormals/nextflow.config b/tests/modules/gatk4/createsomaticpanelofnormals/nextflow.config index 6fda39ec..d73e78ad 100644 --- a/tests/modules/gatk4/createsomaticpanelofnormals/nextflow.config +++ b/tests/modules/gatk4/createsomaticpanelofnormals/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: GATK4_CREATESOMATICPANELOFNORMALS { - ext.suffix = '.pon' + ext.prefix = { "${meta.id}.pon" } } } diff --git a/tests/modules/gatk4/filtermutectcalls/nextflow.config b/tests/modules/gatk4/filtermutectcalls/nextflow.config index c830fdc6..3d4148d2 100644 --- a/tests/modules/gatk4/filtermutectcalls/nextflow.config +++ b/tests/modules/gatk4/filtermutectcalls/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: GATK4_FILTERMUTECTCALLS { - ext.suffix = '.filtered' + ext.prefix = { "${meta.id}.filtered" } } } diff --git a/tests/modules/gatk4/genotypegvcfs/nextflow.config b/tests/modules/gatk4/genotypegvcfs/nextflow.config index aaa704da..97396a74 100644 --- a/tests/modules/gatk4/genotypegvcfs/nextflow.config +++ b/tests/modules/gatk4/genotypegvcfs/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: GATK4_GENOTYPEGVCFS { - ext.suffix = '.genotyped' + ext.prefix = { "${meta.id}.genotyped" } } } diff --git a/tests/modules/gatk4/learnreadorientationmodel/nextflow.config b/tests/modules/gatk4/learnreadorientationmodel/nextflow.config index 3a74623a..463e2d54 100644 --- a/tests/modules/gatk4/learnreadorientationmodel/nextflow.config +++ b/tests/modules/gatk4/learnreadorientationmodel/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: GATK4_LEARNREADORIENTATIONMODEL { - ext.suffix = '.artifact-prior' + ext.prefix = { "${meta.id}.artifact-prior" } } } diff --git a/tests/modules/gatk4/variantfiltration/nextflow.config b/tests/modules/gatk4/variantfiltration/nextflow.config index ff2feb9c..4b930f28 100644 --- a/tests/modules/gatk4/variantfiltration/nextflow.config +++ b/tests/modules/gatk4/variantfiltration/nextflow.config @@ -4,7 +4,7 @@ process { withName: GATK4_VARIANTFILTRATION { ext.args = "--filter-name \'test_filter\' --filter-expression \'MQ0 > 0\'" - ext.suffix = '.filtered' + ext.prefix = { "${meta.id}.filtered" } } } diff --git a/tests/modules/gffread/nextflow.config b/tests/modules/gffread/nextflow.config index 00c052f5..c020f934 100644 --- a/tests/modules/gffread/nextflow.config +++ b/tests/modules/gffread/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: GFFREAD { - ext.suffix = '.out' + ext.prefix = { "${meta.id}.out" } } } diff --git a/tests/modules/gstama/collapse/nextflow.config b/tests/modules/gstama/collapse/nextflow.config index 0455c8b2..a68f33f2 100644 --- a/tests/modules/gstama/collapse/nextflow.config +++ b/tests/modules/gstama/collapse/nextflow.config @@ -4,7 +4,7 @@ process { withName: GSTAMA_COLLAPSE { ext.args = '-x capped -b BAM' - ext.suffix = '_tc' + ext.prefix = { "${meta.id}_tc" } } } diff --git a/tests/modules/gstama/merge/nextflow.config b/tests/modules/gstama/merge/nextflow.config index a9c63fcf..e0d7c8ef 100644 --- a/tests/modules/gstama/merge/nextflow.config +++ b/tests/modules/gstama/merge/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: GSTAMA_MERGE { - ext.suffix = '_merged' + ext.prefix = { "${meta.id}_merged" } } } diff --git a/tests/modules/isoseq3/refine/nextflow.config b/tests/modules/isoseq3/refine/nextflow.config index 88f1bdc4..6a4dea9f 100644 --- a/tests/modules/isoseq3/refine/nextflow.config +++ b/tests/modules/isoseq3/refine/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: ISOSEQ3_REFINE { - ext.suffix = '.refine' + ext.prefix = { "${meta.id}.refine" } } } diff --git a/tests/modules/last/postmask/nextflow.config b/tests/modules/last/postmask/nextflow.config index dc021264..70c3f35b 100644 --- a/tests/modules/last/postmask/nextflow.config +++ b/tests/modules/last/postmask/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: LAST_POSTMASK { - ext.suffix = '.postmask' + ext.prefix = { "${meta.id}.postmask" } } } diff --git a/tests/modules/last/split/nextflow.config b/tests/modules/last/split/nextflow.config index 8b31ca0f..6252ec14 100644 --- a/tests/modules/last/split/nextflow.config +++ b/tests/modules/last/split/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: LAST_SPLIT { - ext.suffix = '.split' + ext.prefix = { "${meta.id}.split" } } } diff --git a/tests/modules/lima/nextflow.config b/tests/modules/lima/nextflow.config index 5091b034..8da2613f 100644 --- a/tests/modules/lima/nextflow.config +++ b/tests/modules/lima/nextflow.config @@ -4,7 +4,7 @@ process { withName: LIMA { ext.args = '--isoseq --peek-guess' - ext.suffix = '.fl' + ext.prefix = { "${meta.id}.fl" } } } diff --git a/tests/modules/lofreq/indelqual/nextflow.config b/tests/modules/lofreq/indelqual/nextflow.config index b9ad2787..c50c1363 100644 --- a/tests/modules/lofreq/indelqual/nextflow.config +++ b/tests/modules/lofreq/indelqual/nextflow.config @@ -4,7 +4,7 @@ process { withName: LOFREQ_INDELQUAL { ext.args = '--dindel' - ext.suffix = '.indelqual' + ext.prefix = { "${meta.id}.indelqual" } } } diff --git a/tests/modules/medaka/nextflow.config b/tests/modules/medaka/nextflow.config index 1f89be62..c0b1b507 100644 --- a/tests/modules/medaka/nextflow.config +++ b/tests/modules/medaka/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: MEDAKA { - ext.suffix = '.polished.genome' + ext.prefix = { "${meta.id}.polished.genome" } } } diff --git a/tests/modules/metaphlan3/nextflow.config b/tests/modules/metaphlan3/nextflow.config index 2dde2212..a47b46e0 100644 --- a/tests/modules/metaphlan3/nextflow.config +++ b/tests/modules/metaphlan3/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: SAMTOOLS_VIEW { - ext.suffix = '.sam' + ext.prefix = { "${meta.id}.sam" } } withName: METAPHLAN3 { diff --git a/tests/modules/miniasm/nextflow.config b/tests/modules/miniasm/nextflow.config index 844a0120..23f0a8d0 100644 --- a/tests/modules/miniasm/nextflow.config +++ b/tests/modules/miniasm/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: MINIASM { - ext.suffix = '.assembly' + ext.prefix = { "${meta.id}.assembly" } } } diff --git a/tests/modules/nanolyse/nextflow.config b/tests/modules/nanolyse/nextflow.config index ede080cc..5f7b5bed 100644 --- a/tests/modules/nanolyse/nextflow.config +++ b/tests/modules/nanolyse/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: NANOLYSE { - ext.suffix = '.clean' + ext.prefix = { "${meta.id}.clean" } } } diff --git a/tests/modules/pairtools/dedup/nextflow.config b/tests/modules/pairtools/dedup/nextflow.config index 1de3348f..b47fab16 100644 --- a/tests/modules/pairtools/dedup/nextflow.config +++ b/tests/modules/pairtools/dedup/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: PAIRTOOLS_DEDUP { - ext.suffix = '.dedup' + ext.prefix = { "${meta.id}.dedup" } } } diff --git a/tests/modules/pairtools/parse/nextflow.config b/tests/modules/pairtools/parse/nextflow.config index 1a1182f6..a5d3ef9d 100644 --- a/tests/modules/pairtools/parse/nextflow.config +++ b/tests/modules/pairtools/parse/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: PAIRTOOLS_PARSE { - ext.suffix = '.raw' + ext.prefix = { "${meta.id}.raw" } } } diff --git a/tests/modules/pairtools/restrict/nextflow.config b/tests/modules/pairtools/restrict/nextflow.config index 857d7534..fa8217bc 100644 --- a/tests/modules/pairtools/restrict/nextflow.config +++ b/tests/modules/pairtools/restrict/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: PAIRTOOLS_RESTRICT { - ext.suffix = '.restrict' + ext.prefix = { "${meta.id}.restrict" } } } diff --git a/tests/modules/pairtools/sort/nextflow.config b/tests/modules/pairtools/sort/nextflow.config index 86b3d802..dfaf6053 100644 --- a/tests/modules/pairtools/sort/nextflow.config +++ b/tests/modules/pairtools/sort/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: PAIRTOOLS_SORT { - ext.suffix = '.sorted' + ext.prefix = { "${meta.id}.sorted" } } } diff --git a/tests/modules/pbbam/pbmerge/nextflow.config b/tests/modules/pbbam/pbmerge/nextflow.config index c897068b..4fc270a9 100644 --- a/tests/modules/pbbam/pbmerge/nextflow.config +++ b/tests/modules/pbbam/pbmerge/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: PBBAM_PBMERGE { - ext.suffix = '.merged' + ext.prefix = { "${meta.id}.merged" } } } diff --git a/tests/modules/picard/filtersamreads/nextflow.config b/tests/modules/picard/filtersamreads/nextflow.config index e9ce4914..653e9633 100644 --- a/tests/modules/picard/filtersamreads/nextflow.config +++ b/tests/modules/picard/filtersamreads/nextflow.config @@ -3,11 +3,11 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: PICARD_SORTSAM { - ext.suffix = '.sorted' + ext.prefix = { "${meta.id}.sorted" } } withName: PICARD_FILTERSAMREADS { - ext.suffix = '.filtered' + ext.prefix = { "${meta.id}.filtered" } } } diff --git a/tests/modules/picard/sortsam/nextflow.config b/tests/modules/picard/sortsam/nextflow.config index 2c290cbe..ca572c2f 100644 --- a/tests/modules/picard/sortsam/nextflow.config +++ b/tests/modules/picard/sortsam/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: PICARD_SORTSAM { - ext.suffix = '.sorted' + ext.prefix = { "${meta.id}.sorted" } } } diff --git a/tests/modules/plink/extract/nextflow.config b/tests/modules/plink/extract/nextflow.config index 12668b01..6a7f6d42 100644 --- a/tests/modules/plink/extract/nextflow.config +++ b/tests/modules/plink/extract/nextflow.config @@ -7,7 +7,7 @@ process { } withName: PLINK_EXTRACT { - ext.suffix = '.extract' + ext.prefix = { "${meta.id}.extract" } } } diff --git a/tests/modules/porechop/nextflow.config b/tests/modules/porechop/nextflow.config index 3a0536b0..85eb257a 100644 --- a/tests/modules/porechop/nextflow.config +++ b/tests/modules/porechop/nextflow.config @@ -4,7 +4,7 @@ process { withName: PORECHOP { ext.args = '' - ext.suffix = '_porechop' + ext.prefix = { "${meta.id}_porechop" } } } diff --git a/tests/modules/rasusa/nextflow.config b/tests/modules/rasusa/nextflow.config index fea844ae..50c32e5c 100644 --- a/tests/modules/rasusa/nextflow.config +++ b/tests/modules/rasusa/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: RASUSA { - ext.suffix = '_100X' + ext.prefix = { "${meta.id}_100X" } } } diff --git a/tests/modules/samblaster/nextflow.config b/tests/modules/samblaster/nextflow.config index 3018088b..7ba8b23b 100644 --- a/tests/modules/samblaster/nextflow.config +++ b/tests/modules/samblaster/nextflow.config @@ -4,7 +4,7 @@ process { withName: SAMBLASTER { ext.args = '-M --addMateTags' - ext.suffix = '.processed' + ext.prefix = { "${meta.id}.processed" } } } diff --git a/tests/modules/samtools/merge/nextflow.config b/tests/modules/samtools/merge/nextflow.config index cb350bf7..4ac70fa0 100644 --- a/tests/modules/samtools/merge/nextflow.config +++ b/tests/modules/samtools/merge/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: SAMTOOLS_MERGE { - ext.suffix = '_merged' + ext.prefix = { "${meta.id}_merged" } } } diff --git a/tests/modules/samtools/sort/nextflow.config b/tests/modules/samtools/sort/nextflow.config index 57ae6280..230bec5f 100644 --- a/tests/modules/samtools/sort/nextflow.config +++ b/tests/modules/samtools/sort/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: SAMTOOLS_SORT { - ext.suffix = '.sorted' + ext.prefix = { "${meta.id}.sorted" } } } diff --git a/tests/modules/seqtk/mergepe/nextflow.config b/tests/modules/seqtk/mergepe/nextflow.config index b14e72ff..04eeef72 100644 --- a/tests/modules/seqtk/mergepe/nextflow.config +++ b/tests/modules/seqtk/mergepe/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: SEQTK_MERGEPE { - ext.suffix = '.processed' + ext.prefix = { "${meta.id}.processed" } } } diff --git a/tests/modules/seqtk/sample/nextflow.config b/tests/modules/seqtk/sample/nextflow.config index 3efac50d..a79ad290 100644 --- a/tests/modules/seqtk/sample/nextflow.config +++ b/tests/modules/seqtk/sample/nextflow.config @@ -4,7 +4,7 @@ process { withName: SEQTK_SAMPLE { ext.args = '-s100' - ext.suffix = '.sampled' + ext.prefix = { "${meta.id}.sampled" } } } diff --git a/tests/modules/seqtk/subseq/nextflow.config b/tests/modules/seqtk/subseq/nextflow.config index c61c4a74..24f16bad 100644 --- a/tests/modules/seqtk/subseq/nextflow.config +++ b/tests/modules/seqtk/subseq/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: SEQTK_SUBSEQ { - ext.suffix = '.filtered' + ext.prefix = { "${meta.id}.filtered" } } } diff --git a/tests/modules/ucsc/bedclip/nextflow.config b/tests/modules/ucsc/bedclip/nextflow.config index 4adc3b8f..46af4b0a 100644 --- a/tests/modules/ucsc/bedclip/nextflow.config +++ b/tests/modules/ucsc/bedclip/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: UCSC_BEDCLIP { - ext.suffix = '.clip' + ext.prefix = { "${meta.id}.clip" } } } diff --git a/tests/modules/ultra/pipeline/nextflow.config b/tests/modules/ultra/pipeline/nextflow.config index a3b88ea3..16ed7f9b 100644 --- a/tests/modules/ultra/pipeline/nextflow.config +++ b/tests/modules/ultra/pipeline/nextflow.config @@ -4,7 +4,7 @@ process { withName: GFFREAD { ext.args = '--sort-alpha --keep-genes -T' - ext.suffix = '_sorted' + ext.prefix = { "${meta.id}_sorted" } } }