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style: Remove newline at end of files

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Edmund Miller 2021-02-03 13:22:42 -06:00
parent 5f810beaa4
commit b62d01285e
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229 changed files with 18304 additions and 18310 deletions
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2
.editorconfig
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@ -3,7 +3,7 @@ root = true
[*]
charset = utf-8
end_of_line = lf
insert_final_newline = true
insert_final_newline = false
trim_trailing_whitespace = true
indent_size = 4
indent_style = space

22
README.md
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@ -40,11 +40,11 @@ We have written a helper command in the `nf-core/tools` package that uses the Gi
```console
$ nf-core modules list
,--./,-.
___ __ __ __ ___ /,-._.--~\
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
`._,._,'
nf-core/tools version 1.10.2
@ -67,11 +67,11 @@ We have written a helper command in the `nf-core/tools` package that uses the Gi
```console
$ nf-core modules install . fastqc
,--./,-.
___ __ __ __ ___ /,-._.--~\
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
`._,._,'
nf-core/tools version 1.10.2
@ -99,11 +99,11 @@ We have written a helper command in the `nf-core/tools` package that uses the Gi
...truncated...
Commands:
list List available software modules.
install Add a DSL2 software wrapper module to a pipeline.
update Update one or all software wrapper modules. (NOT YET IMPLEMENTED)
remove Remove a software wrapper from a pipeline. (NOT YET IMPLEMENTED)
check Check that imported module code has not been modified. (NOT YET IMPLEMENTED)
list List available software modules.
install Add a DSL2 software wrapper module to a pipeline.
update Update one or all software wrapper modules. (NOT YET IMPLEMENTED)
remove Remove a software wrapper from a pipeline. (NOT YET IMPLEMENTED)
check Check that imported module code has not been modified. (NOT YET IMPLEMENTED)
```
## Adding a new module file

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tests/data/bam/test.paired_end.sorted.bam.bai
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tests/data/bam/test.single_end.sorted.bam.bai
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2
tests/data/bed/A.bed
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@ -1,5 +1,3 @@
chr1 951 1061
chr1 1300 1420
chr1 1400 1500

22
tests/data/fastqc/test_1_fastqc.html
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@ -41,9 +41,9 @@
background-color: #EEE;
border:0;
margin:0;
padding:0.5em;
padding:0.5em;
height: 1.3em;
overflow:hidden;
overflow:hidden;
font-size: 100%;
font-weight: bold;
position:fixed;
@ -58,15 +58,15 @@
}
@media print {
img {
max-width:100% !important;
page-break-inside: avoid;
}
h2, h3 {
page-break-after: avoid;
}
div.header {
background-color: #FFF;
img {
max-width:100% !important;
page-break-inside: avoid;
}
h2, h3 {
page-break-after: avoid;
}
div.header {
background-color: #FFF;
}
}

22
tests/data/fastqc/test_2_fastqc.html
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@ -41,9 +41,9 @@
background-color: #EEE;
border:0;
margin:0;
padding:0.5em;
padding:0.5em;
height: 1.3em;
overflow:hidden;
overflow:hidden;
font-size: 100%;
font-weight: bold;
position:fixed;
@ -58,15 +58,15 @@
}
@media print {
img {
max-width:100% !important;
page-break-inside: avoid;
}
h2, h3 {
page-break-after: avoid;
}
div.header {
background-color: #FFF;
img {
max-width:100% !important;
page-break-inside: avoid;
}
h2, h3 {
page-break-after: avoid;
}
div.header {
background-color: #FFF;
}
}

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tests/data/index/E_coli/bwa/NC_010473.fa.bwt
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tests/data/index/E_coli/bwa/NC_010473.fa.pac
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tests/data/index/E_coli/bwa/NC_010473.fa.sa
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4
tests/software/bowtie/align/main.nf
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@ -12,7 +12,7 @@ workflow test_bowtie_align_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ]
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ]
BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
}
@ -23,7 +23,7 @@ workflow test_bowtie_align_paired_end {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
}

4
tests/software/bowtie2/align/main.nf
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@ -12,7 +12,7 @@ workflow test_bowtie2_align_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ]
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ]
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index )
}
@ -23,7 +23,7 @@ workflow test_bowtie2_align_paired_end {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index )
}

4
tests/software/bwa/mem/main.nf
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@ -11,7 +11,7 @@ workflow test_bwa_mem_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ]
[ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ]
BWA_MEM (
input,
@ -27,7 +27,7 @@ workflow test_bwa_mem_paired_end {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true),
[ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz", checkIfExists: true) ] ]
BWA_MEM (

5
tests/software/cutadapt/main.nf
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@ -11,7 +11,7 @@ workflow test_cutadapt_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
[ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
CUTADAPT( input )
}
@ -23,8 +23,7 @@ workflow test_cutadapt_paired_end {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
CUTADAPT( input )
}

2
tests/software/dsh/filterbed/main.nf
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@ -8,7 +8,7 @@ workflow test_dsh_filterbed {
def input = []
input = [ [ id:'A' ], // meta map
[ file("${launchDir}/tests/data/bed/A.bed.gz", checkIfExists: true) ] ]
[ file("${launchDir}/tests/data/bed/A.bed.gz", checkIfExists: true) ] ]
DSH_FILTERBED ( input )
}

2
tests/software/dsh/splitbed/main.nf
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@ -8,7 +8,7 @@ workflow test_dsh_splitbed {
def input = []
input = [ [ id:'A' ], // meta map
[ file("${launchDir}/tests/data/bed/A.bed.gz", checkIfExists: true) ] ]
[ file("${launchDir}/tests/data/bed/A.bed.gz", checkIfExists: true) ] ]
DSH_SPLITBED ( input )
}

5
tests/software/fastp/main.nf
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@ -11,7 +11,7 @@ workflow test_fastp_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
[ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
FASTP ( input )
}
@ -22,8 +22,7 @@ workflow test_fastp_paired_end {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
FASTP ( input )
}

6
tests/software/fastqc/main.nf
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@ -11,7 +11,7 @@ workflow test_fastqc_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
[ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
FASTQC ( input )
}
@ -22,7 +22,7 @@ workflow test_fastqc_paired_end {
def input = []
input = [[id: 'test', single_end: false], // meta map
[file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true)]]
[file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true)]]
FASTQC (input)
}

2
tests/software/multiqc/main.nf
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@ -9,7 +9,7 @@ workflow test_multiqc {
def input = []
input = [ [ id: 'test', single_end: false ],
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
FASTQC ( input )
MULTIQC ( FASTQC.out.zip.collect { it[1] } )

1
tests/software/multiqc/test.yml
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@ -4,4 +4,3 @@
- multiqc
files:
- path: output/multiqc/multiqc_report.html

2
tests/software/pangolin/main.nf
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@ -6,7 +6,7 @@ include { PANGOLIN } from '../../../software/pangolin/main.nf' addParams(options
workflow test_pangolin {
input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true) ] ]
[ file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true) ] ]
PANGOLIN( input )
}

2
tests/software/picard/collectmultiplemetrics/main.nf
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@ -8,7 +8,7 @@ workflow test_picard_collectmultiplemetrics {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ]
file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ]
PICARD_COLLECTMULTIPLEMETRICS (
input,

4
tests/software/picard/markduplicates/main.nf
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@ -8,7 +8,7 @@ workflow test_picard_markduplicates_sorted_bam {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
PICARD_MARKDUPLICATES ( input )
}
@ -17,7 +17,7 @@ workflow test_picard_markduplicates_unsorted_bam {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ]
file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ]
PICARD_MARKDUPLICATES ( input )
}

2
tests/software/picard/mergesamfiles/main.nf
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@ -8,7 +8,7 @@ workflow test_picard_mergesamfiles {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
[ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true), ] ]
PICARD_MERGESAMFILES ( input )

5
tests/software/preseq/lcextrap/main.nf
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@ -11,7 +11,7 @@ workflow test_preseq_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file('https://github.com/smithlabcode/preseq/raw/master/data/SRR1003759_5M_subset.mr', checkIfExists: true), ] ]
[ file('https://github.com/smithlabcode/preseq/raw/master/data/SRR1003759_5M_subset.mr', checkIfExists: true), ] ]
PRESEQ_LCEXTRAP ( input )
}
@ -22,8 +22,7 @@ workflow test_preseq_paired_end {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file('https://github.com/smithlabcode/preseq/raw/master/data/SRR1003759_5M_subset.mr', checkIfExists: true), ] ]
[ file('https://github.com/smithlabcode/preseq/raw/master/data/SRR1003759_5M_subset.mr', checkIfExists: true), ] ]
PRESEQ_LCEXTRAP ( input )
}

4
tests/software/salmon/quant/main.nf
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@ -11,7 +11,7 @@ workflow test_salmon_quant_single_end {
def transcript_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
def gtf = file("${launchDir}/tests/data/gff/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true)
def input = [ [ id:'test', single_end:true ], // meta map
file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_1.fastq.gz", checkIfExists: true) ]
file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_1.fastq.gz", checkIfExists: true) ]
SALMON_INDEX ( genome_fasta, transcript_fasta )
SALMON_QUANT ( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false )
@ -24,7 +24,7 @@ workflow test_salmon_quant_paired_end {
def transcript_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
def gtf = file("${launchDir}/tests/data/gff/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true)
def input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_1.fastq.gz", checkIfExists: true),
[ file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_2.fastq.gz", checkIfExists: true) ] ]
SALMON_INDEX ( genome_fasta, transcript_fasta )

4
tests/software/samtools/flagstat/main.nf
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@ -8,7 +8,7 @@ workflow test_samtools_flagstat {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
SAMTOOLS_FLAGSTAT ( input )
}

4
tests/software/samtools/idxstats/main.nf
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@ -8,7 +8,7 @@ workflow test_samtools_idxstats {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
SAMTOOLS_IDXSTATS ( input )
}

2
tests/software/samtools/index/main.nf
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@ -8,6 +8,6 @@ workflow test_samtools_index {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
SAMTOOLS_INDEX ( input )
}

2
tests/software/samtools/mpileup/main.nf
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@ -9,7 +9,7 @@ workflow test_samtools_mpileup {
def input = []
def fasta = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
fasta = [ file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) ]
SAMTOOLS_MPILEUP ( input, fasta )
}

2
tests/software/samtools/sort/main.nf
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@ -8,6 +8,6 @@ workflow test_samtools_sort {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
SAMTOOLS_SORT ( input )
}

4
tests/software/samtools/stats/main.nf
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@ -8,7 +8,7 @@ workflow test_samtools_stats {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
SAMTOOLS_STATS ( input )
}

2
tests/software/samtools/view/main.nf
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@ -8,6 +8,6 @@ workflow test_samtools_view {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
SAMTOOLS_VIEW ( input )
}

4
tests/software/seacr/callpeak/main.nf
View file

@ -8,8 +8,8 @@ workflow test_seacr_callpeak {
def input = []
input = [[ id:'test_1'],
file("${launchDir}/tests/data/bedgraph/K27me3_1_to_chr20.bedgraph", checkIfExists: true),
file("${launchDir}/tests/data/bedgraph/IgG_1_to_chr20.bedgraph", checkIfExists: true) ]
file("${launchDir}/tests/data/bedgraph/K27me3_1_to_chr20.bedgraph", checkIfExists: true),
file("${launchDir}/tests/data/bedgraph/IgG_1_to_chr20.bedgraph", checkIfExists: true) ]
SEACR_CALLPEAK ( input )
}

6
tests/software/star/align/main.nf
View file

@ -12,7 +12,7 @@ workflow test_star_alignment_single_end {
STAR_GENOMEGENERATE ( fasta, gtf )
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
[ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
}
@ -23,7 +23,7 @@ workflow test_star_alignment_paired_end {
STAR_GENOMEGENERATE ( fasta, gtf )
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
}

4
tests/software/stringtie/main.nf
View file

@ -11,7 +11,7 @@ include { STRINGTIE as STRINGTIE_REVERSE } from '../../../software/stringtie/mai
workflow test_stringtie_forward {
def input = []
input = [ [ id:'test', strandedness:'forward' ], // meta map
[ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] ]
[ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] ]
STRINGTIE_FORWARD (
input,
@ -25,7 +25,7 @@ workflow test_stringtie_forward {
workflow test_stringtie_reverse {
def input = []
input = [ [ id:'test', strandedness:'reverse' ], // meta map
[ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] ]
[ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] ]
STRINGTIE_REVERSE (
input,

4
tests/software/trimgalore/main.nf
View file

@ -11,7 +11,7 @@ workflow test_trimgalore_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
[ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
TRIMGALORE ( input )
}
@ -22,7 +22,7 @@ workflow test_trimgalore_paired_end {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
TRIMGALORE ( input )

2
tests/software/ucsc/bedgraphtobigwig/main.nf
View file

@ -7,7 +7,7 @@ include { UCSC_BEDGRAPHTOBIGWIG } from '../../../../software/ucsc/bedgraphtobig
workflow test_ucsc_bedgraphtobigwig {
def input = []
input = [ [ id:'test' ], // meta map
[ file('https://raw.githubusercontent.com/igvteam/igv.js/master/test/data/wig/bedgraph-example-uscs.bedgraph', checkIfExists: true) ] ]
[ file('https://raw.githubusercontent.com/igvteam/igv.js/master/test/data/wig/bedgraph-example-uscs.bedgraph', checkIfExists: true) ] ]
UCSC_BEDGRAPHTOBIGWIG (
input,