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Fix relative paths

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This commit is contained in:
drpatelh 2021-02-03 16:20:02 +00:00
parent 38c3ecfac6
commit 239cbe17ad
25 changed files with 29 additions and 29 deletions
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4
tests/software/bowtie/align/main.nf
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@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
include { BOWTIE_BUILD } from '../../../software/bowtie/build/main.nf' addParams( options: [:] )
include { BOWTIE_ALIGN } from '../../../software/bowtie/align/main.nf' addParams( options: [:] )
include { BOWTIE_BUILD } from '../../../../software/bowtie/build/main.nf' addParams( options: [:] )
include { BOWTIE_ALIGN } from '../../../../software/bowtie/align/main.nf' addParams( options: [:] )
workflow test_bowtie_alignment_single_end {

2
tests/software/bowtie/build/main.nf
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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { BOWTIE_BUILD } from '../../../software/bowtie/build/main.nf' addParams( options: [:] )
include { BOWTIE_BUILD } from '../../../../software/bowtie/build/main.nf' addParams( options: [:] )
workflow test_bowtie_build {
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)

4
tests/software/bowtie2/align/main.nf
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@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
include { BOWTIE2_BUILD } from '../../../software/bowtie2/build/main.nf' addParams( options: [:] )
include { BOWTIE2_ALIGN } from '../../../software/bowtie2/align/main.nf' addParams( options: [:] )
include { BOWTIE2_BUILD } from '../../../../software/bowtie2/build/main.nf' addParams( options: [:] )
include { BOWTIE2_ALIGN } from '../../../../software/bowtie2/align/main.nf' addParams( options: [:] )
workflow test_bowtie2_align_single_end {

2
tests/software/bowtie2/build/main.nf
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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { BOWTIE2_BUILD } from '../../../software/bowtie2/build/main.nf' addParams( options: [:] )
include { BOWTIE2_BUILD } from '../../../../software/bowtie2/build/main.nf' addParams( options: [:] )
workflow test_bowtie2_build {
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)

2
tests/software/bwa/index/main.nf
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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { BWA_INDEX } from '../../../software/bwa/index/main.nf' addParams( options: [:] )
include { BWA_INDEX } from '../../../../software/bwa/index/main.nf' addParams( options: [:] )
workflow test_bwa_index {
BWA_INDEX ( file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) )

2
tests/software/bwa/mem/main.nf
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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { BWA_MEM } from '../../../software/bwa/mem/main.nf' addParams( options: [:] )
include { BWA_MEM } from '../../../../software/bwa/mem/main.nf' addParams( options: [:] )
/*
* Test with single-end data

2
tests/software/dsh/filterbed/main.nf
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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { DSH_FILTERBED } from '../../../software/dsh/filterbed/main.nf' addParams( options: [suffix: '.filtered', args: '--range chr1:0-1000'] )
include { DSH_FILTERBED } from '../../../../software/dsh/filterbed/main.nf' addParams( options: [suffix: '.filtered', args: '--range chr1:0-1000'] )
workflow test_dsh_filterbed {

2
tests/software/dsh/splitbed/main.nf
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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { DSH_SPLITBED } from '../../../software/dsh/splitbed/main.nf' addParams( options: [suffix: '.', args: '--records 2'] )
include { DSH_SPLITBED } from '../../../../software/dsh/splitbed/main.nf' addParams( options: [suffix: '.', args: '--records 2'] )
workflow test_dsh_splitbed {

2
tests/software/picard/collectmultiplemetrics/main.nf
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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../software/picard/collectmultiplemetrics/main.nf' addParams( options: [:] )
include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../../software/picard/collectmultiplemetrics/main.nf' addParams( options: [:] )
workflow test_picard_collectmultiplemetrics {

2
tests/software/picard/markduplicates/main.nf
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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { PICARD_MARKDUPLICATES } from '../../../software/picard/markduplicates/main.nf' addParams( options: [:] )
include { PICARD_MARKDUPLICATES } from '../../../../software/picard/markduplicates/main.nf' addParams( options: [:] )
workflow test_picard_markduplicates_sorted_bam {

2
tests/software/picard/mergesamfiles/main.nf
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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { PICARD_MERGESAMFILES } from '../../../software/picard/mergesamfiles/main.nf' addParams( options: [:] )
include { PICARD_MERGESAMFILES } from '../../../../../software/picard/mergesamfiles/main.nf' addParams( options: [:] )
workflow test_picard_mergesamfiles {

2
tests/software/preseq/lcextrap/main.nf
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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { PRESEQ_LCEXTRAP } from '../../../software/preseq/lcextrap/main.nf' addParams( options: [:] )
include { PRESEQ_LCEXTRAP } from '../../../../software/preseq/lcextrap/main.nf' addParams( options: [:] )
/*
* Test with single-end data

2
tests/software/salmon/index/main.nf
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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { SALMON_INDEX } from '../../../software/salmon/index/main.nf' addParams( options: [args: '--minAssignedFrags 1'] )
include { SALMON_INDEX } from '../../../../software/salmon/index/main.nf' addParams( options: [args: '--minAssignedFrags 1'] )
workflow test_salmon_index {
def genome_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)

4
tests/software/salmon/quant/main.nf
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@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
include { SALMON_INDEX } from '../../../software/salmon/index/main.nf' addParams( options: [:] )
include { SALMON_QUANT } from '../../../software/salmon/quant/main.nf' addParams( options: [args: '--minAssignedFrags 1'] )
include { SALMON_INDEX } from '../../../../software/salmon/index/main.nf' addParams( options: [:] )
include { SALMON_QUANT } from '../../../../software/salmon/quant/main.nf' addParams( options: [args: '--minAssignedFrags 1'] )
workflow test_salmon_quant_single_end {

2
tests/software/samtools/flagstat/main.nf
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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { SAMTOOLS_FLAGSTAT } from '../../../software/samtools/flagstat/main.nf' addParams( options: [:] )
include { SAMTOOLS_FLAGSTAT } from '../../../../software/samtools/flagstat/main.nf' addParams( options: [:] )
workflow test_samtools_flagstat {

2
tests/software/samtools/idxstats/main.nf
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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { SAMTOOLS_IDXSTATS } from '../../../software/samtools/idxstats/main.nf' addParams( options: [:] )
include { SAMTOOLS_IDXSTATS } from '../../../../software/samtools/idxstats/main.nf' addParams( options: [:] )
workflow test_samtools_idxstats {

2
tests/software/samtools/index/main.nf
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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { SAMTOOLS_INDEX } from '../../../software/samtools/index/main.nf' addParams( options: [:] )
include { SAMTOOLS_INDEX } from '../../../../software/samtools/index/main.nf' addParams( options: [:] )
workflow test_samtools_index {

2
tests/software/samtools/mpileup/main.nf
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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { SAMTOOLS_MPILEUP } from '../../../software/samtools/mpileup/main.nf' addParams( options: [:] )
include { SAMTOOLS_MPILEUP } from '../../../../software/samtools/mpileup/main.nf' addParams( options: [:] )
workflow test_samtools_mpileup {

2
tests/software/samtools/sort/main.nf
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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { SAMTOOLS_SORT } from '../../../software/samtools/sort/main.nf' addParams( options: [:] )
include { SAMTOOLS_SORT } from '../../../../software/samtools/sort/main.nf' addParams( options: [:] )
workflow test_samtools_sort {

2
tests/software/samtools/stats/main.nf
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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { SAMTOOLS_STATS } from '../../../software/samtools/stats/main.nf' addParams( options: [:] )
include { SAMTOOLS_STATS } from '../../../../software/samtools/stats/main.nf' addParams( options: [:] )
workflow test_samtools_stats {

2
tests/software/samtools/view/main.nf
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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { SAMTOOLS_VIEW } from '../../../software/samtools/view/main.nf' addParams( options: [:] )
include { SAMTOOLS_VIEW } from '../../../../software/samtools/view/main.nf' addParams( options: [:] )
workflow test_samtools_view {

2
tests/software/seacr/callpeak/main.nf
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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { SEACR_CALLPEAK } from '../../../software/seacr/callpeak/main.nf' addParams( options: [ args:'norm stringent' ] )
include { SEACR_CALLPEAK } from '../../../../software/seacr/callpeak/main.nf' addParams( options: [ args:'norm stringent' ] )
workflow test_seacr_callpeak {

4
tests/software/star/align/main.nf
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@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
include { STAR_GENOMEGENERATE } from '../../../software/star/genomegenerate/main.nf' addParams( options: [args: '--genomeSAindexNbases 9'] )
include { STAR_ALIGN } from '../../../software/star/align/main.nf' addParams( options: [args: '--readFilesCommand zcat'] )
include { STAR_GENOMEGENERATE } from '../../../../software/star/genomegenerate/main.nf' addParams( options: [args: '--genomeSAindexNbases 9'] )
include { STAR_ALIGN } from '../../../../software/star/align/main.nf' addParams( options: [args: '--readFilesCommand zcat'] )
workflow test_star_alignment_single_end {

2
tests/software/star/genomegenerate/main.nf
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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { STAR_GENOMEGENERATE } from '../../../software/star/genomegenerate/main.nf' addParams( options: [args: '--genomeSAindexNbases 9'] )
include { STAR_GENOMEGENERATE } from '../../../../software/star/genomegenerate/main.nf' addParams( options: [args: '--genomeSAindexNbases 9'] )
workflow test_star_genomegenerate {

2
tests/software/ucsc/bedgraphtobigwig/main.nf
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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { UCSC_BEDGRAPHTOBIGWIG } from '../../../software/ucsc/bedgraphtobigwig/main.nf' addParams( options: [:] )
include { UCSC_BEDGRAPHTOBIGWIG } from '../../../../software/ucsc/bedgraphtobigwig/main.nf' addParams( options: [:] )
workflow test_ucsc_bedgraphtobigwig {
def input = []