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Get tests passing

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This commit is contained in:
drpatelh 2020-10-15 10:47:15 +01:00
parent c32fcb39fc
commit 530789ba85
26 changed files with 62 additions and 61 deletions
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7
software/SOFTWARE/TOOL/test/main.nf
View file

@ -2,7 +2,8 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { FASTQC } from '../main.nf' include { FASTQC as FASTQC_SE } from '../main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
include { FASTQC as FASTQC_PE } from '../main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
/* /*
* Test with single-end data * Test with single-end data
@ -13,7 +14,7 @@ workflow test_single_end {
input = [ [ id:'test', single_end:true ], // meta map input = [ [ id:'test', single_end:true ], // meta map
[ file("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ] [ file("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ]
FASTQC ( input, [ publish_dir:'test_single_end' ] ) FASTQC_SE ( input )
} }
/* /*
@ -26,7 +27,7 @@ workflow test_paired_end {
[ file("${baseDir}/input/test_R1.fastq.gz", checkIfExists: true), [ file("${baseDir}/input/test_R1.fastq.gz", checkIfExists: true),
file("${baseDir}/input/test_R2.fastq.gz", checkIfExists: true) ] ] file("${baseDir}/input/test_R2.fastq.gz", checkIfExists: true) ] ]
FASTQC ( input, [ publish_dir:'test_paired_end' ] ) FASTQC_PE ( input )
} }
workflow { workflow {

4
software/SOFTWARE/TOOL/test/nextflow.config
View file

@ -2,12 +2,12 @@
params { params {
outdir = "output/" outdir = "output/"
publish_dir_mode = "copy" publish_dir_mode = "copy"
conda = false enable_conda = false
} }
profiles { profiles {
conda { conda {
params.conda = true params.enable_conda = true
} }
docker { docker {
docker.enabled = true docker.enabled = true

4
software/bwa/index/test/main.nf
View file

@ -2,10 +2,10 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { BWA_INDEX } from '../main.nf' include { BWA_INDEX } from '../main.nf' addParams( options: [:] )
workflow test { workflow test {
BWA_INDEX ( file("${baseDir}/input/NC_010473.fa", checkIfExists: true), [:] ) BWA_INDEX ( file("${baseDir}/input/NC_010473.fa", checkIfExists: true) )
} }
workflow { workflow {

4
software/bwa/index/test/nextflow.config
View file

@ -2,12 +2,12 @@
params { params {
outdir = "output/" outdir = "output/"
publish_dir_mode = "copy" publish_dir_mode = "copy"
conda = false enable_conda = false
} }
profiles { profiles {
conda { conda {
params.conda = true params.enable_conda = true
} }
docker { docker {
docker.enabled = true docker.enabled = true

13
software/bwa/mem/test/main.nf
View file

@ -2,7 +2,8 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { BWA_MEM } from '../main.nf' include { BWA_MEM as BWA_MEM_SE } from '../main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
include { BWA_MEM as BWA_MEM_PE } from '../main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
/* /*
* Test with single-end data * Test with single-end data
@ -13,11 +14,10 @@ workflow test_single_end {
input = [ [ id:'test', single_end:true ], // meta map input = [ [ id:'test', single_end:true ], // meta map
[ file("${baseDir}/input/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ] [ file("${baseDir}/input/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ]
BWA_MEM ( BWA_MEM_SE (
input, input,
file("${baseDir}/input/index/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true), file("${baseDir}/input/index/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
file("${baseDir}/input/NC_010473.fa", checkIfExists: true), file("${baseDir}/input/NC_010473.fa", checkIfExists: true)
[ publish_dir:'test_single_end' ]
) )
} }
@ -31,11 +31,10 @@ workflow test_paired_end {
[ file("${baseDir}/input/Ecoli_DNA_R1.fastq.gz", checkIfExists: true), [ file("${baseDir}/input/Ecoli_DNA_R1.fastq.gz", checkIfExists: true),
file("${baseDir}/input/Ecoli_DNA_R2.fastq.gz", checkIfExists: true) ] ] file("${baseDir}/input/Ecoli_DNA_R2.fastq.gz", checkIfExists: true) ] ]
BWA_MEM ( BWA_MEM_PE (
input, input,
file("${baseDir}/input/index/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true), file("${baseDir}/input/index/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
file("${baseDir}/input/NC_010473.fa", checkIfExists: true), file("${baseDir}/input/NC_010473.fa", checkIfExists: true)
[ publish_dir:'test_paired_end' ]
) )
} }

4
software/bwa/mem/test/nextflow.config
View file

@ -2,12 +2,12 @@
params { params {
outdir = "output/" outdir = "output/"
publish_dir_mode = "copy" publish_dir_mode = "copy"
conda = false enable_conda = false
} }
profiles { profiles {
conda { conda {
params.conda = true params.enable_conda = true
} }
docker { docker {
docker.enabled = true docker.enabled = true

7
software/fastqc/test/main.nf
View file

@ -2,7 +2,8 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { FASTQC } from '../main.nf' include { FASTQC as FASTQC_SE } from '../main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
include { FASTQC as FASTQC_PE } from '../main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
/* /*
* Test with single-end data * Test with single-end data
@ -13,7 +14,7 @@ workflow test_single_end {
input = [ [ id:'test', single_end:true ], // meta map input = [ [ id:'test', single_end:true ], // meta map
[ file("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ] [ file("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ]
FASTQC ( input, [ publish_dir:'test_single_end' ] ) FASTQC_SE ( input )
} }
/* /*
@ -26,7 +27,7 @@ workflow test_paired_end {
[ file("${baseDir}/input/test_R1.fastq.gz", checkIfExists: true), [ file("${baseDir}/input/test_R1.fastq.gz", checkIfExists: true),
file("${baseDir}/input/test_R2.fastq.gz", checkIfExists: true) ] ] file("${baseDir}/input/test_R2.fastq.gz", checkIfExists: true) ] ]
FASTQC ( input, [ publish_dir:'test_paired_end' ] ) FASTQC_PE ( input )
} }
workflow { workflow {

4
software/fastqc/test/nextflow.config
View file

@ -2,12 +2,12 @@
params { params {
outdir = "output/" outdir = "output/"
publish_dir_mode = "copy" publish_dir_mode = "copy"
conda = false enable_conda = false
} }
profiles { profiles {
conda { conda {
params.conda = true params.enable_conda = true
} }
docker { docker {
docker.enabled = true docker.enabled = true

5
software/picard/collectmultiplemetrics/test/main.nf
View file

@ -2,7 +2,7 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { PICARD_COLLECTMULTIPLEMETRICS } from '../main.nf' include { PICARD_COLLECTMULTIPLEMETRICS } from '../main.nf' addParams( options: [:] )
workflow test { workflow test {
@ -12,8 +12,7 @@ workflow test {
PICARD_COLLECTMULTIPLEMETRICS ( PICARD_COLLECTMULTIPLEMETRICS (
input, input,
file("${baseDir}/input/NC_010473.fa", checkIfExists: true), file("${baseDir}/input/NC_010473.fa", checkIfExists: true)
[:]
) )
} }

4
software/picard/collectmultiplemetrics/test/nextflow.config
View file

@ -2,12 +2,12 @@
params { params {
outdir = "output/" outdir = "output/"
publish_dir_mode = "copy" publish_dir_mode = "copy"
conda = false enable_conda = false
} }
profiles { profiles {
conda { conda {
params.conda = true params.enable_conda = true
} }
docker { docker {
docker.enabled = true docker.enabled = true

4
software/picard/markduplicates/test/main.nf
View file

@ -2,7 +2,7 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { PICARD_MARKDUPLICATES } from '../main.nf' include { PICARD_MARKDUPLICATES } from '../main.nf' addParams( options: [:] )
workflow test { workflow test {
@ -10,7 +10,7 @@ workflow test {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true) ] file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true) ]
PICARD_MARKDUPLICATES ( input, [:] ) PICARD_MARKDUPLICATES ( input )
} }
workflow { workflow {

4
software/picard/markduplicates/test/nextflow.config
View file

@ -2,12 +2,12 @@
params { params {
outdir = "output/" outdir = "output/"
publish_dir_mode = "copy" publish_dir_mode = "copy"
conda = false enable_conda = false
} }
profiles { profiles {
conda { conda {
params.conda = true params.enable_conda = true
} }
docker { docker {
docker.enabled = true docker.enabled = true

4
software/picard/mergesamfiles/test/main.nf
View file

@ -2,7 +2,7 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { PICARD_MERGESAMFILES } from '../main.nf' include { PICARD_MERGESAMFILES } from '../main.nf' addParams( options: [:] )
workflow test { workflow test {
@ -11,7 +11,7 @@ workflow test {
[ file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true), [ file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
file("${baseDir}/input/test.paired_end.COPY.sorted.bam", checkIfExists: true), ] ] file("${baseDir}/input/test.paired_end.COPY.sorted.bam", checkIfExists: true), ] ]
PICARD_MERGESAMFILES ( input, [:] ) PICARD_MERGESAMFILES ( input )
} }
workflow { workflow {

4
software/picard/mergesamfiles/test/nextflow.config
View file

@ -2,12 +2,12 @@
params { params {
outdir = "output/" outdir = "output/"
publish_dir_mode = "copy" publish_dir_mode = "copy"
conda = false enable_conda = false
} }
profiles { profiles {
conda { conda {
params.conda = true params.enable_conda = true
} }
docker { docker {
docker.enabled = true docker.enabled = true

4
software/samtools/flagstat/test/main.nf
View file

@ -2,7 +2,7 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { SAMTOOLS_FLAGSTAT } from '../main.nf' include { SAMTOOLS_FLAGSTAT } from '../main.nf' addParams( options: [:] )
workflow test { workflow test {
@ -11,7 +11,7 @@ workflow test {
file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true), file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
file("${baseDir}/input/test.paired_end.sorted.bam.bai", checkIfExists: true) ] file("${baseDir}/input/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
SAMTOOLS_FLAGSTAT ( input, [:] ) SAMTOOLS_FLAGSTAT ( input )
} }
workflow { workflow {

4
software/samtools/flagstat/test/nextflow.config
View file

@ -2,12 +2,12 @@
params { params {
outdir = "output/" outdir = "output/"
publish_dir_mode = "copy" publish_dir_mode = "copy"
conda = false enable_conda = false
} }
profiles { profiles {
conda { conda {
params.conda = true params.enable_conda = true
} }
docker { docker {
docker.enabled = true docker.enabled = true

4
software/samtools/idxstats/test/main.nf
View file

@ -2,7 +2,7 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { SAMTOOLS_IDXSTATS } from '../main.nf' include { SAMTOOLS_IDXSTATS } from '../main.nf' addParams( options: [:] )
workflow test { workflow test {
@ -11,7 +11,7 @@ workflow test {
file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true), file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
file("${baseDir}/input/test.paired_end.sorted.bam.bai", checkIfExists: true) ] file("${baseDir}/input/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
SAMTOOLS_IDXSTATS ( input, [:] ) SAMTOOLS_IDXSTATS ( input )
} }
workflow { workflow {

4
software/samtools/idxstats/test/nextflow.config
View file

@ -2,12 +2,12 @@
params { params {
outdir = "output/" outdir = "output/"
publish_dir_mode = "copy" publish_dir_mode = "copy"
conda = false enable_conda = false
} }
profiles { profiles {
conda { conda {
params.conda = true params.enable_conda = true
} }
docker { docker {
docker.enabled = true docker.enabled = true

4
software/samtools/index/test/main.nf
View file

@ -2,7 +2,7 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { SAMTOOLS_INDEX } from '../main.nf' include { SAMTOOLS_INDEX } from '../main.nf' addParams( options: [:] )
workflow test { workflow test {
@ -10,7 +10,7 @@ workflow test {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true) ] file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true) ]
SAMTOOLS_INDEX ( input, [:] ) SAMTOOLS_INDEX ( input )
} }
workflow { workflow {

4
software/samtools/index/test/nextflow.config
View file

@ -2,12 +2,12 @@
params { params {
outdir = "output/" outdir = "output/"
publish_dir_mode = "copy" publish_dir_mode = "copy"
conda = false enable_conda = false
} }
profiles { profiles {
conda { conda {
params.conda = true params.enable_conda = true
} }
docker { docker {
docker.enabled = true docker.enabled = true

4
software/samtools/sort/test/main.nf
View file

@ -2,7 +2,7 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { SAMTOOLS_SORT } from '../main.nf' include { SAMTOOLS_SORT } from '../main.nf' addParams( options: [:] )
workflow test { workflow test {
@ -10,7 +10,7 @@ workflow test {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
file("${baseDir}/input/test.paired_end.name.sorted.bam", checkIfExists: true) ] file("${baseDir}/input/test.paired_end.name.sorted.bam", checkIfExists: true) ]
SAMTOOLS_SORT ( input, [:] ) SAMTOOLS_SORT ( input )
} }
workflow { workflow {

4
software/samtools/sort/test/nextflow.config
View file

@ -2,12 +2,12 @@
params { params {
outdir = "output/" outdir = "output/"
publish_dir_mode = "copy" publish_dir_mode = "copy"
conda = false enable_conda = false
} }
profiles { profiles {
conda { conda {
params.conda = true params.enable_conda = true
} }
docker { docker {
docker.enabled = true docker.enabled = true

4
software/samtools/stats/test/main.nf
View file

@ -2,7 +2,7 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { SAMTOOLS_STATS } from '../main.nf' include { SAMTOOLS_STATS } from '../main.nf' addParams( options: [:] )
workflow test { workflow test {
@ -11,7 +11,7 @@ workflow test {
file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true), file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
file("${baseDir}/input/test.paired_end.sorted.bam.bai", checkIfExists: true) ] file("${baseDir}/input/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
SAMTOOLS_STATS ( input, [:] ) SAMTOOLS_STATS ( input )
} }
workflow { workflow {

4
software/samtools/stats/test/nextflow.config
View file

@ -2,12 +2,12 @@
params { params {
outdir = "output/" outdir = "output/"
publish_dir_mode = "copy" publish_dir_mode = "copy"
conda = false enable_conda = false
} }
profiles { profiles {
conda { conda {
params.conda = true params.enable_conda = true
} }
docker { docker {
docker.enabled = true docker.enabled = true

7
software/trimgalore/test/main.nf
View file

@ -2,7 +2,8 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { TRIMGALORE } from '../main.nf' include { TRIMGALORE as TRIMGALORE_SE } from '../main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
include { TRIMGALORE as TRIMGALORE_PE } from '../main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
/* /*
* Test with single-end data * Test with single-end data
@ -13,7 +14,7 @@ workflow test_single_end {
input = [ [ id:'test', single_end:true ], // meta map input = [ [ id:'test', single_end:true ], // meta map
[ file("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ] [ file("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ]
TRIMGALORE ( input, [ publish_dir:'test_single_end' ] ) TRIMGALORE_SE ( input )
} }
/* /*
@ -26,7 +27,7 @@ workflow test_paired_end {
[ file("${baseDir}/input/test_R1.fastq.gz", checkIfExists: true), [ file("${baseDir}/input/test_R1.fastq.gz", checkIfExists: true),
file("${baseDir}/input/test_R2.fastq.gz", checkIfExists: true) ] ] file("${baseDir}/input/test_R2.fastq.gz", checkIfExists: true) ] ]
TRIMGALORE ( input, [ publish_dir:'test_paired_end' ] ) TRIMGALORE_PE ( input )
} }
workflow { workflow {

4
software/trimgalore/test/nextflow.config
View file

@ -2,7 +2,7 @@
params { params {
outdir = "output/" outdir = "output/"
publish_dir_mode = "copy" publish_dir_mode = "copy"
conda = false enable_conda = false
clip_r1 = 0 clip_r1 = 0
clip_r2 = 0 clip_r2 = 0
@ -12,7 +12,7 @@ params {
profiles { profiles {
conda { conda {
params.conda = true params.enable_conda = true
} }
docker { docker {
docker.enabled = true docker.enabled = true