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Merge pull request #142 from drpatelh/split_tests

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Split tests
This commit is contained in:
Harshil Patel 2021-02-03 18:09:30 +00:00 committed by GitHub
commit 5f810beaa4
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GPG key ID: 4AEE18F83AFDEB23
76 changed files with 783 additions and 752 deletions
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70
.github/filters.yml vendored
View file

@ -1,28 +1,28 @@
bowtie2_align:
- software/bowtie2/align/**
- software/bowtie2/build/**
- tests/software/bowtie2/**
bowtie2_build:
- software/bowtie2/build/**
- tests/software/bowtie2/**
bowtie_align:
- software/bowtie/align/**
- software/bowtie/build/**
- tests/software/bowtie/**
- tests/software/bowtie/align/**
bowtie_build:
- software/bowtie/build/**
- tests/software/bowtie/**
- tests/software/bowtie/build/**
bowtie2_align:
- software/bowtie2/align/**
- software/bowtie2/build/**
- tests/software/bowtie2/align/**
bowtie2_build:
- software/bowtie2/build/**
- tests/software/bowtie2/build/**
bwa_index:
- software/bwa/index/**
- tests/software/bwa/**
- tests/software/bwa/index/**
bwa_mem:
- software/bwa/mem/**
- tests/software/bwa/**
- tests/software/bwa/mem/**
cutadapt:
- software/cutadapt/**
@ -30,11 +30,11 @@ cutadapt:
dsh_filterbed:
- software/dsh/filterbed/**
- tests/software/dsh/**
- tests/software/dsh/filterbed/**
dsh_splitbed:
- software/dsh/splitbed/**
- tests/software/dsh/**
- tests/software/dsh/splitbed/**
fastp:
- software/fastp/**
@ -49,6 +49,7 @@ gffread:
- tests/software/gffread/**
multiqc:
- software/fastqc/**
- software/multiqc/**
- tests/software/multiqc/**
@ -58,19 +59,19 @@ pangolin:
picard_collectmultiplemetrics:
- software/picard/collectmultiplemetrics/**
- tests/software/picard/**
- tests/software/picard/collectmultiplemetrics/**
picard_markduplicates:
- software/picard/markduplicates/**
- tests/software/picard/**
- tests/software/picard/markduplicates/**
picard_mergesamfiles:
- software/picard/mergesamfiles/**
- tests/software/picard/**
- tests/software/picard/mergesamfiles/**
preseq_lcextrap:
- software/preseq/lcextrap/**
- tests/software/preseq/**
- tests/software/preseq/lcextrap/**
quast:
- software/quast/**
@ -78,56 +79,55 @@ quast:
salmon_index:
- software/salmon/index/**
- tests/software/salmon/**
- tests/software/salmon/index/**
salmon_quant:
- software/salmon/quant/**
- tests/software/salmon/**
- tests/software/salmon/quant/**
samtools_flagstat:
- software/samtools/flagstat/**
- tests/software/samtools/**
- tests/software/samtools/flagstat/**
samtools_idxstats:
- software/samtools/idxstats/**
- tests/software/samtools/**
- tests/software/samtools/idxstats/**
samtools_index:
- software/samtools/index/**
- tests/software/samtools/**
- tests/software/samtools/index/**
samtools_mpileup:
- software/samtools/mpileup/**
- tests/software/samtools/**
- tests/software/samtools/mpileup/**
samtools_sort:
- software/samtools/sort/**
- tests/software/samtools/**
- tests/software/samtools/sort/**
samtools_stats:
- software/samtools/stats/**
- tests/software/samtools/**
- tests/software/samtools/stats/**
samtools_view:
- software/samtools/view/**
- tests/software/samtools/**
- tests/software/samtools/view/**
seacr_callpeak:
- software/seacr/callpeak/**
- tests/software/seacr/**
- tests/software/seacr/callpeak/**
star_align:
- software/star/align/**
- tests/software/star/**
- tests/software/star/align/**
star_genomegenerate:
- software/star/genomegenerate/**
- tests/software/star/**
- tests/software/star/genomegenerate/**
stringtie:
- software/stringtie/**
- tests/software/stringtie/**
- software/stringtie/**
- tests/software/stringtie/**
trimgalore:
- software/trimgalore/**
@ -135,4 +135,4 @@ trimgalore:
ucsc_bedgraphtobigwig:
- software/ucsc/bedgraphtobigwig/**
- tests/software/ucsc/**
- tests/software/ucsc/bedgraphtobigwig/**

18
tests/software/bowtie/main.nf → tests/software/bowtie/align/main.nf
View file

@ -2,17 +2,12 @@
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_build {
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
BOWTIE_BUILD ( fasta )
}
workflow test_bowtie_align_single_end {
workflow test_bowtie_alignment_single_end {
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
BOWTIE_BUILD ( fasta )
def input = []
@ -21,8 +16,9 @@ workflow test_bowtie_alignment_single_end {
BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
}
workflow test_bowtie_alignment_paired_end {
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
workflow test_bowtie_align_paired_end {
def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
BOWTIE_BUILD ( fasta )
def input = []

35
tests/software/bowtie/test.yml → tests/software/bowtie/align/test.yml
View file

@ -1,27 +1,9 @@
- name: Run bowtie build
command: nextflow run ./tests/software/bowtie -entry test_bowtie_build -c tests/config/nextflow.config
tags:
- bowtie
- bowtie_build
files:
- path: output/bowtie/bowtie/NC_010473.1.ebwt
md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
- path: output/bowtie/bowtie/NC_010473.2.ebwt
md5sum: bfd10c5319c6a0dbc540fd789254a5dd
- path: output/bowtie/bowtie/NC_010473.3.ebwt
md5sum: cd201e81724f3099131aec16ef2cc53b
- path: output/bowtie/bowtie/NC_010473.4.ebwt
md5sum: bbb9d6d21ad765d135f95290204e8433
- path: output/bowtie/bowtie/NC_010473.rev.1.ebwt
md5sum: 44f719c2fe42e1f35d54e798775846d1
- path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
md5sum: f3c398bba5158f4039334a932d79c051
- name: Run bowtie build and align single-end
command: nextflow run ./tests/software/bowtie -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
- name: bowtie align single-end
command: nextflow run ./tests/software/bowtie/align -entry test_bowtie_align_single_end -c tests/config/nextflow.config
tags:
- bowtie
- bowtie_align
- bowtie_align_single_end
files:
- path: output/bowtie/bowtie/NC_010473.1.ebwt
md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
@ -37,12 +19,15 @@
md5sum: f3c398bba5158f4039334a932d79c051
- path: output/bowtie/test.out
md5sum: a81cb18024616415a6cec3108a36fccd
- path: output/bowtie/test.bam
should_exist: true
- name: Run bowtie index and align paired-end
command: nextflow run ./tests/software/bowtie -entry test_bowtie_alignment_paired_end -c tests/config/nextflow.config
- name: bowtie align paired-end
command: nextflow run ./tests/software/bowtie/align -entry test_bowtie_align_single_end -c tests/config/nextflow.config
tags:
- bowtie
- bowtie_align
- bowtie_align_paired_end
files:
- path: output/bowtie/bowtie/NC_010473.1.ebwt
md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
@ -57,4 +42,6 @@
- path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
md5sum: f3c398bba5158f4039334a932d79c051
- path: output/bowtie/test.out
md5sum: a23e9a2a76e949aeb3693bcfae41a615
md5sum: a23e9a2a76e949aeb3693bcfae41a615
- path: output/bowtie/test.bam
should_exist: true

10
tests/software/bowtie/build/main.nf Normal file
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@ -0,0 +1,10 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
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)
BOWTIE_BUILD ( fasta )
}

18
tests/software/bowtie/build/test.yml Normal file
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@ -0,0 +1,18 @@
- name: bowtie build
command: nextflow run ./tests/software/bowtie/build -entry test_bowtie_build -c tests/config/nextflow.config
tags:
- bowtie
- bowtie_build
files:
- path: output/bowtie/bowtie/NC_010473.1.ebwt
md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
- path: output/bowtie/bowtie/NC_010473.2.ebwt
md5sum: bfd10c5319c6a0dbc540fd789254a5dd
- path: output/bowtie/bowtie/NC_010473.3.ebwt
md5sum: cd201e81724f3099131aec16ef2cc53b
- path: output/bowtie/bowtie/NC_010473.4.ebwt
md5sum: bbb9d6d21ad765d135f95290204e8433
- path: output/bowtie/bowtie/NC_010473.rev.1.ebwt
md5sum: 44f719c2fe42e1f35d54e798775846d1
- path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
md5sum: f3c398bba5158f4039334a932d79c051

18
tests/software/bowtie2/main.nf → tests/software/bowtie2/align/main.nf
View file

@ -2,17 +2,12 @@
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_build {
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
BOWTIE2_BUILD ( fasta )
}
workflow test_bowtie2_align_single_end {
workflow test_bowtie2_alignment_single_end {
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
BOWTIE2_BUILD ( fasta )
def input = []
@ -21,8 +16,9 @@ workflow test_bowtie2_alignment_single_end {
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index )
}
workflow test_bowtie2_alignment_paired_end {
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
workflow test_bowtie2_align_paired_end {
def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
BOWTIE2_BUILD ( fasta )
def input = []

33
tests/software/bowtie2/test.yml → tests/software/bowtie2/align/test.yml
View file

@ -1,27 +1,9 @@
- name: Run bowtie2 build
command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_build -c tests/config/nextflow.config
tags:
- bowtie2
- bowtie2_build
files:
- path: output/bowtie2/bowtie2/NC_010473.1.bt2
md5sum: 4db22d92e72111a5fbf609b3d9a43015
- path: output/bowtie2/bowtie2/NC_010473.2.bt2
md5sum: f4429ec74ee0064732c4bb26718a3eb1
- path: output/bowtie2/bowtie2/NC_010473.3.bt2
md5sum: cd201e81724f3099131aec16ef2cc53b
- path: output/bowtie2/bowtie2/NC_010473.4.bt2
md5sum: bbb9d6d21ad765d135f95290204e8433
- path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2
md5sum: 4ccfee8857c3b1c69857e5ecdef597aa
- path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2
md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72
- name: Run bowtie2 index and align single-end
command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_alignment_single_end -c tests/config/nextflow.config
- name: bowtie2 align single-end
command: nextflow run ./tests/software/bowtie2/align -entry test_bowtie2_align_single_end -c tests/config/nextflow.config
tags:
- bowtie2
- bowtie2_align
- bowtie2_align_single_end
files:
- path: output/bowtie2/bowtie2/NC_010473.1.bt2
md5sum: 4db22d92e72111a5fbf609b3d9a43015
@ -37,12 +19,15 @@
md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72
- path: output/bowtie2/test.bowtie2.log
md5sum: 90041c264231be535042adb93a279356
- path: output/bowtie2/test.bam
should_exist: true
- name: Run bowtie2 index and align paired-end
command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_alignment_paired_end -c tests/config/nextflow.config
- name: bowtie2 align paired-end
command: nextflow run ./tests/software/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config
tags:
- bowtie2
- bowtie2_align
- bowtie2_align_paired_end
files:
- path: output/bowtie2/bowtie2/NC_010473.1.bt2
md5sum: 4db22d92e72111a5fbf609b3d9a43015
@ -58,3 +43,5 @@
md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72
- path: output/bowtie2/test.bowtie2.log
md5sum: 9f9eb40b5f57e0f2d5c874f2c1b5cfd5
- path: output/bowtie2/test.bam
should_exist: true

10
tests/software/bowtie2/build/main.nf Normal file
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@ -0,0 +1,10 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
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)
BOWTIE2_BUILD ( fasta )
}

18
tests/software/bowtie2/build/test.yml Normal file
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@ -0,0 +1,18 @@
- name: bowtie2 build
command: nextflow run ./tests/software/bowtie2/build -entry test_bowtie2_build -c tests/config/nextflow.config
tags:
- bowtie2
- bowtie2_build
files:
- path: output/bowtie2/bowtie2/NC_010473.1.bt2
md5sum: 4db22d92e72111a5fbf609b3d9a43015
- path: output/bowtie2/bowtie2/NC_010473.2.bt2
md5sum: f4429ec74ee0064732c4bb26718a3eb1
- path: output/bowtie2/bowtie2/NC_010473.3.bt2
md5sum: cd201e81724f3099131aec16ef2cc53b
- path: output/bowtie2/bowtie2/NC_010473.4.bt2
md5sum: bbb9d6d21ad765d135f95290204e8433
- path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2
md5sum: 4ccfee8857c3b1c69857e5ecdef597aa
- path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2
md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72

9
tests/software/bwa/index/main.nf Normal file
View file

@ -0,0 +1,9 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
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) )
}

14
tests/software/bwa/index/test.yml Normal file
View file

@ -0,0 +1,14 @@
- name: bwa index
command: nextflow run ./tests/software/bwa/index -entry test_bwa_index -c tests/config/nextflow.config
tags:
- bwa
- bwa_index
files:
- path: output/bwa/NC_010473.fa.amb
md5sum: 942a990ae872f1c0b8d72dda2db405d5
- path: output/bwa/NC_010473.fa.bwt
md5sum: 7301b52e2ecb893d429a49fa692447ae
- path: output/bwa/NC_010473.fa.pac
md5sum: 4d5e6fc45bbc968f7f859e9ca2cc89ad
- path: output/bwa/NC_010473.fa.sa
md5sum: a47dcc92e750e2f16fbd979b8ff9538e

12
tests/software/bwa/main.nf → tests/software/bwa/mem/main.nf
View file

@ -2,13 +2,7 @@
nextflow.enable.dsl = 2
include { BWA_INDEX } from '../../../software/bwa/index/main.nf' addParams( options: [:] )
include { BWA_MEM as BWA_MEM_SE } from '../../../software/bwa/mem/main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
include { BWA_MEM as BWA_MEM_PE } from '../../../software/bwa/mem/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
workflow test_bwa_index {
BWA_INDEX ( file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) )
}
include { BWA_MEM } from '../../../../software/bwa/mem/main.nf' addParams( options: [:] )
/*
* Test with single-end data
@ -19,7 +13,7 @@ workflow test_bwa_mem_single_end {
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ]
BWA_MEM_SE (
BWA_MEM (
input,
file("${launchDir}/tests/data/index/E_coli/bwa/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
@ -36,7 +30,7 @@ workflow test_bwa_mem_paired_end {
[ 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_PE (
BWA_MEM (
input,
file("${launchDir}/tests/data/index/E_coli/bwa/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)

19
tests/software/bwa/mem/test.yml Normal file
View file

@ -0,0 +1,19 @@
- name: bwa mem single-end
command: nextflow run ./tests/software/bwa/mem -entry test_bwa_mem_single_end -c tests/config/nextflow.config
tags:
- bwa
- bwa_mem
- bwa_mem_single_end
files:
- path: output/bwa/test.bam
md5sum: 3ee21210bac387e0335008146e4728bc
- name: bwa mem paired-end
command: nextflow run ./tests/software/bwa/mem -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
tags:
- bwa
- bwa_mem
- bwa_mem_paired_end
files:
- path: output/bwa/test.bam
md5sum: 510d8acc6448c07cdacce8e64ec0904c

32
tests/software/bwa/test.yml
View file

@ -1,32 +0,0 @@
- name: Run bwa index
command: nextflow run ./tests/software/bwa -entry test_bwa_index -c tests/config/nextflow.config
tags:
- bwa
- bwa_index
files:
- path: output/bwa/NC_010473.fa.amb
md5sum: 942a990ae872f1c0b8d72dda2db405d5
- path: output/bwa/NC_010473.fa.bwt
md5sum: 7301b52e2ecb893d429a49fa692447ae
- path: output/bwa/NC_010473.fa.pac
md5sum: 4d5e6fc45bbc968f7f859e9ca2cc89ad
- path: output/bwa/NC_010473.fa.sa
md5sum: a47dcc92e750e2f16fbd979b8ff9538e
- name: Run bwa mem single-end
command: nextflow run ./tests/software/bwa -entry test_bwa_mem_single_end -c tests/config/nextflow.config
tags:
- bwa
- bwa_mem
files:
- path: output/test_single_end/test.bam
md5sum: 3ee21210bac387e0335008146e4728bc
- name: Run bwa mem paired-end
command: nextflow run ./tests/software/bwa -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
tags:
- bwa
- bwa_mem
files:
- path: output/test_paired_end/test.bam
md5sum: 510d8acc6448c07cdacce8e64ec0904c

8
tests/software/cutadapt/main.nf
View file

@ -7,11 +7,11 @@ include { CUTADAPT } from '../../../software/cutadapt/main.nf' addParams( optio
/*
* Test with single-end data
*/
workflow test_cutadapt_se {
workflow test_cutadapt_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
CUTADAPT( input )
}
@ -19,12 +19,12 @@ workflow test_cutadapt_se {
* Test with paired-end data
*/
workflow test_cutadapt_pe {
workflow test_cutadapt_paired_end {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
CUTADAPT( input )
}

12
tests/software/cutadapt/test.yml
View file

@ -1,17 +1,17 @@
- name: Run cutadapt single-end test workflow
command: nextflow run ./tests/software/cutadapt -entry test_cutadapt_se -c tests/config/nextflow.config
- name: cutadapt single-end
command: nextflow run ./tests/software/cutadapt -entry test_cutadapt_single_end -c tests/config/nextflow.config
tags:
- cutadapt
- cutadapt_se
- cutadapt_single_end
files:
- path: ./output/cutadapt/test.cutadapt.log
- path: ./output/cutadapt/test.trim.fastq.gz
- name: Run cutadapt paired-end test workflow
command: nextflow run ./tests/software/cutadapt -entry test_cutadapt_pe -c tests/config/nextflow.config
- name: cutadapt paired-end
command: nextflow run ./tests/software/cutadapt -entry test_cutadapt_paired_end -c tests/config/nextflow.config
tags:
- cutadapt
- cutadapt_pe
- cutadapt_paired_end
files:
- path: ./output/cutadapt/test.cutadapt.log
- path: ./output/cutadapt/test_1.trim.fastq.gz

14
tests/software/dsh/filterbed/main.nf Normal file
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@ -0,0 +1,14 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { DSH_FILTERBED } from '../../../../software/dsh/filterbed/main.nf' addParams( options: [suffix: '.filtered', args: '--range chr1:0-1000'] )
workflow test_dsh_filterbed {
def input = []
input = [ [ id:'A' ], // meta map
[ file("${launchDir}/tests/data/bed/A.bed.gz", checkIfExists: true) ] ]
DSH_FILTERBED ( input )
}

8
tests/software/dsh/filterbed/test.yml Normal file
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@ -0,0 +1,8 @@
- name: dsh filterbed
command: nextflow run ./tests/software/dsh/filterbed -entry test_dsh_filterbed -c tests/config/nextflow.config
tags:
- dsh
- dsh_filterbed
files:
- path: output/dsh/A.filtered.bed.gz
md5sum: 91cee4392d6034793f99f6c53891d866

24
tests/software/dsh/main.nf
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@ -1,24 +0,0 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { DSH_FILTERBED } from '../../../software/dsh/filterbed/main.nf' addParams( options: [suffix: '.filtered', args: '--range chr1:0-1000'] )
include { DSH_SPLITBED } from '../../../software/dsh/splitbed/main.nf' addParams( options: [suffix: '.', args: '--records 2'] )
workflow test_dsh_filterbed {
def input = []
input = [ [ id:'A' ], // meta map
[ file("${launchDir}/tests/data/bed/A.bed.gz", checkIfExists: true) ] ]
DSH_FILTERBED ( input )
}
workflow test_dsh_splitbed {
def input = []
input = [ [ id:'A' ], // meta map
[ file("${launchDir}/tests/data/bed/A.bed.gz", checkIfExists: true) ] ]
DSH_SPLITBED ( input )
}

14
tests/software/dsh/splitbed/main.nf Normal file
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@ -0,0 +1,14 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { DSH_SPLITBED } from '../../../../software/dsh/splitbed/main.nf' addParams( options: [suffix: '.', args: '--records 2'] )
workflow test_dsh_splitbed {
def input = []
input = [ [ id:'A' ], // meta map
[ file("${launchDir}/tests/data/bed/A.bed.gz", checkIfExists: true) ] ]
DSH_SPLITBED ( input )
}

10
tests/software/dsh/splitbed/test.yml Normal file
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@ -0,0 +1,10 @@
- name: dsh splitbed
command: nextflow run ./tests/software/dsh/splitbed -entry test_dsh_splitbed -c tests/config/nextflow.config
tags:
- dsh
- dsh_splitbed
files:
- path: output/dsh/A.0.bed.gz
md5sum: 619e51c435d0e7138ca41b660ed07e3a
- path: output/dsh/A.1.bed.gz
md5sum: 223bba025a0bb859de9a1bf385550a7e

19
tests/software/dsh/test.yml
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@ -1,19 +0,0 @@
- name: Run dsh filterbed
command: nextflow run ./tests/software/dsh -entry test_dsh_filterbed -c tests/config/nextflow.config
tags:
- dsh
- dsh_filterbed
files:
- path: output/dsh/A.filtered.bed.gz
md5sum: 91cee4392d6034793f99f6c53891d866
- name: Run dsh splitbed
command: nextflow run ./tests/software/dsh -entry test_dsh_splitbed -c tests/config/nextflow.config
tags:
- dsh
- dsh_splitbed
files:
- path: output/dsh/A.0.bed.gz
md5sum: 619e51c435d0e7138ca41b660ed07e3a
- path: output/dsh/A.1.bed.gz
md5sum: 223bba025a0bb859de9a1bf385550a7e

11
tests/software/fastp/main.nf
View file

@ -7,24 +7,23 @@ include { FASTP } from '../../../software/fastp/main.nf' addParams( options: [:
/*
* Test with single-end data
*/
workflow test_fastp_se {
workflow test_fastp_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
FASTP( input )
FASTP ( input )
}
/*
* Test with paired-end data
*/
workflow test_fastp_paired_end {
workflow test_fastp_pe {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
FASTP( input )
FASTP ( input )
}

12
tests/software/fastp/test.yml
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@ -1,8 +1,8 @@
- name: fastp_se
command: nextflow run ./tests/software/fastp -entry test_fastp_se -c ./tests/config/nextflow.config
- name: fastp single-end
command: nextflow run ./tests/software/fastp -entry test_fastp_single_end -c ./tests/config/nextflow.config
tags:
- fastp
- fastp_se
- fastp_single_end
files:
- path: ./output/fastp/test.fastp.json
md5sum: b81d53bfa5c1553bed89f6475edcf437
@ -11,11 +11,11 @@
- path: ./output/fastp/test.fastp.log
- path: ./output/fastp/test.fastp.html
- name: fastp_pe
command: nextflow run ./tests/software/fastp -entry test_fastp_pe -c ./tests/config/nextflow.config
- name: fastp paired-end
command: nextflow run ./tests/software/fastp -entry test_fastp_paired_end -c ./tests/config/nextflow.config
tags:
- fastp
- fastp_pe
- fastp_paired_end
files:
- path: ./output/fastp/test.fastp.html
- path: ./output/fastp/test.fastp.json

18
tests/software/fastqc/main.nf
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@ -2,35 +2,27 @@
nextflow.enable.dsl = 2
include { FASTQC as FASTQC_SE } from '../../../software/fastqc/main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
include { FASTQC as FASTQC_PE } from '../../../software/fastqc/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
include { FASTQC } from '../../../software/fastqc/main.nf' addParams( options: [:] )
/*
* Test with single-end data
*/
workflow test_single_end {
workflow test_fastqc_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
FASTQC_SE ( input )
FASTQC ( input )
}
/*
* Test with paired-end data
*/
workflow test_paired_end {
workflow test_fastqc_paired_end {
def input = []
input = [[id: 'test', single_end: false], // meta map
[file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true)]]
FASTQC_PE(input)
emit:
html = FASTQC_PE.out.html
zip = FASTQC_PE.out.zip
FASTQC (input)
}

22
tests/software/fastqc/test.yml
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@ -1,17 +1,19 @@
- name: Run fastqc single-end test workflow
command: nextflow run ./tests/software/fastqc/ -entry test_single_end -c tests/config/nextflow.config
- name: fastqc single-end
command: nextflow run ./tests/software/fastqc/ -entry test_fastqc_single_end -c tests/config/nextflow.config
tags:
- fastqc
- fastqc_single_end
files:
- path: output/test_single_end/test_fastqc.html
- path: output/test_single_end/test_fastqc.zip
- path: output/fastqc/test_fastqc.html
- path: output/fastqc/test_fastqc.zip
- name: Run fastqc paired-end test workflow
command: nextflow run ./tests/software/fastqc/ -entry test_paired_end -c tests/config/nextflow.config
- name: fastqc paired-end
command: nextflow run ./tests/software/fastqc/ -entry test_fastqc_paired_end -c tests/config/nextflow.config
tags:
- fastqc
- fastqc_paired_end
files:
- path: output/test_paired_end/test_1_fastqc.html
- path: output/test_paired_end/test_2_fastqc.html
- path: output/test_paired_end/test_1_fastqc.zip
- path: output/test_paired_end/test_2_fastqc.zip
- path: output/fastqc/test_1_fastqc.html
- path: output/fastqc/test_2_fastqc.html
- path: output/fastqc/test_1_fastqc.zip
- path: output/fastqc/test_2_fastqc.zip

2
tests/software/gffread/test.yml
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@ -1,4 +1,4 @@
- name: Run gffread test workflow
- name: gffread
command: nextflow run ./tests/software/gffread/ -entry test_gffread -c tests/config/nextflow.config
tags:
- gffread

18
tests/software/multiqc/main.nf
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@ -2,15 +2,15 @@
nextflow.enable.dsl = 2
include { MULTIQC } from '../../../software/multiqc/main.nf' addParams(options: [publish_dir: 'test_multiqc'])
include { test_paired_end } from '../fastqc/main.nf' addParams(options: [publish_dir: 'test_paired_end'])
include { FASTQC } from '../../../software/fastqc/main.nf' addParams( options: [:] )
include { MULTIQC } from '../../../software/multiqc/main.nf' addParams( options: [:] )
workflow test_multiqc {
test_paired_end()
input = [
test_paired_end.out.zip.collect { it[1] }.ifEmpty([])
]
MULTIQC(*input)
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_R2.fastq.gz", checkIfExists: true) ] ]
FASTQC ( input )
MULTIQC ( FASTQC.out.zip.collect { it[1] } )
}

6
tests/software/multiqc/test.yml
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@ -1,7 +1,7 @@
- name: Run multiqc test workflow
command: nextflow run ./tests/software/multiqc/ -entry test_multiqc -c tests/config/nextflow.config
- name: multiqc
command: nextflow run ./tests/software/multiqc -entry test_multiqc -c tests/config/nextflow.config
tags:
- multiqc
files:
- path: output/test_multiqc/multiqc_report.html
- path: output/multiqc/multiqc_report.html

17
tests/software/picard/collectmultiplemetrics/main.nf Normal file
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@ -0,0 +1,17 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../../software/picard/collectmultiplemetrics/main.nf' addParams( options: [:] )
workflow test_picard_collectmultiplemetrics {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ]
PICARD_COLLECTMULTIPLEMETRICS (
input,
file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
)
}

16
tests/software/picard/collectmultiplemetrics/test.yml Normal file
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@ -0,0 +1,16 @@
- name: picard collectmultiplemetrics
command: nextflow run ./tests/software/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics -c tests/config/nextflow.config
tags:
- picard
- picard_collectmultiplemetrics
files:
# These can't be md5'd consistently
- path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
- path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
- path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
- path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
- path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
- path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
- path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
- path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
- path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics

48
tests/software/picard/main.nf
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@ -1,48 +0,0 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { PICARD_MERGESAMFILES } from '../../../software/picard/mergesamfiles/main.nf' addParams( options: [:] )
include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../software/picard/collectmultiplemetrics/main.nf' addParams( options: [:] )
include { PICARD_MARKDUPLICATES } from '../../../software/picard/markduplicates/main.nf' addParams( options: [:] )
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.name.sorted.bam", checkIfExists: true), ] ]
PICARD_MERGESAMFILES ( input )
}
workflow test_picard_collectmultiplemetrics {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ]
PICARD_COLLECTMULTIPLEMETRICS (
input,
file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
)
}
workflow test_picard_markduplicates {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
PICARD_MARKDUPLICATES ( input )
}
workflow test_picard_markduplicates_not_sorted {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ]
PICARD_MARKDUPLICATES ( input )
}

23
tests/software/picard/markduplicates/main.nf Normal file
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@ -0,0 +1,23 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { PICARD_MARKDUPLICATES } from '../../../../software/picard/markduplicates/main.nf' addParams( options: [:] )
workflow test_picard_markduplicates_sorted_bam {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
PICARD_MARKDUPLICATES ( input )
}
workflow test_picard_markduplicates_unsorted_bam {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ]
PICARD_MARKDUPLICATES ( input )
}

17
tests/software/picard/markduplicates/test.yml Normal file
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@ -0,0 +1,17 @@
- name: picard markduplicates on sorted bam
command: nextflow run ./tests/software/picard/markduplicates -entry test_picard_markduplicates_sorted_bam -c tests/config/nextflow.config
tags:
- picard
- picard_markduplicates
files:
- path: output/picard/test.MarkDuplicates.metrics.txt
- path: output/picard/test.bam
md5sum: 0ed0bfc94069380334ccd595f6d8207c
- name: picard markduplicates on unsorted bam
command: nextflow run ./tests/software/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c tests/config/nextflow.config
tags:
- picard
- picard_markduplicates
- should fail
exit_code: 1

15
tests/software/picard/mergesamfiles/main.nf Normal file
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@ -0,0 +1,15 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { PICARD_MERGESAMFILES } from '../../../../software/picard/mergesamfiles/main.nf' addParams( options: [:] )
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.name.sorted.bam", checkIfExists: true), ] ]
PICARD_MERGESAMFILES ( input )
}

8
tests/software/picard/mergesamfiles/test.yml Normal file
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@ -0,0 +1,8 @@
- name: picard mergesamfiles
command: nextflow run ./tests/software/picard/mergesamfiles -entry test_picard_mergesamfiles -c tests/config/nextflow.config
tags:
- picard
- picard_mergesamfiles
files:
- path: output/picard/test.bam
md5sum: a9c8a28d1aac362df5973ba2d9923f86

43
tests/software/picard/test.yml
View file

@ -1,43 +0,0 @@
- name: Run picard mergesamfiles
command: nextflow run ./tests/software/picard -entry test_picard_mergesamfiles -c tests/config/nextflow.config
tags:
- picard
- picard_mergesamfiles
files:
- path: output/picard/test.bam
md5sum: a9c8a28d1aac362df5973ba2d9923f86
- name: Run picard collectmultiplemetrics
command: nextflow run ./tests/software/picard -entry test_picard_collectmultiplemetrics -c tests/config/nextflow.config
tags:
- picard
- picard_collectmultiplemetrics
files:
# These can't be md5'd consistently
- path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
- path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
- path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
- path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
- path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
- path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
- path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
- path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
- path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
- name: Run picard MarkDuplicates
command: nextflow run ./tests/software/picard -entry test_picard_markduplicates -c tests/config/nextflow.config
tags:
- picard
- picard_markduplicates
files:
- path: output/picard/test.MarkDuplicates.metrics.txt
- path: output/picard/test.bam
md5sum: 0ed0bfc94069380334ccd595f6d8207c
- name: Run picard MarkDuplicates without a sorted bam file so it fails
command: nextflow run ./tests/software/picard -entry test_picard_markduplicates_not_sorted -c tests/config/nextflow.config
tags:
- picard
- picard_markduplicates
- should fail
exit_code: 1

9
tests/software/preseq/main.nf → tests/software/preseq/lcextrap/main.nf
View file

@ -2,31 +2,28 @@
nextflow.enable.dsl = 2
include { PRESEQ_LCEXTRAP as PRESEQ_LCEXTRAP_SE } from '../../../software/preseq/lcextrap/main.nf' addParams( options: [ publish_dir:'test_preseq_single_end' ] )
include { PRESEQ_LCEXTRAP as PRESEQ_LCEXTRAP_PE } from '../../../software/preseq/lcextrap/main.nf' addParams( options: [ publish_dir:'test_preseq_paired_end' ] )
include { PRESEQ_LCEXTRAP } from '../../../../software/preseq/lcextrap/main.nf' addParams( options: [:] )
/*
* Test with single-end data
*/
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), ] ]
PRESEQ_LCEXTRAP_SE ( input )
PRESEQ_LCEXTRAP ( input )
}
/*
* Test with paired-end data
*/
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), ] ]
PRESEQ_LCEXTRAP_PE ( input )
PRESEQ_LCEXTRAP ( input )
}

21
tests/software/preseq/lcextrap/test.yml Normal file
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@ -0,0 +1,21 @@
- name: preseq lcextrap single-end
command: nextflow run ./tests/software/preseq/lcextrap -entry test_preseq_single_end -c tests/config/nextflow.config
tags:
- preseq
- preseq_lcextrap
- preseq_lcextrap_single_end
files:
- path: output/preseq/test.ccurve.txt
md5sum: 76ae04c8eaf19c94e3210bb69da38498
- path: output/preseq/test.command.log
- name: preseq lcextrap paired-end
command: nextflow run ./tests/software/preseq/lcextrap -entry test_preseq_paired_end -c tests/config/nextflow.config
tags:
- preseq
- preseq_lcextrap
- preseq_lcextrap_paired_end
files:
- path: output/preseq/test.ccurve.txt
md5sum: 2836d2fabd2213f097fd7063db550276
- path: output/preseq/test.command.log

21
tests/software/preseq/test.yml
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@ -1,21 +0,0 @@
- name: Run preseq single-end lcextrap
command: nextflow run ./tests/software/preseq -entry test_preseq_single_end -c tests/config/nextflow.config
tags:
- preseq
- preseq_lcextrap
files:
- path: output/test_preseq_single_end/test.ccurve.txt
md5sum: 76ae04c8eaf19c94e3210bb69da38498
- path: output/test_preseq_single_end/test.command.log
- name: Run preseq paired-end lcextrap
command: nextflow run ./tests/software/preseq -entry test_preseq_paired_end -c tests/config/nextflow.config
tags:
- preseq
- preseq_lcextrap
files:
- path: output/test_preseq_paired_end/test.ccurve.txt
md5sum: 2836d2fabd2213f097fd7063db550276
- path: output/test_preseq_paired_end/test.command.log

4
tests/software/quast/test.yml
View file

@ -1,4 +1,4 @@
- name: quast_ref
- name: quast with reference
command: nextflow run ./tests/software/quast -entry test_quast_ref -c ./tests/config/nextflow.config
tags:
- quast
@ -87,7 +87,7 @@
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: ./output/quast/quast/aligned_stats/NAx_plot.pdf
- name: quast_noref
- name: quast without reference
command: nextflow run ./tests/software/quast -entry test_quast_noref -c ./tests/config/nextflow.config
tags:
- quast

11
tests/software/salmon/index/main.nf Normal file
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@ -0,0 +1,11 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SALMON_INDEX } from '../../../../software/salmon/index/main.nf' addParams( options: [:] )
workflow test_salmon_index {
def genome_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
def transcript_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
SALMON_INDEX ( genome_fasta, transcript_fasta )
}

31
tests/software/salmon/index/test.yml Normal file
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@ -0,0 +1,31 @@
- name: salmon index
command: nextflow run ./tests/software/salmon/index -entry test_salmon_index -c tests/config/nextflow.config
tags:
- salmon
- salmon_index
files:
- path: ./output/salmon/salmon/info.json
md5sum: 61ff4d3471134c280668355ddd39e99f
- path: ./output/salmon/salmon/mphf.bin
md5sum: 53669a47610e33e031faafd32703b714
- path: ./output/salmon/salmon/complete_ref_lens.bin
md5sum: f57562f1fca3ae7b133f895ae13c3d08
- path: ./output/salmon/salmon/ref_indexing.log
- path: ./output/salmon/salmon/versionInfo.json
md5sum: 204865f645102587c4953fccb256797c
- path: ./output/salmon/salmon/seq.bin
- path: ./output/salmon/salmon/pre_indexing.log
- path: ./output/salmon/salmon/rank.bin
md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
- path: ./output/salmon/salmon/reflengths.bin
md5sum: f57562f1fca3ae7b133f895ae13c3d08
- path: ./output/salmon/salmon/ctable.bin
- path: ./output/salmon/salmon/ctg_offsets.bin
md5sum: 27a76542337df436436e66017f66dd25
- path: ./output/salmon/salmon/pos.bin
- path: ./output/salmon/salmon/duplicate_clusters.tsv
md5sum: 51b5292e3a874119c0e1aa566e95d70c
- path: ./output/salmon/salmon/refAccumLengths.bin
md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
- path: ./output/salmon/salmon/refseq.bin
md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7

35
tests/software/salmon/main.nf
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@ -1,35 +0,0 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
def quant_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: quant_options )
workflow test_salmon_index {
genome_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
transcript_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
SALMON_INDEX ( genome_fasta, transcript_fasta )
}
workflow test_salmon_quant_pe {
genome_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
transcript_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
gtf = file("${launchDir}/tests/data/gff/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true)
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_2.fastq.gz", checkIfExists: true) ] ]
SALMON_INDEX ( genome_fasta, transcript_fasta )
SALMON_QUANT( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false)
}
workflow test_salmon_quant_se {
genome_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
transcript_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
gtf = file("${launchDir}/tests/data/gff/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true)
input = [ [ id:'test', single_end:true ], // meta map
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)
}

33
tests/software/salmon/quant/main.nf Normal file
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@ -0,0 +1,33 @@
#!/usr/bin/env nextflow
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'] )
workflow test_salmon_quant_single_end {
def genome_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
def transcript_fasta = file("${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) ]
SALMON_INDEX ( genome_fasta, transcript_fasta )
SALMON_QUANT ( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false )
}
workflow test_salmon_quant_paired_end {
def genome_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
def transcript_fasta = file("${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_2.fastq.gz", checkIfExists: true) ] ]
SALMON_INDEX ( genome_fasta, transcript_fasta )
SALMON_QUANT ( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false )
}

144
tests/software/salmon/test.yml → tests/software/salmon/quant/test.yml
View file

@ -1,95 +1,9 @@
- name: salmon index
command: nextflow run ./tests/software/salmon -entry test_salmon_index -c tests/config/nextflow.config
tags:
- salmon
- salmon_index
files:
- path: ./output/salmon/salmon/info.json
md5sum: 61ff4d3471134c280668355ddd39e99f
- path: ./output/salmon/salmon/mphf.bin
md5sum: 53669a47610e33e031faafd32703b714
- path: ./output/salmon/salmon/complete_ref_lens.bin
md5sum: f57562f1fca3ae7b133f895ae13c3d08
- path: ./output/salmon/salmon/ref_indexing.log
- path: ./output/salmon/salmon/versionInfo.json
md5sum: 204865f645102587c4953fccb256797c
- path: ./output/salmon/salmon/seq.bin
- path: ./output/salmon/salmon/pre_indexing.log
- path: ./output/salmon/salmon/rank.bin
md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
- path: ./output/salmon/salmon/reflengths.bin
md5sum: f57562f1fca3ae7b133f895ae13c3d08
- path: ./output/salmon/salmon/ctable.bin
- path: ./output/salmon/salmon/ctg_offsets.bin
md5sum: 27a76542337df436436e66017f66dd25
- path: ./output/salmon/salmon/pos.bin
- path: ./output/salmon/salmon/duplicate_clusters.tsv
md5sum: 51b5292e3a874119c0e1aa566e95d70c
- path: ./output/salmon/salmon/refAccumLengths.bin
md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
- path: ./output/salmon/salmon/refseq.bin
md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
- name: salmon quant paired end
command: nextflow run ./tests/software/salmon -entry test_salmon_quant_pe -c tests/config/nextflow.config
tags:
- salmon
- salmon_quant
- salmon_quant_pe
files:
- path: ./output/salmon/salmon/pos.bin
- path: ./output/salmon/salmon/versionInfo.json
md5sum: 204865f645102587c4953fccb256797c
- path: ./output/salmon/salmon/complete_ref_lens.bin
md5sum: f57562f1fca3ae7b133f895ae13c3d08
- path: ./output/salmon/test/lib_format_counts.json
md5sum: a8b6e6bfbc28c6e790ddaec559fad9ea
- path: ./output/salmon/test/aux_info/expected_bias.gz
md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
- path: ./output/salmon/test/libParams/flenDist.txt
md5sum: f90c7256c9b18d4131f4d4ecb69d0f55
- path: ./output/salmon/salmon/ref_indexing.log
- path: ./output/salmon/test/aux_info/observed_bias_3p.gz
md5sum: ef13c06a538e9c34ca9f84212c82f44e
- path: ./output/salmon/salmon/ctable.bin
- path: ./output/salmon/test/aux_info/meta_info.json
- path: ./output/salmon/test/aux_info/fld.gz
- path: ./output/salmon/salmon/refseq.bin
md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
- path: ./output/salmon/salmon/info.json
md5sum: 61ff4d3471134c280668355ddd39e99f
- path: ./output/salmon/salmon/seq.bin
- path: ./output/salmon/test/cmd_info.json
md5sum: 007676e4d79de0809a03e0ea045ed4a1
- path: ./output/salmon/test/aux_info/observed_bias.gz
md5sum: ef13c06a538e9c34ca9f84212c82f44e
- path: ./output/salmon/salmon/duplicate_clusters.tsv
md5sum: 51b5292e3a874119c0e1aa566e95d70c
- path: ./output/salmon/test/quant.genes.sf
md5sum: eb3e7b44801a0b3af07c25963927e20d
- path: ./output/salmon/salmon/rank.bin
md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
- path: ./output/salmon/salmon/mphf.bin
md5sum: 53669a47610e33e031faafd32703b714
- path: ./output/salmon/test/aux_info/ambig_info.tsv
md5sum: 950001575c24fb6bc2c7a6848043b126
- path: ./output/salmon/test/logs/salmon_quant.log
- path: ./output/salmon/salmon/pre_indexing.log
- path: ./output/salmon/salmon/refAccumLengths.bin
md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
- path: ./output/salmon/test/quant.sf
md5sum: addb78e233f248b8f62cae3e217bf689
- path: ./output/salmon/salmon/reflengths.bin
md5sum: f57562f1fca3ae7b133f895ae13c3d08
- path: ./output/salmon/salmon/ctg_offsets.bin
md5sum: 27a76542337df436436e66017f66dd25
- name: salmon quant single-end
command: nextflow run ./tests/software/salmon -entry test_salmon_quant_se -c tests/config/nextflow.config
command: nextflow run ./tests/software/salmon/quant -entry test_salmon_quant_single_end -c tests/config/nextflow.config
tags:
- salmon
- salmon_quant
- salmon_quant_se
- salmon_quant_single_end
files:
- path: ./output/salmon/salmon/versionInfo.json
md5sum: 204865f645102587c4953fccb256797c
@ -137,3 +51,57 @@
md5sum: c3306d26186ffe018ad4f19d52256180
- path: ./output/salmon/test/quant.sf
md5sum: b08095ac70f89efc3146cdf488d0eb73
- name: salmon quant paired end
command: nextflow run ./tests/software/salmon/quant -entry test_salmon_quant_paired_end -c tests/config/nextflow.config
tags:
- salmon
- salmon_quant
- salmon_quant_paired_end
files:
- path: ./output/salmon/salmon/pos.bin
- path: ./output/salmon/salmon/versionInfo.json
md5sum: 204865f645102587c4953fccb256797c
- path: ./output/salmon/salmon/complete_ref_lens.bin
md5sum: f57562f1fca3ae7b133f895ae13c3d08
- path: ./output/salmon/test/lib_format_counts.json
md5sum: a8b6e6bfbc28c6e790ddaec559fad9ea
- path: ./output/salmon/test/aux_info/expected_bias.gz
md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
- path: ./output/salmon/test/libParams/flenDist.txt
md5sum: f90c7256c9b18d4131f4d4ecb69d0f55
- path: ./output/salmon/salmon/ref_indexing.log
- path: ./output/salmon/test/aux_info/observed_bias_3p.gz
md5sum: ef13c06a538e9c34ca9f84212c82f44e
- path: ./output/salmon/salmon/ctable.bin
- path: ./output/salmon/test/aux_info/meta_info.json
- path: ./output/salmon/test/aux_info/fld.gz
- path: ./output/salmon/salmon/refseq.bin
md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
- path: ./output/salmon/salmon/info.json
md5sum: 61ff4d3471134c280668355ddd39e99f
- path: ./output/salmon/salmon/seq.bin
- path: ./output/salmon/test/cmd_info.json
md5sum: 007676e4d79de0809a03e0ea045ed4a1
- path: ./output/salmon/test/aux_info/observed_bias.gz
md5sum: ef13c06a538e9c34ca9f84212c82f44e
- path: ./output/salmon/salmon/duplicate_clusters.tsv
md5sum: 51b5292e3a874119c0e1aa566e95d70c
- path: ./output/salmon/test/quant.genes.sf
md5sum: eb3e7b44801a0b3af07c25963927e20d
- path: ./output/salmon/salmon/rank.bin
md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
- path: ./output/salmon/salmon/mphf.bin
md5sum: 53669a47610e33e031faafd32703b714
- path: ./output/salmon/test/aux_info/ambig_info.tsv
md5sum: 950001575c24fb6bc2c7a6848043b126
- path: ./output/salmon/test/logs/salmon_quant.log
- path: ./output/salmon/salmon/pre_indexing.log
- path: ./output/salmon/salmon/refAccumLengths.bin
md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
- path: ./output/salmon/test/quant.sf
md5sum: addb78e233f248b8f62cae3e217bf689
- path: ./output/salmon/salmon/reflengths.bin
md5sum: f57562f1fca3ae7b133f895ae13c3d08
- path: ./output/salmon/salmon/ctg_offsets.bin
md5sum: 27a76542337df436436e66017f66dd25

14
tests/software/samtools/flagstat/main.nf Normal file
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@ -0,0 +1,14 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SAMTOOLS_FLAGSTAT } from '../../../../software/samtools/flagstat/main.nf' addParams( options: [:] )
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) ]
SAMTOOLS_FLAGSTAT ( input )
}

8
tests/software/samtools/flagstat/test.yml Normal file
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@ -0,0 +1,8 @@
- name: samtools flagstat
command: nextflow run ./tests/software/samtools/flagstat -entry test_samtools_flagstat -c tests/config/nextflow.config
tags:
- samtools
- samtools_flagstat
files:
- path: output/samtools/test.paired_end.sorted.bam.flagstat
md5sum: 80590621c74f5ee43ada20d010a3837f

14
tests/software/samtools/idxstats/main.nf Normal file
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@ -0,0 +1,14 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SAMTOOLS_IDXSTATS } from '../../../../software/samtools/idxstats/main.nf' addParams( options: [:] )
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) ]
SAMTOOLS_IDXSTATS ( input )
}

8
tests/software/samtools/idxstats/test.yml Normal file
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@ -0,0 +1,8 @@
- name: samtools idxstats
command: nextflow run ./tests/software/samtools/idxstats -entry test_samtools_idxstats -c tests/config/nextflow.config
tags:
- samtools
- samtools_idxstats
files:
- path: output/samtools/test.paired_end.sorted.bam.idxstats
md5sum: 3bee8b7d55e412da2b3816c5a18d60d5

13
tests/software/samtools/index/main.nf Normal file
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@ -0,0 +1,13 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SAMTOOLS_INDEX } from '../../../../software/samtools/index/main.nf' addParams( options: [:] )
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) ]
SAMTOOLS_INDEX ( input )
}

8
tests/software/samtools/index/test.yml Normal file
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@ -0,0 +1,8 @@
- name: samtools index
command: nextflow run ./tests/software/samtools/index -entry test_samtools_index -c tests/config/nextflow.config
tags:
- samtools
- samtools_index
files:
- path: output/samtools/test.paired_end.sorted.bam.bai
md5sum: 67338c2995eae82c849830ca55aa7bd1

80
tests/software/samtools/main.nf
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@ -1,80 +0,0 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SAMTOOLS_FLAGSTAT } from '../../../software/samtools/flagstat/main.nf' addParams( options: [:] )
include { SAMTOOLS_IDXSTATS } from '../../../software/samtools/idxstats/main.nf' addParams( options: [:] )
include { SAMTOOLS_INDEX } from '../../../software/samtools/index/main.nf' addParams( options: [:] )
include { SAMTOOLS_SORT } from '../../../software/samtools/sort/main.nf' addParams( options: [:] )
include { SAMTOOLS_STATS } from '../../../software/samtools/stats/main.nf' addParams( options: [:] )
include { SAMTOOLS_VIEW } from '../../../software/samtools/view/main.nf' addParams( options: [:] )
include { SAMTOOLS_MPILEUP } from '../../../software/samtools/mpileup/main.nf' addParams( options: [:] )
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) ]
SAMTOOLS_FLAGSTAT ( input )
}
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) ]
SAMTOOLS_IDXSTATS ( input )
}
workflow test_samtools_index {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
SAMTOOLS_INDEX ( input )
}
// FIXME Why is this passing it an already sorted bam?
workflow test_samtools_sort {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
SAMTOOLS_SORT ( input )
}
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) ]
SAMTOOLS_STATS ( input )
}
workflow test_samtools_view {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
SAMTOOLS_VIEW ( input )
}
workflow test_samtools_mpileup {
def input = []
def fasta = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
fasta = [ file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) ]
SAMTOOLS_MPILEUP ( input, fasta )
}

15
tests/software/samtools/mpileup/main.nf Normal file
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@ -0,0 +1,15 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SAMTOOLS_MPILEUP } from '../../../../software/samtools/mpileup/main.nf' addParams( options: [:] )
workflow test_samtools_mpileup {
def input = []
def fasta = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
fasta = [ file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) ]
SAMTOOLS_MPILEUP ( input, fasta )
}

8
tests/software/samtools/mpileup/test.yml Normal file
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@ -0,0 +1,8 @@
- name: samtools mpileup
command: nextflow run ./tests/software/samtools/mpileup -entry test_samtools_mpileup -c tests/config/nextflow.config
tags:
- samtools
- samtools_mpileup
files:
- path: output/samtools/test.mpileup
md5sum: 95c2646fa7bd535207722008c581c81d

13
tests/software/samtools/sort/main.nf Normal file
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@ -0,0 +1,13 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SAMTOOLS_SORT } from '../../../../software/samtools/sort/main.nf' addParams( options: [:] )
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) ]
SAMTOOLS_SORT ( input )
}

8
tests/software/samtools/sort/test.yml Normal file
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@ -0,0 +1,8 @@
- name: samtools sort
command: nextflow run ./tests/software/samtools/sort -entry test_samtools_sort -c tests/config/nextflow.config
tags:
- samtools
- samtools_sort
files:
- path: output/samtools/test.bam
md5sum: a41bfadacd2eeef1d31e05c135cc4f4e

14
tests/software/samtools/stats/main.nf Normal file
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@ -0,0 +1,14 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SAMTOOLS_STATS } from '../../../../software/samtools/stats/main.nf' addParams( options: [:] )
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) ]
SAMTOOLS_STATS ( input )
}

8
tests/software/samtools/stats/test.yml Normal file
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@ -0,0 +1,8 @@
- name: samtools stats
command: nextflow run ./tests/software/samtools/stats -entry test_samtools_stats -c tests/config/nextflow.config
tags:
- samtools
- samtools_stats
files:
- path: output/samtools/test.paired_end.sorted.bam.stats
md5sum: 06c183864d6e47ab89b0650cae831a93

62
tests/software/samtools/test.yml
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@ -1,62 +0,0 @@
- name: Run samtools flagstat test workflow
command: nextflow run ./tests/software/samtools/ -entry test_samtools_flagstat -c tests/config/nextflow.config
tags:
- samtools
- samtools_flagstat
files:
- path: output/samtools/test.paired_end.sorted.bam.flagstat
md5sum: 80590621c74f5ee43ada20d010a3837f
- name: Run samtools idxstats test workflow
command: nextflow run ./tests/software/samtools/ -entry test_samtools_idxstats -c tests/config/nextflow.config
tags:
- samtools
- samtools_idxstats
files:
- path: output/samtools/test.paired_end.sorted.bam.idxstats
md5sum: 3bee8b7d55e412da2b3816c5a18d60d5
- name: Run samtools index test workflow
command: nextflow run ./tests/software/samtools/ -entry test_samtools_index -c tests/config/nextflow.config
tags:
- samtools
- samtools_index
files:
- path: output/samtools/test.paired_end.sorted.bam.bai
md5sum: 67338c2995eae82c849830ca55aa7bd1
- name: Run samtools sort test workflow
command: nextflow run ./tests/software/samtools/ -entry test_samtools_sort -c tests/config/nextflow.config
tags:
- samtools
- samtools_sort
files:
- path: output/samtools/test.bam
md5sum: a41bfadacd2eeef1d31e05c135cc4f4e
- name: Run samtools stats test workflow
command: nextflow run ./tests/software/samtools/ -entry test_samtools_stats -c tests/config/nextflow.config
tags:
- samtools
- samtools_stats
files:
- path: output/samtools/test.paired_end.sorted.bam.stats
md5sum: 06c183864d6e47ab89b0650cae831a93
- name: Run samtools view test workflow
command: nextflow run ./tests/software/samtools/ -entry test_samtools_view -c tests/config/nextflow.config
tags:
- samtools
- samtools_view
files:
- path: output/samtools/test.bam
md5sum: 7ea2c325e2249ed7ef44e1d9fdc4f8ff
- name: Run samtools mpileup test workflow
command: nextflow run ./tests/software/samtools/ -entry test_samtools_mpileup -c tests/config/nextflow.config
tags:
- samtools
- samtools_mpileup
files:
- path: output/samtools/test.mpileup
md5sum: 95c2646fa7bd535207722008c581c81d

13
tests/software/samtools/view/main.nf Normal file
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@ -0,0 +1,13 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SAMTOOLS_VIEW } from '../../../../software/samtools/view/main.nf' addParams( options: [:] )
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) ]
SAMTOOLS_VIEW ( input )
}

8
tests/software/samtools/view/test.yml Normal file
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@ -0,0 +1,8 @@
- name: samtools view
command: nextflow run ./tests/software/samtools/view -entry test_samtools_view -c tests/config/nextflow.config
tags:
- samtools
- samtools_view
files:
- path: output/samtools/test.bam
md5sum: 7ea2c325e2249ed7ef44e1d9fdc4f8ff

7
tests/software/seacr/main.nf → tests/software/seacr/callpeak/main.nf
View file

@ -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 {
@ -12,9 +12,4 @@ workflow test_seacr_callpeak {
file("${launchDir}/tests/data/bedgraph/IgG_1_to_chr20.bedgraph", checkIfExists: true) ]
SEACR_CALLPEAK ( input )
}
// For local testing
workflow {
test_seacr_callpeak()
}

8
tests/software/seacr/callpeak/test.yml Normal file
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@ -0,0 +1,8 @@
- name: seacr callpeak
command: nextflow run ./tests/software/seacr/callpeak -entry test_seacr_callpeak -c tests/config/nextflow.config
tags:
- seacr
- seacr_callpeak
files:
- path: output/seacr/test_1.stringent.bed
md5sum: 3ac70475669eb6a7b8ca89e19a08a28e

8
tests/software/seacr/test.yml
View file

@ -1,8 +0,0 @@
- name: Run seacr call peak test workflow
command: nextflow run ./tests/software/seacr/ -entry test_seacr_callpeak -c tests/config/nextflow.config
tags:
- seacr
- seacr_callpeak
files:
- path: output/seacr/test_1.stringent.bed
md5sum: 3ac70475669eb6a7b8ca89e19a08a28e

29
tests/software/star/align/main.nf Normal file
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@ -0,0 +1,29 @@
#!/usr/bin/env nextflow
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'] )
workflow test_star_alignment_single_end {
def fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
def gtf = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
STAR_GENOMEGENERATE ( fasta, gtf )
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
}
workflow test_star_alignment_paired_end {
def fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
def gtf = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
STAR_GENOMEGENERATE ( fasta, gtf )
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
}

45
tests/software/star/test.yml → tests/software/star/align/test.yml
View file

@ -1,42 +1,9 @@
- name: Run star genomegenerate
command: nextflow run ./tests/software/star -entry test_star_genomegenerate -c tests/config/nextflow.config
tags:
- star
- star_genomegenerate
files:
- path: output/star/star/Genome
md5sum: 323c992bac354f93073ce0fc43f222f8
- path: output/star/star/SA
md5sum: 3e70e4fc6d031e1915bb510727f2c559
- path: output/star/star/SAindex
md5sum: a94198b95a245d4f64af2a7133b6ec7b
- path: output/star/star/chrLength.txt
md5sum: f2bea3725fe1c01420c57fb73bdeb31a
- path: output/star/star/chrNameLength.txt
md5sum: c7ceb0a8827b2ea91c386933bee48742
- path: output/star/star/chrStart.txt
md5sum: faf5c55020c99eceeef3e34188ac0d2f
- path: output/star/star/exonGeTrInfo.tab
md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6
- path: output/star/star/exonInfo.tab
md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343
- path: output/star/star/genomeParameters.txt
md5sum: ed47b8b034cae2fefcdb39321aea47cd
- path: output/star/star/sjdbInfo.txt
md5sum: 1082ab459363b3f2f7aabcef0979c1ed
- path: output/star/star/sjdbList.fromGTF.out.tab
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/star/star/sjdbList.out.tab
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/star/star/transcriptInfo.tab
md5sum: 8fbe69abbbef4f89da3854873984dbac
- name: Run star single-end alignment
command: nextflow run ./tests/software/star -entry test_star_alignment_single_end -c tests/config/nextflow.config
- name: star align single-end
command: nextflow run ./tests/software/star/align -entry test_star_alignment_single_end -c tests/config/nextflow.config
tags:
- star
- star_align
- star_alignment_single_end
- star_align_single_end
files:
- path: output/star/star/Genome
md5sum: 323c992bac354f93073ce0fc43f222f8
@ -69,12 +36,12 @@
- path: output/star/test.SJ.out.tab
md5sum: d41d8cd98f00b204e9800998ecf8427e
- name: Run star paired-end alignment
command: nextflow run ./tests/software/star -entry test_star_alignment_paired_end -c tests/config/nextflow.config
- name: star align paired-end
command: nextflow run ./tests/software/star/align -entry test_star_alignment_paired_end -c tests/config/nextflow.config
tags:
- star
- star_align
- star_alignment_paired_end
- star_align_paired_end
files:
- path: output/star/star/Genome
md5sum: 323c992bac354f93073ce0fc43f222f8

12
tests/software/star/genomegenerate/main.nf Normal file
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@ -0,0 +1,12 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { STAR_GENOMEGENERATE } from '../../../../software/star/genomegenerate/main.nf' addParams( options: [args: '--genomeSAindexNbases 9'] )
workflow test_star_genomegenerate {
def fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
def gtf = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
STAR_GENOMEGENERATE ( fasta, gtf )
}

32
tests/software/star/genomegenerate/test.yml Normal file
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@ -0,0 +1,32 @@
- name: star genomegenerate
command: nextflow run ./tests/software/star/genomegenerate -entry test_star_genomegenerate -c tests/config/nextflow.config
tags:
- star
- star_genomegenerate
files:
- path: output/star/star/Genome
md5sum: 323c992bac354f93073ce0fc43f222f8
- path: output/star/star/SA
md5sum: 3e70e4fc6d031e1915bb510727f2c559
- path: output/star/star/SAindex
md5sum: a94198b95a245d4f64af2a7133b6ec7b
- path: output/star/star/chrLength.txt
md5sum: f2bea3725fe1c01420c57fb73bdeb31a
- path: output/star/star/chrNameLength.txt
md5sum: c7ceb0a8827b2ea91c386933bee48742
- path: output/star/star/chrStart.txt
md5sum: faf5c55020c99eceeef3e34188ac0d2f
- path: output/star/star/exonGeTrInfo.tab
md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6
- path: output/star/star/exonInfo.tab
md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343
- path: output/star/star/genomeParameters.txt
md5sum: ed47b8b034cae2fefcdb39321aea47cd
- path: output/star/star/sjdbInfo.txt
md5sum: 1082ab459363b3f2f7aabcef0979c1ed
- path: output/star/star/sjdbList.fromGTF.out.tab
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/star/star/sjdbList.out.tab
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/star/star/transcriptInfo.tab
md5sum: 8fbe69abbbef4f89da3854873984dbac

36
tests/software/star/main.nf
View file

@ -1,36 +0,0 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
def options_align = [args: '--readFilesCommand zcat']
def options_gg = [args: '--genomeSAindexNbases 9']
include { STAR_ALIGN } from '../../../software/star/align/main.nf' addParams( options: options_align )
include { STAR_GENOMEGENERATE } from '../../../software/star/genomegenerate/main.nf' addParams( options: options_gg )
workflow test_star_genomegenerate {
fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
gtf = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
STAR_GENOMEGENERATE ( fasta, gtf )
}
workflow test_star_alignment_single_end {
fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
gtf = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
STAR_GENOMEGENERATE ( fasta, gtf )
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
STAR_ALIGN( input, STAR_GENOMEGENERATE.out.index, gtf)
}
workflow test_star_alignment_paired_end {
fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
gtf = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
STAR_GENOMEGENERATE ( fasta, gtf )
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
STAR_ALIGN( input, STAR_GENOMEGENERATE.out.index, gtf)
}

4
tests/software/stringtie/test.yml
View file

@ -1,4 +1,4 @@
- name: Run stringtie forward strand test workflow
- name: stringtie forward-strand
command: nextflow run ./tests/software/stringtie/ -entry test_stringtie_forward -c tests/config/nextflow.config
tags:
- stringtie
@ -20,7 +20,7 @@
- path: output/test_stringtie_forward/test.ballgown/t_data.ctab
md5sum: 0106f70121a8b520d98b8739aed92915
- name: Run stringtie reverse strand test workflow
- name: stringtie reverse-strand
command: nextflow run ./tests/software/stringtie/ -entry test_stringtie_reverse -c tests/config/nextflow.config
tags:
- stringtie

17
tests/software/trimgalore/main.nf
View file

@ -2,8 +2,7 @@
nextflow.enable.dsl = 2
include { TRIMGALORE as TRIMGALORE_SE } from '../../../software/trimgalore/main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
include { TRIMGALORE as TRIMGALORE_PE } from '../../../software/trimgalore/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
include { TRIMGALORE } from '../../../software/trimgalore/main.nf' addParams( options: [:] )
/*
* Test with single-end data
@ -13,19 +12,9 @@ workflow test_trimgalore_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
TRIMGALORE_SE ( input )
TRIMGALORE ( input )
}
// workflow test_trimgalore_single_end {
// def input = []
// input = [ [ id:'test', single_end:false ], // meta map
// [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
// TRIMGALORE_SE ( input )
// }
/*
* Test with paired-end data
*/
@ -36,5 +25,5 @@ workflow test_trimgalore_paired_end {
[ 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_PE ( input )
TRIMGALORE ( input )
}

16
tests/software/trimgalore/test.yml
View file

@ -1,21 +1,21 @@
- name: Run trimgalore single-end test workflow
- name: trimgalore single-end
command: nextflow run ./tests/software/trimgalore/ -entry test_trimgalore_single_end -c tests/config/nextflow.config
tags:
- trimgalore
files:
# These can't be md5'd reliably
# TODO Test for includes
- path: output/test_single_end/test.fastq.gz_trimming_report.txt
- path: output/test_single_end/test_trimmed.fq.gz
- path: output/trimgalore/test.fastq.gz_trimming_report.txt
- path: output/trimgalore/test_trimmed.fq.gz
- name: Run trimgalore paired-end test workflow
- name: trimgalore paired-end
command: nextflow run ./tests/software/trimgalore/ -entry test_trimgalore_paired_end -c tests/config/nextflow.config
tags:
- trimgalore
files:
# These can't be md5'd reliably
# TODO Test for includes
- path: output/test_paired_end/test_1.fastq.gz_trimming_report.txt
- path: output/test_paired_end/test_1_val_1.fq.gz
- path: output/test_paired_end/test_2.fastq.gz_trimming_report.txt
- path: output/test_paired_end/test_2_val_2.fq.gz
- path: output/trimgalore/test_1.fastq.gz_trimming_report.txt
- path: output/trimgalore/test_1_val_1.fq.gz
- path: output/trimgalore/test_2.fastq.gz_trimming_report.txt
- path: output/trimgalore/test_2_val_2.fq.gz

3
tests/software/ucsc/main.nf → tests/software/ucsc/bedgraphtobigwig/main.nf
View file

@ -2,12 +2,13 @@
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 = []
input = [ [ id:'test' ], // meta map
[ file('https://raw.githubusercontent.com/igvteam/igv.js/master/test/data/wig/bedgraph-example-uscs.bedgraph', checkIfExists: true) ] ]
UCSC_BEDGRAPHTOBIGWIG (
input,
file('https://raw.githubusercontent.com/igvteam/igv.js/master/test/data/wig/chrom.sizes', checkIfExists: true)

7
tests/software/ucsc/bedgraphtobigwig/test.yml Normal file
View file

@ -0,0 +1,7 @@
- name: ucsc bedgraphtobigwig
command: nextflow run ./tests/software/ucsc/bedgraphtobigwig -entry test_ucsc_bedgraphtobigwig -c tests/config/nextflow.config
tags:
- ucsc_bedgraphtobigwig
files:
- path: output/ucsc/test.bigWig
md5sum: 5346de25b01ecbff91b63178b3bfbeec

7
tests/software/ucsc/test.yml
View file

@ -1,7 +0,0 @@
- name: Run bedgraphtobigwig test workflow
command: nextflow run ./tests/software/ucsc/ -entry test_ucsc_bedgraphtobigwig -c tests/config/nextflow.config
tags:
- ucsc_bedgraphtobigwig
files:
- path: output/ucsc/test.bigWig
md5sum: 5346de25b01ecbff91b63178b3bfbeec