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remove deprecated test tags (#440)

Browse source 
* remove deprecated test tags

* fix bowtie, gatk4/applybsqr

* fix gatk4 baserecalibrator

* fixed shovill

* fixed yara/mapper

* fixed kallistobustools/ref paths
This commit is contained in:
Kevin Menden 2021-04-13 19:03:09 +02:00 committed by GitHub
parent a9fcbd93cc
commit 043a7d1e3c
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GPG key ID: 4AEE18F83AFDEB23
41 changed files with 49 additions and 124 deletions
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2
software/gatk4/applybqsr/main.nf
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@ -19,7 +19,7 @@ process GATK4_APPLYBQSR {
} }
input: input:
tuple val(meta), path(bam), path(bqsr_table) tuple val(meta), path(bam), path(bai), path(bqsr_table)
path fasta path fasta
path fastaidx path fastaidx
path dict path dict

2
software/gatk4/baserecalibrator/main.nf
View file

@ -19,7 +19,7 @@ process GATK4_BASERECALIBRATOR {
} }
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam), path(bai)
path fasta path fasta
path fastaidx path fastaidx
path dict path dict

3
tests/software/adapterremoval/test.yml
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@ -1,7 +1,6 @@
- name: adapterremoval test_adapterremoval_single_end - name: adapterremoval test_adapterremoval_single_end
command: nextflow run tests/software/adapterremoval -entry test_adapterremoval_single_end -c tests/config/nextflow.config command: nextflow run tests/software/adapterremoval -entry test_adapterremoval_single_end -c tests/config/nextflow.config
tags: tags:
- adapterremoval_single_end
- adapterremoval - adapterremoval
files: files:
- path: output/adapterremoval/test.log - path: output/adapterremoval/test.log
@ -12,7 +11,6 @@
- name: adapterremoval test_adapterremoval_paired_end - name: adapterremoval test_adapterremoval_paired_end
command: nextflow run tests/software/adapterremoval -entry test_adapterremoval_paired_end -c tests/config/nextflow.config command: nextflow run tests/software/adapterremoval -entry test_adapterremoval_paired_end -c tests/config/nextflow.config
tags: tags:
- adapterremoval_paired_end
- adapterremoval - adapterremoval
files: files:
- path: output/adapterremoval/test.pair2.trimmed.fastq.gz - path: output/adapterremoval/test.pair2.trimmed.fastq.gz
@ -25,7 +23,6 @@
- name: adapterremoval test_adapterremoval_paired_end_collapse - name: adapterremoval test_adapterremoval_paired_end_collapse
command: nextflow run tests/software/adapterremoval -entry test_adapterremoval_paired_end_collapse -c tests/config/nextflow.config command: nextflow run tests/software/adapterremoval -entry test_adapterremoval_paired_end_collapse -c tests/config/nextflow.config
tags: tags:
- adapterremoval_paired_end_collapse
- adapterremoval - adapterremoval
files: files:
- path: output/adapterremoval/test.log - path: output/adapterremoval/test.log

4
tests/software/bowtie/align/main.nf
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@ -7,9 +7,9 @@ include { BOWTIE_ALIGN } from '../../../../software/bowtie/align/main.nf' addPar
workflow test_bowtie_align_single_end { workflow test_bowtie_align_single_end {
input = [ [ id:'test', single_end:true ], // meta map input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
] ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BOWTIE_BUILD ( fasta ) BOWTIE_BUILD ( fasta )
BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index ) BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )

2
tests/software/bowtie/align/test.yml
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@ -3,7 +3,6 @@
tags: tags:
- bowtie - bowtie
- bowtie/align - bowtie/align
- bowtie_align_single_end
files: files:
- path: ./output/bowtie/test.bam - path: ./output/bowtie/test.bam
- path: ./output/bowtie/test.out - path: ./output/bowtie/test.out
@ -26,7 +25,6 @@
tags: tags:
- bowtie - bowtie
- bowtie/align - bowtie/align
- bowtie_align_paired_end
files: files:
- path: ./output/bowtie/test.bam - path: ./output/bowtie/test.bam
- path: ./output/bowtie/test.out - path: ./output/bowtie/test.out

2
tests/software/bowtie2/align/test.yml
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@ -3,7 +3,6 @@
tags: tags:
- bowtie2 - bowtie2
- bowtie2/align - bowtie2/align
- bowtie2_align_single_end
files: files:
- path: ./output/bowtie2/test.bam - path: ./output/bowtie2/test.bam
- path: ./output/bowtie2/test.bowtie2.log - path: ./output/bowtie2/test.bowtie2.log
@ -25,7 +24,6 @@
tags: tags:
- bowtie2 - bowtie2
- bowtie2/align - bowtie2/align
- bowtie2_align_paired_end
files: files:
- path: ./output/bowtie2/test.bam - path: ./output/bowtie2/test.bam
- path: ./output/bowtie2/test.bowtie2.log - path: ./output/bowtie2/test.bowtie2.log

2
tests/software/bwa/mem/test.yml
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@ -3,7 +3,6 @@
tags: tags:
- bwa - bwa
- bwa/mem - bwa/mem
- bwa_mem_single_end
files: files:
- path: ./output/bwa/test.bam - path: ./output/bwa/test.bam
md5sum: 9165508bf914baee0e6347711aa7b23a md5sum: 9165508bf914baee0e6347711aa7b23a
@ -23,7 +22,6 @@
tags: tags:
- bwa - bwa
- bwa/mem - bwa/mem
- bwa_mem_paired_end
files: files:
- path: ./output/bwa/test.bam - path: ./output/bwa/test.bam
md5sum: 670a53bddee62d6bd14ed7adaf103e7c md5sum: 670a53bddee62d6bd14ed7adaf103e7c

2
tests/software/bwamem2/mem/test.yml
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@ -3,7 +3,6 @@
tags: tags:
- bwamem2 - bwamem2
- bwamem2/mem - bwamem2/mem
- bwamem2_mem_single_end
files: files:
- path: ./output/bwamem2/test.bam - path: ./output/bwamem2/test.bam
md5sum: 2133c011119ea11f06f0a9b1621ba05b md5sum: 2133c011119ea11f06f0a9b1621ba05b
@ -23,7 +22,6 @@
tags: tags:
- bwamem2 - bwamem2
- bwamem2/mem - bwamem2/mem
- bwamem2_mem_paired_end
files: files:
- path: ./output/bwamem2/test.bam - path: ./output/bwamem2/test.bam
md5sum: d8fadab5cef04faff1851a8162fc30b5 md5sum: d8fadab5cef04faff1851a8162fc30b5

2
tests/software/cat/fastq/test.yml
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@ -3,7 +3,6 @@
tags: tags:
- cat - cat
- cat/fastq - cat/fastq
- cat_fastqc_single_end
files: files:
- path: ./output/merged_fastq/test.merged.fastq.gz - path: ./output/merged_fastq/test.merged.fastq.gz
md5sum: 59f6dbe193741bb40f498f254aeb2e99 md5sum: 59f6dbe193741bb40f498f254aeb2e99
@ -13,7 +12,6 @@
tags: tags:
- cat - cat
- cat/fastq - cat/fastq
- cat_fastqc_paired_end
files: files:
- path: ./output/merged_fastq/test_2.merged.fastq.gz - path: ./output/merged_fastq/test_2.merged.fastq.gz
md5sum: d2b1a836eef1058738ecab36c907c5ba md5sum: d2b1a836eef1058738ecab36c907c5ba

2
tests/software/cutadapt/test.yml
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@ -2,7 +2,6 @@
command: nextflow run ./tests/software/cutadapt -entry test_cutadapt_single_end -c tests/config/nextflow.config command: nextflow run ./tests/software/cutadapt -entry test_cutadapt_single_end -c tests/config/nextflow.config
tags: tags:
- cutadapt - cutadapt
- cutadapt_single_end
files: files:
- path: ./output/cutadapt/test.cutadapt.log - path: ./output/cutadapt/test.cutadapt.log
- path: ./output/cutadapt/test.trim.fastq.gz - path: ./output/cutadapt/test.trim.fastq.gz
@ -11,7 +10,6 @@
command: nextflow run ./tests/software/cutadapt -entry test_cutadapt_paired_end -c tests/config/nextflow.config command: nextflow run ./tests/software/cutadapt -entry test_cutadapt_paired_end -c tests/config/nextflow.config
tags: tags:
- cutadapt - cutadapt
- cutadapt_paired_end
files: files:
- path: ./output/cutadapt/test.cutadapt.log - path: ./output/cutadapt/test.cutadapt.log
- path: ./output/cutadapt/test_1.trim.fastq.gz - path: ./output/cutadapt/test_1.trim.fastq.gz

2
tests/software/fastp/test.yml
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@ -1,7 +1,6 @@
- name: fastp test_fastp_single_end - name: fastp test_fastp_single_end
command: nextflow run tests/software/fastp -entry test_fastp_single_end -c tests/config/nextflow.config command: nextflow run tests/software/fastp -entry test_fastp_single_end -c tests/config/nextflow.config
tags: tags:
- fastp_single_end
- fastp - fastp
files: files:
- path: output/fastp/test.fastp.html - path: output/fastp/test.fastp.html
@ -20,7 +19,6 @@
- name: fastp test_fastp_paired_end - name: fastp test_fastp_paired_end
command: nextflow run tests/software/fastp -entry test_fastp_paired_end -c tests/config/nextflow.config command: nextflow run tests/software/fastp -entry test_fastp_paired_end -c tests/config/nextflow.config
tags: tags:
- fastp_paired_end
- fastp - fastp
files: files:
- path: output/fastp/test.fastp.html - path: output/fastp/test.fastp.html

2
tests/software/fastqc/test.yml
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@ -2,7 +2,6 @@
command: nextflow run ./tests/software/fastqc/ -entry test_fastqc_single_end -c tests/config/nextflow.config command: nextflow run ./tests/software/fastqc/ -entry test_fastqc_single_end -c tests/config/nextflow.config
tags: tags:
- fastqc - fastqc
- fastqc_single_end
files: files:
- path: ./output/fastqc/test_fastqc.html - path: ./output/fastqc/test_fastqc.html
- path: ./output/fastqc/test_fastqc.zip - path: ./output/fastqc/test_fastqc.zip
@ -11,7 +10,6 @@
command: nextflow run ./tests/software/fastqc/ -entry test_fastqc_paired_end -c tests/config/nextflow.config command: nextflow run ./tests/software/fastqc/ -entry test_fastqc_paired_end -c tests/config/nextflow.config
tags: tags:
- fastqc - fastqc
- fastqc_paired_end
files: files:
- path: ./output/fastqc/test_1_fastqc.html - path: ./output/fastqc/test_1_fastqc.html
- path: ./output/fastqc/test_2_fastqc.html - path: ./output/fastqc/test_2_fastqc.html

2
tests/software/gatk4/applybqsr/main.nf
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@ -7,6 +7,7 @@ include { GATK4_APPLYBQSR } from '../../../../software/gatk4/applybqsr/main.nf'
workflow test_gatk4_applybqsr { workflow test_gatk4_applybqsr {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true)
] ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
@ -19,6 +20,7 @@ workflow test_gatk4_applybqsr {
workflow test_gatk4_applybqsr_intervals { workflow test_gatk4_applybqsr_intervals {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true)
] ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)

1
tests/software/gatk4/applybqsr/test.yml
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@ -11,7 +11,6 @@
command: nextflow run tests/software/gatk4/applybqsr -entry test_gatk4_applybqsr_intervals -c tests/config/nextflow.config command: nextflow run tests/software/gatk4/applybqsr -entry test_gatk4_applybqsr_intervals -c tests/config/nextflow.config
tags: tags:
- gatk4 - gatk4
- gatk4/applybqsr/intervals
- gatk4/applybqsr - gatk4/applybqsr
files: files:
- path: output/gatk4/test.bam - path: output/gatk4/test.bam

9
tests/software/gatk4/baserecalibrator/main.nf
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@ -6,7 +6,8 @@ include { GATK4_BASERECALIBRATOR } from '../../../../software/gatk4/baserecalibr
workflow test_gatk4_baserecalibrator { workflow test_gatk4_baserecalibrator {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
] ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
@ -19,7 +20,8 @@ workflow test_gatk4_baserecalibrator {
workflow test_gatk4_baserecalibrator_intervals { workflow test_gatk4_baserecalibrator_intervals {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
] ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
@ -33,7 +35,8 @@ workflow test_gatk4_baserecalibrator_intervals {
workflow test_gatk4_baserecalibrator_multiple_sites { workflow test_gatk4_baserecalibrator_multiple_sites {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
] ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)

2
tests/software/gatk4/baserecalibrator/test.yml
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@ -10,7 +10,6 @@
- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_intervals - name: gatk4 baserecalibrator test_gatk4_baserecalibrator_intervals
command: nextflow run tests/software/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_intervals -c tests/config/nextflow.config command: nextflow run tests/software/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_intervals -c tests/config/nextflow.config
tags: tags:
- gatk4/baserecalibrator/intervals
- gatk4/baserecalibrator - gatk4/baserecalibrator
- gatk4 - gatk4
files: files:
@ -20,7 +19,6 @@
- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_multiple_sites - name: gatk4 baserecalibrator test_gatk4_baserecalibrator_multiple_sites
command: nextflow run tests/software/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_multiple_sites -c tests/config/nextflow.config command: nextflow run tests/software/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_multiple_sites -c tests/config/nextflow.config
tags: tags:
- gatk4_baserecalibrator_multiple_sites
- gatk4/baserecalibrator - gatk4/baserecalibrator
- gatk4 - gatk4
files: files:

2
tests/software/gatk4/fastqtosam/test.yml
View file

@ -1,7 +1,6 @@
- name: gatk4 fastqtosam test_gatk4_fastqtosam_single_end - name: gatk4 fastqtosam test_gatk4_fastqtosam_single_end
command: nextflow run tests/software/gatk4/fastqtosam -entry test_gatk4_fastqtosam_single_end -c tests/config/nextflow.config command: nextflow run tests/software/gatk4/fastqtosam -entry test_gatk4_fastqtosam_single_end -c tests/config/nextflow.config
tags: tags:
- gatk4_fastqtosam_single_end
- gatk4/fastqtosam - gatk4/fastqtosam
- gatk4 - gatk4
files: files:
@ -11,7 +10,6 @@
- name: gatk4 fastqtosam test_gatk4_fastqtosam_paired_end - name: gatk4 fastqtosam test_gatk4_fastqtosam_paired_end
command: nextflow run tests/software/gatk4/fastqtosam -entry test_gatk4_fastqtosam_paired_end -c tests/config/nextflow.config command: nextflow run tests/software/gatk4/fastqtosam -entry test_gatk4_fastqtosam_paired_end -c tests/config/nextflow.config
tags: tags:
- gatk4_fastqtosam_paired_end
- gatk4 - gatk4
- gatk4/fastqtosam - gatk4/fastqtosam
files: files:

1
tests/software/gatk4/mergevcfs/test.yml
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@ -12,7 +12,6 @@
tags: tags:
- gatk4/mergevcfs - gatk4/mergevcfs
- gatk4 - gatk4
- gatk4/mergevcfs_refdict
files: files:
- path: output/gatk4/test.merged.vcf.gz - path: output/gatk4/test.merged.vcf.gz
md5sum: ff48f175e26db2d4b2957762f6d1c715 md5sum: ff48f175e26db2d4b2957762f6d1c715

2
tests/software/gatk4/samtofastq/test.yml
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@ -3,7 +3,6 @@
tags: tags:
- gatk4 - gatk4
- gatk4/samtofastq - gatk4/samtofastq
- gatk4_samtofastq_single_end
files: files:
- path: output/gatk4/test.fastq.gz - path: output/gatk4/test.fastq.gz
md5sum: 50ace41d4c24467f24f8b929540a7797 md5sum: 50ace41d4c24467f24f8b929540a7797
@ -13,7 +12,6 @@
tags: tags:
- gatk4 - gatk4
- gatk4/samtofastq - gatk4/samtofastq
- gatk4_samtofastq_paired_end
files: files:
- path: output/gatk4/test_1.fastq.gz - path: output/gatk4/test_1.fastq.gz
md5sum: cfea607c9d75fd9ea9704780ad3a499c md5sum: cfea607c9d75fd9ea9704780ad3a499c

2
tests/software/hisat2/align/test.yml
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@ -3,7 +3,6 @@
tags: tags:
- hisat2 - hisat2
- hisat2/align - hisat2/align
- hisat2_align_single_end
files: files:
- path: output/hisat2/test.hisat2.summary.log - path: output/hisat2/test.hisat2.summary.log
md5sum: 7b8a9e61b7646da1089b041333c41a87 md5sum: 7b8a9e61b7646da1089b041333c41a87
@ -32,7 +31,6 @@
tags: tags:
- hisat2 - hisat2
- hisat2/align - hisat2/align
- hisat2_align_paired_end
files: files:
- path: output/hisat2/test.hisat2.summary.log - path: output/hisat2/test.hisat2.summary.log
md5sum: 9839b31db795958cc4b70711a3414e9c md5sum: 9839b31db795958cc4b70711a3414e9c

18
tests/software/kallistobustools/ref/main.nf
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@ -6,27 +6,27 @@ include { KALLISTOBUSTOOLS_REF } from '../../../../software/kallistobustools/ref
workflow test_kallistobustools_ref_standard { workflow test_kallistobustools_ref_standard {
fasta = file("${launchDir}/tests/data/delete_me/kallistobustools/GRCm39.chr19_100k.fa.gz", checkIfExists: true) fasta = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kallistobustools/GRCm39.chr19_100k.fa.gz", checkIfExists: true)
gtf = file("${launchDir}/tests/data/delete_me/kallistobustools/gencode.VM26.chr19_10k.gtf.gz", checkIfExists: true) gtf = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kallistobustools/gencode.VM26.chr19_10k.gtf.gz", checkIfExists: true)
workflow = "standard" workflow = "standard"
KALLISTOBUSTOOLS_REF(fasta, gtf, workflow) KALLISTOBUSTOOLS_REF(fasta, gtf, workflow)
} }
workflow test_kallistobustools_ref_lamanno { workflow test_kallistobustools_ref_lamanno {
fasta = file("${launchDir}/tests/data/delete_me/kallistobustools/GRCm39.chr19_100k.fa.gz", checkIfExists: true) fasta = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kallistobustools/GRCm39.chr19_100k.fa.gz", checkIfExists: true)
gtf = file("${launchDir}/tests/data/delete_me/kallistobustools/gencode.VM26.chr19_10k.gtf.gz", checkIfExists: true) gtf = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kallistobustools/gencode.VM26.chr19_10k.gtf.gz", checkIfExists: true)
workflow = "standard" workflow = "standard"
KALLISTOBUSTOOLS_REF( fasta, gtf, workflow) KALLISTOBUSTOOLS_REF( fasta, gtf, workflow)
} }
workflow test_kallistobustools_ref_nucleus { workflow test_kallistobustools_ref_nucleus {
fasta = file("${launchDir}/tests/data/delete_me/kallistobustools/GRCm39.chr19_100k.fa.gz", checkIfExists: true) fasta = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kallistobustools/GRCm39.chr19_100k.fa.gz", checkIfExists: true)
gtf = file("${launchDir}/tests/data/delete_me/kallistobustools/gencode.VM26.chr19_10k.gtf.gz", checkIfExists: true) gtf = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kallistobustools/gencode.VM26.chr19_10k.gtf.gz", checkIfExists: true)
workflow = "standard" workflow = "standard"
KALLISTOBUSTOOLS_REF( fasta, gtf, workflow) KALLISTOBUSTOOLS_REF( fasta, gtf, workflow)
} }

3
tests/software/kallistobustools/ref/test.yml
View file

@ -2,7 +2,6 @@
command: nextflow run tests/software/kallistobustools/ref -entry test_kallistobustools_ref_standard -c tests/config/nextflow.config command: nextflow run tests/software/kallistobustools/ref -entry test_kallistobustools_ref_standard -c tests/config/nextflow.config
tags: tags:
- kallistobustools - kallistobustools
- kallistobustools_ref_standard
- kallistobustools/ref - kallistobustools/ref
files: files:
- path: output/kallistobustools/cdna.fa - path: output/kallistobustools/cdna.fa
@ -16,7 +15,6 @@
command: nextflow run tests/software/kallistobustools/ref -entry test_kallistobustools_ref_lamanno -c tests/config/nextflow.config command: nextflow run tests/software/kallistobustools/ref -entry test_kallistobustools_ref_lamanno -c tests/config/nextflow.config
tags: tags:
- kallistobustools - kallistobustools
- kallistobustools_ref_lamanno
- kallistobustools/ref - kallistobustools/ref
files: files:
- path: output/kallistobustools/cdna.fa - path: output/kallistobustools/cdna.fa
@ -29,7 +27,6 @@
- name: kallistobustools ref test_kallistobustools_ref_nucleus - name: kallistobustools ref test_kallistobustools_ref_nucleus
command: nextflow run tests/software/kallistobustools/ref -entry test_kallistobustools_ref_nucleus -c tests/config/nextflow.config command: nextflow run tests/software/kallistobustools/ref -entry test_kallistobustools_ref_nucleus -c tests/config/nextflow.config
tags: tags:
- kallistobustools_ref_nucleus
- kallistobustools - kallistobustools
- kallistobustools/ref - kallistobustools/ref
files: files:

8
tests/software/minimap2/align/main.nf
View file

@ -6,9 +6,9 @@ include { MINIMAP2_ALIGN } from '../../../../software/minimap2/align/main.nf' ad
workflow test_minimap2_align_single_end { workflow test_minimap2_align_single_end {
input = [ [ id:'test', single_end:true ], // meta map input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
] ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
MINIMAP2_ALIGN ( input, fasta ) MINIMAP2_ALIGN ( input, fasta )
} }
@ -16,9 +16,9 @@ workflow test_minimap2_align_single_end {
workflow test_minimap2_align_paired_end { workflow test_minimap2_align_paired_end {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
] ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
MINIMAP2_ALIGN ( input, fasta ) MINIMAP2_ALIGN ( input, fasta )
} }

2
tests/software/minimap2/align/test.yml
View file

@ -3,7 +3,6 @@
tags: tags:
- minimap2 - minimap2
- minimap2/align - minimap2/align
- minimap2_align_single_end
files: files:
- path: ./output/minimap2/test.paf - path: ./output/minimap2/test.paf
md5sum: 5a9648fc67c30a2c83b0ef094171faa0 md5sum: 5a9648fc67c30a2c83b0ef094171faa0
@ -13,7 +12,6 @@
tags: tags:
- minimap2 - minimap2
- minimap2/align - minimap2/align
- minimap2_align_paired_end
files: files:
- path: ./output/minimap2/test.paf - path: ./output/minimap2/test.paf
md5sum: e7b952be872bdbef16bf99d512690df7 md5sum: e7b952be872bdbef16bf99d512690df7

1
tests/software/picard/markduplicates/test.yml
View file

@ -13,5 +13,4 @@
tags: tags:
- picard - picard
- picard/markduplicates - picard/markduplicates
- should fail
exit_code: 1 exit_code: 1

2
tests/software/preseq/lcextrap/test.yml
View file

@ -3,7 +3,6 @@
tags: tags:
- preseq - preseq
- preseq/lcextrap - preseq/lcextrap
- preseq_lcextrap_single_end
files: files:
- path: output/preseq/test.ccurve.txt - path: output/preseq/test.ccurve.txt
md5sum: 76ae04c8eaf19c94e3210bb69da38498 md5sum: 76ae04c8eaf19c94e3210bb69da38498
@ -14,7 +13,6 @@
tags: tags:
- preseq - preseq
- preseq/lcextrap - preseq/lcextrap
- preseq_lcextrap_paired_end
files: files:
- path: output/preseq/test.ccurve.txt - path: output/preseq/test.ccurve.txt
md5sum: 2836d2fabd2213f097fd7063db550276 md5sum: 2836d2fabd2213f097fd7063db550276

2
tests/software/quast/test.yml
View file

@ -2,7 +2,6 @@
command: nextflow run ./tests/software/quast -entry test_quast_ref -c ./tests/config/nextflow.config command: nextflow run ./tests/software/quast -entry test_quast_ref -c ./tests/config/nextflow.config
tags: tags:
- quast - quast
- quast_reference
files: files:
- path: ./output/quast/report.tsv - path: ./output/quast/report.tsv
- path: ./output/quast/quast/transposed_report.txt - path: ./output/quast/quast/transposed_report.txt
@ -86,7 +85,6 @@
command: nextflow run ./tests/software/quast -entry test_quast_noref -c ./tests/config/nextflow.config command: nextflow run ./tests/software/quast -entry test_quast_noref -c ./tests/config/nextflow.config
tags: tags:
- quast - quast
- quast_no_reference
files: files:
- path: ./output/quast/report.tsv - path: ./output/quast/report.tsv
md5sum: 074e239aac0f298cf4cd2a28a9bb5690 md5sum: 074e239aac0f298cf4cd2a28a9bb5690

2
tests/software/salmon/quant/test.yml
View file

@ -3,7 +3,6 @@
tags: tags:
- salmon - salmon
- salmon/quant - salmon/quant
- salmon_quant_single_end
files: files:
- path: ./output/salmon/test/cmd_info.json - path: ./output/salmon/test/cmd_info.json
- path: ./output/salmon/test/quant.sf - path: ./output/salmon/test/quant.sf
@ -55,7 +54,6 @@
tags: tags:
- salmon - salmon
- salmon/quant - salmon/quant
- salmon_quant_paired_end
files: files:
- path: ./output/salmon/test/cmd_info.json - path: ./output/salmon/test/cmd_info.json
- path: ./output/salmon/test/quant.sf - path: ./output/salmon/test/quant.sf

13
tests/software/seqkit/split2/test.yml
View file

@ -3,22 +3,17 @@
tags: tags:
- seqkit - seqkit
- seqkit/split2 - seqkit/split2
- seqkit_split2_single_end
- length
files: files:
- path: output/seqkit/test.split/test_1.part_001.fastq.gz - path: output/seqkit/test.split/test_1.part_001.fastq.gz
md5sum: 6f7d58ba35c254c0817fe9a7c69862e4 md5sum: 6f7d58ba35c254c0817fe9a7c69862e4
- path: output/seqkit/test.split/test_1.part_002.fastq.gz - path: output/seqkit/test.split/test_1.part_002.fastq.gz
md5sum: cf38c51506e45380fe25abdd1bd5ccc6 md5sum: cf38c51506e45380fe25abdd1bd5ccc6
- name: seqkit split2 single-end size - name: seqkit split2 single-end size
command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_single_end_size -c tests/config/nextflow.config command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_single_end_size -c tests/config/nextflow.config
tags: tags:
- seqkit - seqkit
- seqkit/split2 - seqkit/split2
- seqkit_split2_single_end
- size
files: files:
- path: output/seqkit/test.split/test_1.part_001.fastq.gz - path: output/seqkit/test.split/test_1.part_001.fastq.gz
md5sum: bf835e685d597fc1ab5e5ac7dd689619 md5sum: bf835e685d597fc1ab5e5ac7dd689619
@ -30,8 +25,6 @@
tags: tags:
- seqkit - seqkit
- seqkit/split2 - seqkit/split2
- seqkit_split2_single_end
- part
files: files:
- path: output/seqkit/test.split/test_1.part_001.fastq.gz - path: output/seqkit/test.split/test_1.part_001.fastq.gz
md5sum: fa25951435471238d5567fd2cae31f55 md5sum: fa25951435471238d5567fd2cae31f55
@ -45,8 +38,6 @@
tags: tags:
- seqkit - seqkit
- seqkit/split2 - seqkit/split2
- seqkit_split2_paired_end
- length
files: files:
- path: output/seqkit/test.split/test_1.part_001.fastq.gz - path: output/seqkit/test.split/test_1.part_001.fastq.gz
md5sum: 6f7d58ba35c254c0817fe9a7c69862e4 md5sum: 6f7d58ba35c254c0817fe9a7c69862e4
@ -62,8 +53,6 @@
tags: tags:
- seqkit - seqkit
- seqkit/split2 - seqkit/split2
- seqkit_split2_paired_end
- size
files: files:
- path: output/seqkit/test.split/test_1.part_001.fastq.gz - path: output/seqkit/test.split/test_1.part_001.fastq.gz
md5sum: bf835e685d597fc1ab5e5ac7dd689619 md5sum: bf835e685d597fc1ab5e5ac7dd689619
@ -79,8 +68,6 @@
tags: tags:
- seqkit - seqkit
- seqkit/split2 - seqkit/split2
- seqkit_split2_paired_end
- part
files: files:
- path: output/seqkit/test.split/test_1.part_001.fastq.gz - path: output/seqkit/test.split/test_1.part_001.fastq.gz
md5sum: fa25951435471238d5567fd2cae31f55 md5sum: fa25951435471238d5567fd2cae31f55

14
tests/software/shovill/main.nf
View file

@ -10,7 +10,7 @@ include { SHOVILL as SHOVILL_VELVET } from '../../../software/shovill/main.nf'
workflow test_shovill { workflow test_shovill {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
[ file("https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_1.fastq.gz", checkIfExists: true), [ file("https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_1.fastq.gz", checkIfExists: true),
file("https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_2.fastq.gz", checkIfExists: true) ] file("https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_2.fastq.gz", checkIfExists: true) ]
] ]
SHOVILL ( input ) SHOVILL ( input )
@ -18,8 +18,8 @@ workflow test_shovill {
workflow test_shovill_megahit { workflow test_shovill_megahit {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true), [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ] file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
] ]
SHOVILL_MEGAHIT ( input ) SHOVILL_MEGAHIT ( input )
@ -27,8 +27,8 @@ workflow test_shovill_megahit {
workflow test_shovill_skesa { workflow test_shovill_skesa {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true), [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ] file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
] ]
SHOVILL_SKESA ( input ) SHOVILL_SKESA ( input )
@ -36,8 +36,8 @@ workflow test_shovill_skesa {
workflow test_shovill_velvet { workflow test_shovill_velvet {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true), [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ] file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
] ]
SHOVILL_VELVET ( input ) SHOVILL_VELVET ( input )

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

@ -2,7 +2,6 @@
command: nextflow run ./tests/software/shovill -entry test_shovill -c tests/config/nextflow.config command: nextflow run ./tests/software/shovill -entry test_shovill -c tests/config/nextflow.config
tags: tags:
- shovill - shovill
- shovill/spades
files: files:
- path: output/shovill/contigs.gfa - path: output/shovill/contigs.gfa
md5sum: 277af5d8ae8a0d2432db59a316226828 md5sum: 277af5d8ae8a0d2432db59a316226828
@ -17,7 +16,6 @@
command: nextflow run ./tests/software/shovill -entry test_shovill_megahit -c tests/config/nextflow.config command: nextflow run ./tests/software/shovill -entry test_shovill_megahit -c tests/config/nextflow.config
tags: tags:
- shovill - shovill
- shovill/megahit
files: files:
- path: output/shovill/shovill.corrections - path: output/shovill/shovill.corrections
md5sum: d41d8cd98f00b204e9800998ecf8427e md5sum: d41d8cd98f00b204e9800998ecf8427e
@ -26,17 +24,16 @@
- path: output/shovill/contigs.fastg - path: output/shovill/contigs.fastg
- path: output/shovill/megahit.fasta - path: output/shovill/megahit.fasta
- path: output/shovill/shovill.log - path: output/shovill/shovill.log
- name: shovill with skesa - name: shovill with skesa
command: nextflow run ./tests/software/shovill -entry test_shovill_skesa -c tests/config/nextflow.config command: nextflow run ./tests/software/shovill -entry test_shovill_skesa -c tests/config/nextflow.config
tags: tags:
- shovill - shovill
- shovill/skesa
files: files:
- path: output/shovill/shovill.corrections - path: output/shovill/shovill.corrections
md5sum: d41d8cd98f00b204e9800998ecf8427e md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/shovill/skesa.fasta - path: output/shovill/skesa.fasta
md5sum: c0c2d11b633310eb1437345cb599c33c md5sum: 8157837dbe8315922f588dafa7af5ef8
# MD5sum not reproducible (timestamp) # MD5sum not reproducible (timestamp)
- path: output/shovill/contigs.fa - path: output/shovill/contigs.fa
- path: output/shovill/shovill.log - path: output/shovill/shovill.log
@ -45,7 +42,6 @@
command: nextflow run ./tests/software/shovill -entry test_shovill_velvet -c tests/config/nextflow.config command: nextflow run ./tests/software/shovill -entry test_shovill_velvet -c tests/config/nextflow.config
tags: tags:
- shovill - shovill
- shovill/velvet
files: files:
# MD5sum not reproducible (timestamp, contig order) # MD5sum not reproducible (timestamp, contig order)
- path: output/shovill/contigs.fa - path: output/shovill/contigs.fa

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

@ -2,7 +2,6 @@
command: nextflow run ./tests/software/spades -entry test_spades_single_end -c tests/config/nextflow.config command: nextflow run ./tests/software/spades -entry test_spades_single_end -c tests/config/nextflow.config
tags: tags:
- spades - spades
- spades_single_end
files: files:
- path: output/spades/test.assembly.gfa - path: output/spades/test.assembly.gfa
md5sum: b2616d2beba83ab7d361b54778d1e759 md5sum: b2616d2beba83ab7d361b54778d1e759
@ -16,10 +15,9 @@
command: nextflow run ./tests/software/spades -entry test_spades_paired_end -c tests/config/nextflow.config command: nextflow run ./tests/software/spades -entry test_spades_paired_end -c tests/config/nextflow.config
tags: tags:
- spades - spades
- spades_paired_end
files: files:
- path: output/spades/test.assembly.gfa - path: output/spades/test.assembly.gfa
md5sum: faf76135ee390606b899c0197dc38e04 md5sum: faf76135ee390606b899c0197dc38e04
- path: output/spades/test.contigs.fa - path: output/spades/test.contigs.fa
md5sum: 6148e25b33890c80f176f90f2dd88989 md5sum: 6148e25b33890c80f176f90f2dd88989
- path: output/spades/test.spades.log - path: output/spades/test.spades.log

2
tests/software/star/align/test.yml
View file

@ -3,7 +3,6 @@
tags: tags:
- star - star
- star/align - star/align
- star_align_single_end
files: files:
- path: output/star/star/Genome - path: output/star/star/Genome
md5sum: 323c992bac354f93073ce0fc43f222f8 md5sum: 323c992bac354f93073ce0fc43f222f8
@ -41,7 +40,6 @@
tags: tags:
- star - star
- star/align - star/align
- star_align_paired_end
files: files:
- path: output/star/star/Genome - path: output/star/star/Genome
md5sum: 323c992bac354f93073ce0fc43f222f8 md5sum: 323c992bac354f93073ce0fc43f222f8

3
tests/software/subread/featurecounts/test.yml
View file

@ -3,7 +3,6 @@
tags: tags:
- subread - subread
- subread/featurecounts - subread/featurecounts
- subread_featurecounts_forward
files: files:
- path: output/subread/test.featureCounts.txt.summary - path: output/subread/test.featureCounts.txt.summary
md5sum: d78617192451a57f6ef249ddcaf13720 md5sum: d78617192451a57f6ef249ddcaf13720
@ -15,7 +14,6 @@
tags: tags:
- subread - subread
- subread/featurecounts - subread/featurecounts
- subread_featurecounts_reverse
files: files:
- path: output/subread/test.featureCounts.txt.summary - path: output/subread/test.featureCounts.txt.summary
md5sum: 4217004d0b55f870f77092364f59e44d md5sum: 4217004d0b55f870f77092364f59e44d
@ -27,7 +25,6 @@
tags: tags:
- subread - subread
- subread/featurecounts - subread/featurecounts
- subread_featurecounts_unstranded
files: files:
- path: output/subread/test.featureCounts.txt.summary - path: output/subread/test.featureCounts.txt.summary
md5sum: ee585faeb1edfcd2188a5e486a0e98a9 md5sum: ee585faeb1edfcd2188a5e486a0e98a9

3
tests/software/tabix/tabix/test.yml
View file

@ -3,7 +3,6 @@
tags: tags:
- tabix - tabix
- tabix/tabix - tabix/tabix
- bed
files: files:
- path: ./output/tabix/test.bed.gz.tbi - path: ./output/tabix/test.bed.gz.tbi
md5sum: 115922d881d24879b15d20c3734495ac md5sum: 115922d881d24879b15d20c3734495ac
@ -12,7 +11,6 @@
tags: tags:
- tabix - tabix
- tabix/tabix - tabix/tabix
- gff
files: files:
- path: ./output/tabix/genome.gff3.gz.tbi - path: ./output/tabix/genome.gff3.gz.tbi
md5sum: 4059fe4762568194cf293fc6df7b358b md5sum: 4059fe4762568194cf293fc6df7b358b
@ -21,7 +19,6 @@
tags: tags:
- tabix - tabix
- tabix/tabix - tabix/tabix
- vcf
files: files:
- path: output/tabix/test.vcf.gz.tbi - path: output/tabix/test.vcf.gz.tbi
md5sum: bbec39fd53cf2834909d52094980d094 md5sum: bbec39fd53cf2834909d52094980d094

2
tests/software/tiddit/sv/test.yml
View file

@ -3,7 +3,6 @@
tags: tags:
- tiddit - tiddit
- tiddit/sv - tiddit/sv
- vcf
files: files:
- path: output/tiddit/test.ploidy.tab - path: output/tiddit/test.ploidy.tab
md5sum: 45e050b0e204f0a5a3a99627cc440eaa md5sum: 45e050b0e204f0a5a3a99627cc440eaa
@ -17,7 +16,6 @@
tags: tags:
- tiddit - tiddit
- tiddit/sv - tiddit/sv
- vcf
files: files:
- path: output/tiddit/test.ploidy.tab - path: output/tiddit/test.ploidy.tab
md5sum: 45e050b0e204f0a5a3a99627cc440eaa md5sum: 45e050b0e204f0a5a3a99627cc440eaa

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

@ -6,7 +6,7 @@ include { UNICYCLER } from '../../../software/unicycler/main.nf' addParams( opti
workflow test_unicycler_single_end { workflow test_unicycler_single_end {
input = [ [ id:'test', single_end:true ], // meta map input = [ [ id:'test', single_end:true ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] [ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
] ]
UNICYCLER ( input ) UNICYCLER ( input )
@ -15,7 +15,7 @@ workflow test_unicycler_single_end {
workflow test_unicycler_paired_end { workflow test_unicycler_paired_end {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
] ]
UNICYCLER ( input ) UNICYCLER ( input )

2
tests/software/unicycler/test.yml
View file

@ -2,7 +2,6 @@
command: nextflow run ./tests/software/unicycler -entry test_unicycler_single_end -c tests/config/nextflow.config command: nextflow run ./tests/software/unicycler -entry test_unicycler_single_end -c tests/config/nextflow.config
tags: tags:
- unicycler - unicycler
- unicycler_single_end
files: files:
- path: output/unicycler/test.scaffolds.fa - path: output/unicycler/test.scaffolds.fa
- path: output/unicycler/test.assembly.gfa - path: output/unicycler/test.assembly.gfa
@ -14,7 +13,6 @@
command: nextflow run ./tests/software/unicycler -entry test_unicycler_paired_end -c tests/config/nextflow.config command: nextflow run ./tests/software/unicycler -entry test_unicycler_paired_end -c tests/config/nextflow.config
tags: tags:
- unicycler - unicycler
- unicycler_paired_end
files: files:
- path: output/unicycler/test.scaffolds.fa - path: output/unicycler/test.scaffolds.fa
- path: output/unicycler/test.assembly.gfa - path: output/unicycler/test.assembly.gfa

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

@ -2,7 +2,6 @@
command: nextflow run tests/software/vcftools -entry test_vcftools_vcf_base -c tests/config/nextflow.config command: nextflow run tests/software/vcftools -entry test_vcftools_vcf_base -c tests/config/nextflow.config
tags: tags:
- vcftools - vcftools
- vcftools_vcf_base
files: files:
- path: output/vcftools/test.frq - path: output/vcftools/test.frq
md5sum: 7f126655f17268fd1a338734f62868e9 md5sum: 7f126655f17268fd1a338734f62868e9
@ -10,7 +9,6 @@
- name: vcftools test_vcftools_vcfgz_base - name: vcftools test_vcftools_vcfgz_base
command: nextflow run tests/software/vcftools -entry test_vcftools_vcfgz_base -c tests/config/nextflow.config command: nextflow run tests/software/vcftools -entry test_vcftools_vcfgz_base -c tests/config/nextflow.config
tags: tags:
- vcftools_vcfgz_base
- vcftools - vcftools
files: files:
- path: output/vcftools/test.frq - path: output/vcftools/test.frq
@ -20,7 +18,6 @@
command: nextflow run tests/software/vcftools -entry test_vcftools_vcf_optional -c tests/config/nextflow.config command: nextflow run tests/software/vcftools -entry test_vcftools_vcf_optional -c tests/config/nextflow.config
tags: tags:
- vcftools - vcftools
- vcftools_vcf_optional
files: files:
- path: output/vcftools/test.frq - path: output/vcftools/test.frq
md5sum: 7f126655f17268fd1a338734f62868e9 md5sum: 7f126655f17268fd1a338734f62868e9
@ -29,7 +26,6 @@
command: nextflow run tests/software/vcftools -entry test_vcftools_vcfgz_optional -c tests/config/nextflow.config command: nextflow run tests/software/vcftools -entry test_vcftools_vcfgz_optional -c tests/config/nextflow.config
tags: tags:
- vcftools - vcftools
- vcftools_vcfgz_optional
files: files:
- path: output/vcftools/test.frq - path: output/vcftools/test.frq
md5sum: 7f126655f17268fd1a338734f62868e9 md5sum: 7f126655f17268fd1a338734f62868e9

18
tests/software/yara/mapper/main.nf
View file

@ -8,25 +8,23 @@ include { YARA_MAPPER } from '../../../../software/yara/mapper/main.nf' addParam
workflow test_yara_single_end { workflow test_yara_single_end {
def fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
YARA_INDEX ( fasta )
def input = []
input = [ [ id:'test', single_end:true ], // meta map input = [ [ id:'test', single_end:true ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
YARA_INDEX ( fasta )
YARA_MAPPER ( input, YARA_INDEX.out.index ) YARA_MAPPER ( input, YARA_INDEX.out.index )
} }
workflow test_yara_paired_end { workflow test_yara_paired_end {
def fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
YARA_INDEX ( fasta )
def input = []
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ] ] file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] ]
YARA_INDEX ( fasta )
YARA_MAPPER ( input, YARA_INDEX.out.index ) YARA_MAPPER ( input, YARA_INDEX.out.index )
} }

2
tests/software/yara/mapper/test.yml
View file

@ -1,7 +1,6 @@
- name: yara mapper test_yara_single_end - name: yara mapper test_yara_single_end
command: nextflow run tests/software/yara/mapper -entry test_yara_single_end -c tests/config/nextflow.config command: nextflow run tests/software/yara/mapper -entry test_yara_single_end -c tests/config/nextflow.config
tags: tags:
- yara_single_end
- yara/mapper - yara/mapper
- yara - yara
files: files:
@ -37,7 +36,6 @@
command: nextflow run tests/software/yara/mapper -entry test_yara_paired_end -c tests/config/nextflow.config command: nextflow run tests/software/yara/mapper -entry test_yara_paired_end -c tests/config/nextflow.config
tags: tags:
- yara/mapper - yara/mapper
- yara_paired_end
- yara - yara
files: files:
- path: output/yara/test_2.mapped.bam - path: output/yara/test_2.mapped.bam