mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2025-01-02 20:52:07 -05:00
remove deprecated test tags (#440)
* 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
GitHub
parent
a9fcbd93cc
commit
043a7d1e3c
41 changed files with 49 additions and 124 deletions
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@ -19,7 +19,7 @@ process GATK4_APPLYBQSR {
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}
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input:
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tuple val(meta), path(bam), path(bqsr_table)
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tuple val(meta), path(bam), path(bai), path(bqsr_table)
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path fasta
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path fastaidx
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path dict
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@ -19,7 +19,7 @@ process GATK4_BASERECALIBRATOR {
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}
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input:
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tuple val(meta), path(bam)
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tuple val(meta), path(bam), path(bai)
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path fasta
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path fastaidx
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path dict
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@ -1,7 +1,6 @@
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- name: adapterremoval test_adapterremoval_single_end
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command: nextflow run tests/software/adapterremoval -entry test_adapterremoval_single_end -c tests/config/nextflow.config
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tags:
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- adapterremoval_single_end
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- adapterremoval
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files:
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- path: output/adapterremoval/test.log
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@ -12,7 +11,6 @@
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- name: adapterremoval test_adapterremoval_paired_end
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command: nextflow run tests/software/adapterremoval -entry test_adapterremoval_paired_end -c tests/config/nextflow.config
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tags:
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- adapterremoval_paired_end
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- adapterremoval
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files:
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- path: output/adapterremoval/test.pair2.trimmed.fastq.gz
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@ -25,7 +23,6 @@
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- name: adapterremoval test_adapterremoval_paired_end_collapse
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command: nextflow run tests/software/adapterremoval -entry test_adapterremoval_paired_end_collapse -c tests/config/nextflow.config
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tags:
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- adapterremoval_paired_end_collapse
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- adapterremoval
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files:
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- path: output/adapterremoval/test.log
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@ -7,9 +7,9 @@ include { BOWTIE_ALIGN } from '../../../../software/bowtie/align/main.nf' addPar
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workflow test_bowtie_align_single_end {
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input = [ [ id:'test', single_end:true ], // meta map
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[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
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]
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fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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BOWTIE_BUILD ( fasta )
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BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
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@ -3,7 +3,6 @@
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tags:
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- bowtie
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- bowtie/align
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- bowtie_align_single_end
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files:
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- path: ./output/bowtie/test.bam
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- path: ./output/bowtie/test.out
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@ -26,7 +25,6 @@
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tags:
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- bowtie
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- bowtie/align
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- bowtie_align_paired_end
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files:
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- path: ./output/bowtie/test.bam
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- path: ./output/bowtie/test.out
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@ -3,7 +3,6 @@
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tags:
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- bowtie2
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- bowtie2/align
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- bowtie2_align_single_end
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files:
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- path: ./output/bowtie2/test.bam
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- path: ./output/bowtie2/test.bowtie2.log
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@ -25,7 +24,6 @@
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tags:
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- bowtie2
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- bowtie2/align
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- bowtie2_align_paired_end
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files:
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- path: ./output/bowtie2/test.bam
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- path: ./output/bowtie2/test.bowtie2.log
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@ -3,7 +3,6 @@
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tags:
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- bwa
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- bwa/mem
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- bwa_mem_single_end
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files:
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- path: ./output/bwa/test.bam
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md5sum: 9165508bf914baee0e6347711aa7b23a
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@ -23,7 +22,6 @@
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tags:
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- bwa
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- bwa/mem
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- bwa_mem_paired_end
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files:
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- path: ./output/bwa/test.bam
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md5sum: 670a53bddee62d6bd14ed7adaf103e7c
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@ -3,7 +3,6 @@
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tags:
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- bwamem2
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- bwamem2/mem
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- bwamem2_mem_single_end
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files:
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- path: ./output/bwamem2/test.bam
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md5sum: 2133c011119ea11f06f0a9b1621ba05b
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@ -23,7 +22,6 @@
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tags:
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- bwamem2
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- bwamem2/mem
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- bwamem2_mem_paired_end
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files:
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- path: ./output/bwamem2/test.bam
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md5sum: d8fadab5cef04faff1851a8162fc30b5
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@ -3,7 +3,6 @@
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tags:
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- cat
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- cat/fastq
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- cat_fastqc_single_end
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files:
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- path: ./output/merged_fastq/test.merged.fastq.gz
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md5sum: 59f6dbe193741bb40f498f254aeb2e99
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@ -13,7 +12,6 @@
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tags:
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- cat
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- cat/fastq
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- cat_fastqc_paired_end
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files:
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- path: ./output/merged_fastq/test_2.merged.fastq.gz
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md5sum: d2b1a836eef1058738ecab36c907c5ba
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@ -2,7 +2,6 @@
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command: nextflow run ./tests/software/cutadapt -entry test_cutadapt_single_end -c tests/config/nextflow.config
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tags:
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- cutadapt
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- cutadapt_single_end
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files:
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- path: ./output/cutadapt/test.cutadapt.log
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- path: ./output/cutadapt/test.trim.fastq.gz
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@ -11,7 +10,6 @@
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command: nextflow run ./tests/software/cutadapt -entry test_cutadapt_paired_end -c tests/config/nextflow.config
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tags:
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- cutadapt
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- cutadapt_paired_end
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files:
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- path: ./output/cutadapt/test.cutadapt.log
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- path: ./output/cutadapt/test_1.trim.fastq.gz
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@ -1,7 +1,6 @@
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- name: fastp test_fastp_single_end
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command: nextflow run tests/software/fastp -entry test_fastp_single_end -c tests/config/nextflow.config
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tags:
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- fastp_single_end
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- fastp
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files:
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- path: output/fastp/test.fastp.html
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@ -20,7 +19,6 @@
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- name: fastp test_fastp_paired_end
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command: nextflow run tests/software/fastp -entry test_fastp_paired_end -c tests/config/nextflow.config
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tags:
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- fastp_paired_end
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- fastp
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files:
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- path: output/fastp/test.fastp.html
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@ -2,7 +2,6 @@
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command: nextflow run ./tests/software/fastqc/ -entry test_fastqc_single_end -c tests/config/nextflow.config
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tags:
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- fastqc
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- fastqc_single_end
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files:
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- path: ./output/fastqc/test_fastqc.html
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- path: ./output/fastqc/test_fastqc.zip
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@ -11,7 +10,6 @@
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command: nextflow run ./tests/software/fastqc/ -entry test_fastqc_paired_end -c tests/config/nextflow.config
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tags:
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- fastqc
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- fastqc_paired_end
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files:
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- path: ./output/fastqc/test_1_fastqc.html
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- path: ./output/fastqc/test_2_fastqc.html
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@ -7,6 +7,7 @@ include { GATK4_APPLYBQSR } from '../../../../software/gatk4/applybqsr/main.nf'
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workflow test_gatk4_applybqsr {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true)
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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@ -19,6 +20,7 @@ workflow test_gatk4_applybqsr {
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workflow test_gatk4_applybqsr_intervals {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true)
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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@ -11,7 +11,6 @@
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command: nextflow run tests/software/gatk4/applybqsr -entry test_gatk4_applybqsr_intervals -c tests/config/nextflow.config
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tags:
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- gatk4
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- gatk4/applybqsr/intervals
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- gatk4/applybqsr
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files:
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- path: output/gatk4/test.bam
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@ -6,7 +6,8 @@ include { GATK4_BASERECALIBRATOR } from '../../../../software/gatk4/baserecalibr
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workflow test_gatk4_baserecalibrator {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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@ -19,7 +20,8 @@ workflow test_gatk4_baserecalibrator {
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workflow test_gatk4_baserecalibrator_intervals {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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@ -33,7 +35,8 @@ workflow test_gatk4_baserecalibrator_intervals {
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workflow test_gatk4_baserecalibrator_multiple_sites {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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@ -10,7 +10,6 @@
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- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_intervals
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command: nextflow run tests/software/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_intervals -c tests/config/nextflow.config
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tags:
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- gatk4/baserecalibrator/intervals
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- gatk4/baserecalibrator
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- gatk4
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files:
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@ -20,7 +19,6 @@
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- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_multiple_sites
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command: nextflow run tests/software/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_multiple_sites -c tests/config/nextflow.config
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tags:
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- gatk4_baserecalibrator_multiple_sites
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- gatk4/baserecalibrator
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- gatk4
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files:
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@ -1,7 +1,6 @@
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- name: gatk4 fastqtosam test_gatk4_fastqtosam_single_end
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command: nextflow run tests/software/gatk4/fastqtosam -entry test_gatk4_fastqtosam_single_end -c tests/config/nextflow.config
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tags:
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- gatk4_fastqtosam_single_end
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- gatk4/fastqtosam
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- gatk4
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files:
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@ -11,7 +10,6 @@
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- name: gatk4 fastqtosam test_gatk4_fastqtosam_paired_end
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command: nextflow run tests/software/gatk4/fastqtosam -entry test_gatk4_fastqtosam_paired_end -c tests/config/nextflow.config
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tags:
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- gatk4_fastqtosam_paired_end
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- gatk4
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- gatk4/fastqtosam
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files:
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@ -12,7 +12,6 @@
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tags:
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- gatk4/mergevcfs
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- gatk4
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- gatk4/mergevcfs_refdict
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files:
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- path: output/gatk4/test.merged.vcf.gz
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md5sum: ff48f175e26db2d4b2957762f6d1c715
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@ -3,7 +3,6 @@
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tags:
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- gatk4
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- gatk4/samtofastq
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- gatk4_samtofastq_single_end
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files:
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- path: output/gatk4/test.fastq.gz
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md5sum: 50ace41d4c24467f24f8b929540a7797
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@ -13,7 +12,6 @@
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tags:
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- gatk4
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- gatk4/samtofastq
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- gatk4_samtofastq_paired_end
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files:
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- path: output/gatk4/test_1.fastq.gz
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md5sum: cfea607c9d75fd9ea9704780ad3a499c
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@ -3,7 +3,6 @@
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tags:
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- hisat2
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- hisat2/align
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- hisat2_align_single_end
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files:
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- path: output/hisat2/test.hisat2.summary.log
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md5sum: 7b8a9e61b7646da1089b041333c41a87
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@ -32,7 +31,6 @@
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tags:
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- hisat2
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- hisat2/align
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- hisat2_align_paired_end
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files:
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- path: output/hisat2/test.hisat2.summary.log
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md5sum: 9839b31db795958cc4b70711a3414e9c
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@ -6,8 +6,8 @@ include { KALLISTOBUSTOOLS_REF } from '../../../../software/kallistobustools/ref
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workflow test_kallistobustools_ref_standard {
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fasta = file("${launchDir}/tests/data/delete_me/kallistobustools/GRCm39.chr19_100k.fa.gz", checkIfExists: true)
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gtf = file("${launchDir}/tests/data/delete_me/kallistobustools/gencode.VM26.chr19_10k.gtf.gz", checkIfExists: true)
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fasta = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kallistobustools/GRCm39.chr19_100k.fa.gz", checkIfExists: true)
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gtf = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kallistobustools/gencode.VM26.chr19_10k.gtf.gz", checkIfExists: true)
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workflow = "standard"
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KALLISTOBUSTOOLS_REF(fasta, gtf, workflow)
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@ -15,8 +15,8 @@ workflow test_kallistobustools_ref_standard {
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workflow test_kallistobustools_ref_lamanno {
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fasta = file("${launchDir}/tests/data/delete_me/kallistobustools/GRCm39.chr19_100k.fa.gz", checkIfExists: true)
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gtf = file("${launchDir}/tests/data/delete_me/kallistobustools/gencode.VM26.chr19_10k.gtf.gz", checkIfExists: true)
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fasta = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kallistobustools/GRCm39.chr19_100k.fa.gz", checkIfExists: true)
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gtf = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kallistobustools/gencode.VM26.chr19_10k.gtf.gz", checkIfExists: true)
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workflow = "standard"
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KALLISTOBUSTOOLS_REF( fasta, gtf, workflow)
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@ -24,8 +24,8 @@ workflow test_kallistobustools_ref_lamanno {
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workflow test_kallistobustools_ref_nucleus {
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fasta = file("${launchDir}/tests/data/delete_me/kallistobustools/GRCm39.chr19_100k.fa.gz", checkIfExists: true)
|
||||
gtf = file("${launchDir}/tests/data/delete_me/kallistobustools/gencode.VM26.chr19_10k.gtf.gz", checkIfExists: true)
|
||||
fasta = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kallistobustools/GRCm39.chr19_100k.fa.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"
|
||||
|
||||
KALLISTOBUSTOOLS_REF( fasta, gtf, workflow)
|
||||
|
|
|
|||
|
|
@ -2,7 +2,6 @@
|
|||
command: nextflow run tests/software/kallistobustools/ref -entry test_kallistobustools_ref_standard -c tests/config/nextflow.config
|
||||
tags:
|
||||
- kallistobustools
|
||||
- kallistobustools_ref_standard
|
||||
- kallistobustools/ref
|
||||
files:
|
||||
- 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
|
||||
tags:
|
||||
- kallistobustools
|
||||
- kallistobustools_ref_lamanno
|
||||
- kallistobustools/ref
|
||||
files:
|
||||
- path: output/kallistobustools/cdna.fa
|
||||
|
|
@ -29,7 +27,6 @@
|
|||
- name: kallistobustools ref test_kallistobustools_ref_nucleus
|
||||
command: nextflow run tests/software/kallistobustools/ref -entry test_kallistobustools_ref_nucleus -c tests/config/nextflow.config
|
||||
tags:
|
||||
- kallistobustools_ref_nucleus
|
||||
- kallistobustools
|
||||
- kallistobustools/ref
|
||||
files:
|
||||
|
|
|
|||
|
|
@ -6,9 +6,9 @@ include { MINIMAP2_ALIGN } from '../../../../software/minimap2/align/main.nf' ad
|
|||
|
||||
workflow test_minimap2_align_single_end {
|
||||
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 )
|
||||
}
|
||||
|
|
@ -18,7 +18,7 @@ workflow test_minimap2_align_paired_end {
|
|||
[ file(params.test_data['sarscov2']['illumina']['test_1_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 )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -3,7 +3,6 @@
|
|||
tags:
|
||||
- minimap2
|
||||
- minimap2/align
|
||||
- minimap2_align_single_end
|
||||
files:
|
||||
- path: ./output/minimap2/test.paf
|
||||
md5sum: 5a9648fc67c30a2c83b0ef094171faa0
|
||||
|
|
@ -13,7 +12,6 @@
|
|||
tags:
|
||||
- minimap2
|
||||
- minimap2/align
|
||||
- minimap2_align_paired_end
|
||||
files:
|
||||
- path: ./output/minimap2/test.paf
|
||||
md5sum: e7b952be872bdbef16bf99d512690df7
|
||||
|
|
|
|||
|
|
@ -13,5 +13,4 @@
|
|||
tags:
|
||||
- picard
|
||||
- picard/markduplicates
|
||||
- should fail
|
||||
exit_code: 1
|
||||
|
|
|
|||
|
|
@ -3,7 +3,6 @@
|
|||
tags:
|
||||
- preseq
|
||||
- preseq/lcextrap
|
||||
- preseq_lcextrap_single_end
|
||||
files:
|
||||
- path: output/preseq/test.ccurve.txt
|
||||
md5sum: 76ae04c8eaf19c94e3210bb69da38498
|
||||
|
|
@ -14,7 +13,6 @@
|
|||
tags:
|
||||
- preseq
|
||||
- preseq/lcextrap
|
||||
- preseq_lcextrap_paired_end
|
||||
files:
|
||||
- path: output/preseq/test.ccurve.txt
|
||||
md5sum: 2836d2fabd2213f097fd7063db550276
|
||||
|
|
|
|||
|
|
@ -2,7 +2,6 @@
|
|||
command: nextflow run ./tests/software/quast -entry test_quast_ref -c ./tests/config/nextflow.config
|
||||
tags:
|
||||
- quast
|
||||
- quast_reference
|
||||
files:
|
||||
- path: ./output/quast/report.tsv
|
||||
- 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
|
||||
tags:
|
||||
- quast
|
||||
- quast_no_reference
|
||||
files:
|
||||
- path: ./output/quast/report.tsv
|
||||
md5sum: 074e239aac0f298cf4cd2a28a9bb5690
|
||||
|
|
|
|||
|
|
@ -3,7 +3,6 @@
|
|||
tags:
|
||||
- salmon
|
||||
- salmon/quant
|
||||
- salmon_quant_single_end
|
||||
files:
|
||||
- path: ./output/salmon/test/cmd_info.json
|
||||
- path: ./output/salmon/test/quant.sf
|
||||
|
|
@ -55,7 +54,6 @@
|
|||
tags:
|
||||
- salmon
|
||||
- salmon/quant
|
||||
- salmon_quant_paired_end
|
||||
files:
|
||||
- path: ./output/salmon/test/cmd_info.json
|
||||
- path: ./output/salmon/test/quant.sf
|
||||
|
|
|
|||
|
|
@ -3,22 +3,17 @@
|
|||
tags:
|
||||
- seqkit
|
||||
- seqkit/split2
|
||||
- seqkit_split2_single_end
|
||||
- length
|
||||
files:
|
||||
- path: output/seqkit/test.split/test_1.part_001.fastq.gz
|
||||
md5sum: 6f7d58ba35c254c0817fe9a7c69862e4
|
||||
- path: output/seqkit/test.split/test_1.part_002.fastq.gz
|
||||
md5sum: cf38c51506e45380fe25abdd1bd5ccc6
|
||||
|
||||
|
||||
- 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
|
||||
tags:
|
||||
- seqkit
|
||||
- seqkit/split2
|
||||
- seqkit_split2_single_end
|
||||
- size
|
||||
files:
|
||||
- path: output/seqkit/test.split/test_1.part_001.fastq.gz
|
||||
md5sum: bf835e685d597fc1ab5e5ac7dd689619
|
||||
|
|
@ -30,8 +25,6 @@
|
|||
tags:
|
||||
- seqkit
|
||||
- seqkit/split2
|
||||
- seqkit_split2_single_end
|
||||
- part
|
||||
files:
|
||||
- path: output/seqkit/test.split/test_1.part_001.fastq.gz
|
||||
md5sum: fa25951435471238d5567fd2cae31f55
|
||||
|
|
@ -45,8 +38,6 @@
|
|||
tags:
|
||||
- seqkit
|
||||
- seqkit/split2
|
||||
- seqkit_split2_paired_end
|
||||
- length
|
||||
files:
|
||||
- path: output/seqkit/test.split/test_1.part_001.fastq.gz
|
||||
md5sum: 6f7d58ba35c254c0817fe9a7c69862e4
|
||||
|
|
@ -62,8 +53,6 @@
|
|||
tags:
|
||||
- seqkit
|
||||
- seqkit/split2
|
||||
- seqkit_split2_paired_end
|
||||
- size
|
||||
files:
|
||||
- path: output/seqkit/test.split/test_1.part_001.fastq.gz
|
||||
md5sum: bf835e685d597fc1ab5e5ac7dd689619
|
||||
|
|
@ -79,8 +68,6 @@
|
|||
tags:
|
||||
- seqkit
|
||||
- seqkit/split2
|
||||
- seqkit_split2_paired_end
|
||||
- part
|
||||
files:
|
||||
- path: output/seqkit/test.split/test_1.part_001.fastq.gz
|
||||
md5sum: fa25951435471238d5567fd2cae31f55
|
||||
|
|
|
|||
|
|
@ -18,8 +18,8 @@ workflow test_shovill {
|
|||
|
||||
workflow test_shovill_megahit {
|
||||
input = [ [ id:'test', single_end:false ], // meta map
|
||||
[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true),
|
||||
file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ]
|
||||
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
|
||||
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
|
||||
]
|
||||
|
||||
SHOVILL_MEGAHIT ( input )
|
||||
|
|
@ -27,8 +27,8 @@ workflow test_shovill_megahit {
|
|||
|
||||
workflow test_shovill_skesa {
|
||||
input = [ [ id:'test', single_end:false ], // meta map
|
||||
[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true),
|
||||
file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ]
|
||||
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
|
||||
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
|
||||
]
|
||||
|
||||
SHOVILL_SKESA ( input )
|
||||
|
|
@ -36,8 +36,8 @@ workflow test_shovill_skesa {
|
|||
|
||||
workflow test_shovill_velvet {
|
||||
input = [ [ id:'test', single_end:false ], // meta map
|
||||
[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true),
|
||||
file("${launchDir}/tests/data/generic/fastq/test_R2.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) ]
|
||||
]
|
||||
|
||||
SHOVILL_VELVET ( input )
|
||||
|
|
|
|||
|
|
@ -2,7 +2,6 @@
|
|||
command: nextflow run ./tests/software/shovill -entry test_shovill -c tests/config/nextflow.config
|
||||
tags:
|
||||
- shovill
|
||||
- shovill/spades
|
||||
files:
|
||||
- path: output/shovill/contigs.gfa
|
||||
md5sum: 277af5d8ae8a0d2432db59a316226828
|
||||
|
|
@ -17,7 +16,6 @@
|
|||
command: nextflow run ./tests/software/shovill -entry test_shovill_megahit -c tests/config/nextflow.config
|
||||
tags:
|
||||
- shovill
|
||||
- shovill/megahit
|
||||
files:
|
||||
- path: output/shovill/shovill.corrections
|
||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
||||
|
|
@ -31,12 +29,11 @@
|
|||
command: nextflow run ./tests/software/shovill -entry test_shovill_skesa -c tests/config/nextflow.config
|
||||
tags:
|
||||
- shovill
|
||||
- shovill/skesa
|
||||
files:
|
||||
- path: output/shovill/shovill.corrections
|
||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
||||
- path: output/shovill/skesa.fasta
|
||||
md5sum: c0c2d11b633310eb1437345cb599c33c
|
||||
md5sum: 8157837dbe8315922f588dafa7af5ef8
|
||||
# MD5sum not reproducible (timestamp)
|
||||
- path: output/shovill/contigs.fa
|
||||
- path: output/shovill/shovill.log
|
||||
|
|
@ -45,7 +42,6 @@
|
|||
command: nextflow run ./tests/software/shovill -entry test_shovill_velvet -c tests/config/nextflow.config
|
||||
tags:
|
||||
- shovill
|
||||
- shovill/velvet
|
||||
files:
|
||||
# MD5sum not reproducible (timestamp, contig order)
|
||||
- path: output/shovill/contigs.fa
|
||||
|
|
|
|||
|
|
@ -2,7 +2,6 @@
|
|||
command: nextflow run ./tests/software/spades -entry test_spades_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- spades
|
||||
- spades_single_end
|
||||
files:
|
||||
- path: output/spades/test.assembly.gfa
|
||||
md5sum: b2616d2beba83ab7d361b54778d1e759
|
||||
|
|
@ -16,10 +15,9 @@
|
|||
command: nextflow run ./tests/software/spades -entry test_spades_paired_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- spades
|
||||
- spades_paired_end
|
||||
files:
|
||||
- path: output/spades/test.assembly.gfa
|
||||
md5sum: faf76135ee390606b899c0197dc38e04
|
||||
- path: output/spades/test.contigs.fa
|
||||
md5sum: 6148e25b33890c80f176f90f2dd88989
|
||||
- path: output/spades/test.spades.log
|
||||
- path: output/spades/test.assembly.gfa
|
||||
md5sum: faf76135ee390606b899c0197dc38e04
|
||||
- path: output/spades/test.contigs.fa
|
||||
md5sum: 6148e25b33890c80f176f90f2dd88989
|
||||
- path: output/spades/test.spades.log
|
||||
|
|
|
|||
|
|
@ -3,7 +3,6 @@
|
|||
tags:
|
||||
- star
|
||||
- star/align
|
||||
- star_align_single_end
|
||||
files:
|
||||
- path: output/star/star/Genome
|
||||
md5sum: 323c992bac354f93073ce0fc43f222f8
|
||||
|
|
@ -41,7 +40,6 @@
|
|||
tags:
|
||||
- star
|
||||
- star/align
|
||||
- star_align_paired_end
|
||||
files:
|
||||
- path: output/star/star/Genome
|
||||
md5sum: 323c992bac354f93073ce0fc43f222f8
|
||||
|
|
|
|||
|
|
@ -3,7 +3,6 @@
|
|||
tags:
|
||||
- subread
|
||||
- subread/featurecounts
|
||||
- subread_featurecounts_forward
|
||||
files:
|
||||
- path: output/subread/test.featureCounts.txt.summary
|
||||
md5sum: d78617192451a57f6ef249ddcaf13720
|
||||
|
|
@ -15,7 +14,6 @@
|
|||
tags:
|
||||
- subread
|
||||
- subread/featurecounts
|
||||
- subread_featurecounts_reverse
|
||||
files:
|
||||
- path: output/subread/test.featureCounts.txt.summary
|
||||
md5sum: 4217004d0b55f870f77092364f59e44d
|
||||
|
|
@ -27,7 +25,6 @@
|
|||
tags:
|
||||
- subread
|
||||
- subread/featurecounts
|
||||
- subread_featurecounts_unstranded
|
||||
files:
|
||||
- path: output/subread/test.featureCounts.txt.summary
|
||||
md5sum: ee585faeb1edfcd2188a5e486a0e98a9
|
||||
|
|
|
|||
|
|
@ -3,7 +3,6 @@
|
|||
tags:
|
||||
- tabix
|
||||
- tabix/tabix
|
||||
- bed
|
||||
files:
|
||||
- path: ./output/tabix/test.bed.gz.tbi
|
||||
md5sum: 115922d881d24879b15d20c3734495ac
|
||||
|
|
@ -12,7 +11,6 @@
|
|||
tags:
|
||||
- tabix
|
||||
- tabix/tabix
|
||||
- gff
|
||||
files:
|
||||
- path: ./output/tabix/genome.gff3.gz.tbi
|
||||
md5sum: 4059fe4762568194cf293fc6df7b358b
|
||||
|
|
@ -21,7 +19,6 @@
|
|||
tags:
|
||||
- tabix
|
||||
- tabix/tabix
|
||||
- vcf
|
||||
files:
|
||||
- path: output/tabix/test.vcf.gz.tbi
|
||||
md5sum: bbec39fd53cf2834909d52094980d094
|
||||
|
|
|
|||
|
|
@ -3,7 +3,6 @@
|
|||
tags:
|
||||
- tiddit
|
||||
- tiddit/sv
|
||||
- vcf
|
||||
files:
|
||||
- path: output/tiddit/test.ploidy.tab
|
||||
md5sum: 45e050b0e204f0a5a3a99627cc440eaa
|
||||
|
|
@ -17,7 +16,6 @@
|
|||
tags:
|
||||
- tiddit
|
||||
- tiddit/sv
|
||||
- vcf
|
||||
files:
|
||||
- path: output/tiddit/test.ploidy.tab
|
||||
md5sum: 45e050b0e204f0a5a3a99627cc440eaa
|
||||
|
|
|
|||
|
|
@ -6,7 +6,7 @@ include { UNICYCLER } from '../../../software/unicycler/main.nf' addParams( opti
|
|||
|
||||
workflow test_unicycler_single_end {
|
||||
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 )
|
||||
|
|
|
|||
|
|
@ -2,7 +2,6 @@
|
|||
command: nextflow run ./tests/software/unicycler -entry test_unicycler_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- unicycler
|
||||
- unicycler_single_end
|
||||
files:
|
||||
- path: output/unicycler/test.scaffolds.fa
|
||||
- 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
|
||||
tags:
|
||||
- unicycler
|
||||
- unicycler_paired_end
|
||||
files:
|
||||
- path: output/unicycler/test.scaffolds.fa
|
||||
- path: output/unicycler/test.assembly.gfa
|
||||
|
|
|
|||
|
|
@ -2,7 +2,6 @@
|
|||
command: nextflow run tests/software/vcftools -entry test_vcftools_vcf_base -c tests/config/nextflow.config
|
||||
tags:
|
||||
- vcftools
|
||||
- vcftools_vcf_base
|
||||
files:
|
||||
- path: output/vcftools/test.frq
|
||||
md5sum: 7f126655f17268fd1a338734f62868e9
|
||||
|
|
@ -10,7 +9,6 @@
|
|||
- name: vcftools test_vcftools_vcfgz_base
|
||||
command: nextflow run tests/software/vcftools -entry test_vcftools_vcfgz_base -c tests/config/nextflow.config
|
||||
tags:
|
||||
- vcftools_vcfgz_base
|
||||
- vcftools
|
||||
files:
|
||||
- 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
|
||||
tags:
|
||||
- vcftools
|
||||
- vcftools_vcf_optional
|
||||
files:
|
||||
- path: output/vcftools/test.frq
|
||||
md5sum: 7f126655f17268fd1a338734f62868e9
|
||||
|
|
@ -29,7 +26,6 @@
|
|||
command: nextflow run tests/software/vcftools -entry test_vcftools_vcfgz_optional -c tests/config/nextflow.config
|
||||
tags:
|
||||
- vcftools
|
||||
- vcftools_vcfgz_optional
|
||||
files:
|
||||
- path: output/vcftools/test.frq
|
||||
md5sum: 7f126655f17268fd1a338734f62868e9
|
||||
|
|
|
|||
|
|
@ -8,25 +8,23 @@ include { YARA_MAPPER } from '../../../../software/yara/mapper/main.nf' addParam
|
|||
|
||||
workflow test_yara_single_end {
|
||||
|
||||
def fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
|
||||
YARA_INDEX ( fasta )
|
||||
|
||||
def input = []
|
||||
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
input = [ [ id:'test', single_end:true ], // meta map
|
||||
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
|
||||
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
|
||||
|
||||
|
||||
YARA_INDEX ( fasta )
|
||||
YARA_MAPPER ( input, YARA_INDEX.out.index )
|
||||
}
|
||||
|
||||
workflow test_yara_paired_end {
|
||||
|
||||
def fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
|
||||
YARA_INDEX ( fasta )
|
||||
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
|
||||
def input = []
|
||||
input = [ [ id:'test', single_end:false ], // meta map
|
||||
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
|
||||
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ] ]
|
||||
[ file(params.test_data['sarscov2']['illumina']['test_1_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 )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,7 +1,6 @@
|
|||
- name: yara mapper test_yara_single_end
|
||||
command: nextflow run tests/software/yara/mapper -entry test_yara_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- yara_single_end
|
||||
- yara/mapper
|
||||
- yara
|
||||
files:
|
||||
|
|
@ -37,7 +36,6 @@
|
|||
command: nextflow run tests/software/yara/mapper -entry test_yara_paired_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- yara/mapper
|
||||
- yara_paired_end
|
||||
- yara
|
||||
files:
|
||||
- path: output/yara/test_2.mapped.bam
|
||||
|
|
|
|||
Loading…
Reference in a new issue