mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
Get tests passing
This commit is contained in:
parent
c32fcb39fc
commit
530789ba85
26 changed files with 62 additions and 61 deletions
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@ -2,7 +2,8 @@
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nextflow.enable.dsl = 2
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include { FASTQC } from '../main.nf'
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include { FASTQC as FASTQC_SE } from '../main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
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include { FASTQC as FASTQC_PE } from '../main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
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/*
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* Test with single-end data
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@ -13,7 +14,7 @@ workflow test_single_end {
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input = [ [ id:'test', single_end:true ], // meta map
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[ file("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ]
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FASTQC ( input, [ publish_dir:'test_single_end' ] )
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FASTQC_SE ( input )
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}
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/*
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@ -26,7 +27,7 @@ workflow test_paired_end {
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[ file("${baseDir}/input/test_R1.fastq.gz", checkIfExists: true),
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file("${baseDir}/input/test_R2.fastq.gz", checkIfExists: true) ] ]
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FASTQC ( input, [ publish_dir:'test_paired_end' ] )
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FASTQC_PE ( input )
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}
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workflow {
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@ -2,12 +2,12 @@
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params {
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outdir = "output/"
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publish_dir_mode = "copy"
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conda = false
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enable_conda = false
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}
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profiles {
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conda {
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params.conda = true
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params.enable_conda = true
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}
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docker {
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docker.enabled = true
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@ -2,10 +2,10 @@
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nextflow.enable.dsl = 2
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include { BWA_INDEX } from '../main.nf'
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include { BWA_INDEX } from '../main.nf' addParams( options: [:] )
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workflow test {
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BWA_INDEX ( file("${baseDir}/input/NC_010473.fa", checkIfExists: true), [:] )
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BWA_INDEX ( file("${baseDir}/input/NC_010473.fa", checkIfExists: true) )
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}
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workflow {
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@ -2,12 +2,12 @@
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params {
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outdir = "output/"
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publish_dir_mode = "copy"
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conda = false
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enable_conda = false
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}
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profiles {
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conda {
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params.conda = true
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params.enable_conda = true
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}
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docker {
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docker.enabled = true
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@ -2,7 +2,8 @@
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nextflow.enable.dsl = 2
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include { BWA_MEM } from '../main.nf'
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include { BWA_MEM as BWA_MEM_SE } from '../main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
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include { BWA_MEM as BWA_MEM_PE } from '../main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
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/*
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* Test with single-end data
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@ -13,11 +14,10 @@ workflow test_single_end {
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input = [ [ id:'test', single_end:true ], // meta map
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[ file("${baseDir}/input/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ]
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BWA_MEM (
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BWA_MEM_SE (
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input,
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file("${baseDir}/input/index/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
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file("${baseDir}/input/NC_010473.fa", checkIfExists: true),
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[ publish_dir:'test_single_end' ]
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file("${baseDir}/input/NC_010473.fa", checkIfExists: true)
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)
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}
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@ -31,11 +31,10 @@ workflow test_paired_end {
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[ file("${baseDir}/input/Ecoli_DNA_R1.fastq.gz", checkIfExists: true),
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file("${baseDir}/input/Ecoli_DNA_R2.fastq.gz", checkIfExists: true) ] ]
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BWA_MEM (
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BWA_MEM_PE (
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input,
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file("${baseDir}/input/index/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
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file("${baseDir}/input/NC_010473.fa", checkIfExists: true),
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[ publish_dir:'test_paired_end' ]
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file("${baseDir}/input/NC_010473.fa", checkIfExists: true)
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)
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}
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@ -2,12 +2,12 @@
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params {
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outdir = "output/"
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publish_dir_mode = "copy"
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conda = false
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enable_conda = false
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}
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profiles {
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conda {
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params.conda = true
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params.enable_conda = true
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}
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docker {
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docker.enabled = true
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@ -2,7 +2,8 @@
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nextflow.enable.dsl = 2
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include { FASTQC } from '../main.nf'
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include { FASTQC as FASTQC_SE } from '../main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
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include { FASTQC as FASTQC_PE } from '../main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
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/*
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* Test with single-end data
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@ -13,7 +14,7 @@ workflow test_single_end {
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input = [ [ id:'test', single_end:true ], // meta map
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[ file("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ]
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FASTQC ( input, [ publish_dir:'test_single_end' ] )
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FASTQC_SE ( input )
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}
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/*
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[ file("${baseDir}/input/test_R1.fastq.gz", checkIfExists: true),
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file("${baseDir}/input/test_R2.fastq.gz", checkIfExists: true) ] ]
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FASTQC ( input, [ publish_dir:'test_paired_end' ] )
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FASTQC_PE ( input )
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}
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workflow {
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params {
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outdir = "output/"
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publish_dir_mode = "copy"
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conda = false
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enable_conda = false
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}
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profiles {
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conda {
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params.conda = true
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params.enable_conda = true
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}
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docker {
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docker.enabled = true
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@ -2,7 +2,7 @@
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nextflow.enable.dsl = 2
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include { PICARD_COLLECTMULTIPLEMETRICS } from '../main.nf'
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include { PICARD_COLLECTMULTIPLEMETRICS } from '../main.nf' addParams( options: [:] )
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workflow test {
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PICARD_COLLECTMULTIPLEMETRICS (
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input,
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file("${baseDir}/input/NC_010473.fa", checkIfExists: true),
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[:]
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file("${baseDir}/input/NC_010473.fa", checkIfExists: true)
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)
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}
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@ -2,12 +2,12 @@
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params {
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outdir = "output/"
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publish_dir_mode = "copy"
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conda = false
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enable_conda = false
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}
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profiles {
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conda {
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params.conda = true
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params.enable_conda = true
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}
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docker {
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docker.enabled = true
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@ -2,7 +2,7 @@
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nextflow.enable.dsl = 2
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include { PICARD_MARKDUPLICATES } from '../main.nf'
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include { PICARD_MARKDUPLICATES } from '../main.nf' addParams( options: [:] )
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workflow test {
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input = [ [ id:'test', single_end:false ], // meta map
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file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true) ]
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PICARD_MARKDUPLICATES ( input, [:] )
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PICARD_MARKDUPLICATES ( input )
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}
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workflow {
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params {
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outdir = "output/"
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publish_dir_mode = "copy"
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conda = false
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enable_conda = false
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}
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profiles {
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conda {
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params.conda = true
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params.enable_conda = true
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}
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docker {
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docker.enabled = true
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@ -2,7 +2,7 @@
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nextflow.enable.dsl = 2
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include { PICARD_MERGESAMFILES } from '../main.nf'
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include { PICARD_MERGESAMFILES } from '../main.nf' addParams( options: [:] )
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workflow test {
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[ file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
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file("${baseDir}/input/test.paired_end.COPY.sorted.bam", checkIfExists: true), ] ]
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PICARD_MERGESAMFILES ( input, [:] )
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PICARD_MERGESAMFILES ( input )
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}
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workflow {
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params {
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outdir = "output/"
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publish_dir_mode = "copy"
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conda = false
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enable_conda = false
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}
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profiles {
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conda {
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params.conda = true
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params.enable_conda = true
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}
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docker {
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docker.enabled = true
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@ -2,7 +2,7 @@
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nextflow.enable.dsl = 2
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include { SAMTOOLS_FLAGSTAT } from '../main.nf'
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include { SAMTOOLS_FLAGSTAT } from '../main.nf' addParams( options: [:] )
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workflow test {
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file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
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file("${baseDir}/input/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
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SAMTOOLS_FLAGSTAT ( input, [:] )
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SAMTOOLS_FLAGSTAT ( input )
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}
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workflow {
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params {
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outdir = "output/"
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publish_dir_mode = "copy"
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conda = false
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enable_conda = false
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}
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profiles {
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conda {
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params.conda = true
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params.enable_conda = true
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}
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docker {
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docker.enabled = true
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@ -2,7 +2,7 @@
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nextflow.enable.dsl = 2
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include { SAMTOOLS_IDXSTATS } from '../main.nf'
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include { SAMTOOLS_IDXSTATS } from '../main.nf' addParams( options: [:] )
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workflow test {
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file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
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file("${baseDir}/input/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
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SAMTOOLS_IDXSTATS ( input, [:] )
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SAMTOOLS_IDXSTATS ( input )
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}
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workflow {
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@ -2,12 +2,12 @@
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params {
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outdir = "output/"
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publish_dir_mode = "copy"
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conda = false
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enable_conda = false
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}
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profiles {
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conda {
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params.conda = true
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params.enable_conda = true
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}
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docker {
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docker.enabled = true
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@ -2,7 +2,7 @@
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nextflow.enable.dsl = 2
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include { SAMTOOLS_INDEX } from '../main.nf'
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include { SAMTOOLS_INDEX } from '../main.nf' addParams( options: [:] )
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workflow test {
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input = [ [ id:'test', single_end:false ], // meta map
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file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true) ]
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SAMTOOLS_INDEX ( input, [:] )
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SAMTOOLS_INDEX ( input )
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}
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workflow {
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params {
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outdir = "output/"
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publish_dir_mode = "copy"
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conda = false
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enable_conda = false
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}
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profiles {
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conda {
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params.conda = true
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params.enable_conda = true
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}
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docker {
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docker.enabled = true
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@ -2,7 +2,7 @@
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nextflow.enable.dsl = 2
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include { SAMTOOLS_SORT } from '../main.nf'
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include { SAMTOOLS_SORT } from '../main.nf' addParams( options: [:] )
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workflow test {
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input = [ [ id:'test', single_end:false ], // meta map
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file("${baseDir}/input/test.paired_end.name.sorted.bam", checkIfExists: true) ]
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SAMTOOLS_SORT ( input, [:] )
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SAMTOOLS_SORT ( input )
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}
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workflow {
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params {
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outdir = "output/"
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publish_dir_mode = "copy"
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conda = false
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enable_conda = false
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}
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profiles {
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conda {
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params.conda = true
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params.enable_conda = true
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}
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docker {
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docker.enabled = true
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@ -2,7 +2,7 @@
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nextflow.enable.dsl = 2
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include { SAMTOOLS_STATS } from '../main.nf'
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include { SAMTOOLS_STATS } from '../main.nf' addParams( options: [:] )
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workflow test {
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file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
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file("${baseDir}/input/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
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SAMTOOLS_STATS ( input, [:] )
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SAMTOOLS_STATS ( input )
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}
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workflow {
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@ -2,12 +2,12 @@
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params {
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outdir = "output/"
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publish_dir_mode = "copy"
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conda = false
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enable_conda = false
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}
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profiles {
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conda {
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params.conda = true
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params.enable_conda = true
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}
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docker {
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docker.enabled = true
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@ -2,7 +2,8 @@
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nextflow.enable.dsl = 2
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include { TRIMGALORE } from '../main.nf'
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include { TRIMGALORE as TRIMGALORE_SE } from '../main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
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include { TRIMGALORE as TRIMGALORE_PE } from '../main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
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/*
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* Test with single-end data
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@ -13,7 +14,7 @@ workflow test_single_end {
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input = [ [ id:'test', single_end:true ], // meta map
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[ file("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ]
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TRIMGALORE ( input, [ publish_dir:'test_single_end' ] )
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TRIMGALORE_SE ( input )
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}
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/*
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@ -26,7 +27,7 @@ workflow test_paired_end {
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[ file("${baseDir}/input/test_R1.fastq.gz", checkIfExists: true),
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file("${baseDir}/input/test_R2.fastq.gz", checkIfExists: true) ] ]
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TRIMGALORE ( input, [ publish_dir:'test_paired_end' ] )
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TRIMGALORE_PE ( input )
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}
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workflow {
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@ -2,7 +2,7 @@
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params {
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outdir = "output/"
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publish_dir_mode = "copy"
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conda = false
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enable_conda = false
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clip_r1 = 0
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clip_r2 = 0
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|
@ -12,7 +12,7 @@ params {
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profiles {
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conda {
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params.conda = true
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params.enable_conda = true
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}
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docker {
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docker.enabled = true
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|
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