mirror of
https://github.com/MillironX/nf-core_modules.git
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Pinch docs and delete redundant modules
This commit is contained in:
drpatelh
parent
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commit
1edc58a36b
16 changed files with 0 additions and 451 deletions
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process samtools_index {
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tag "${bam.baseName}"
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container 'quay.io/biocontainers/samtools:1.9--h10a08f8_12'
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input:
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path bam
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output:
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path "*.bam.bai"
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script:
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"""
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samtools index $bam
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samtools --version &> v_samtools.txt
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"""
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}
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name: samtools sort
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description: Sort a BAM or CRAM file
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keywords:
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- sort
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tools:
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- samtools:
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description: |
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SAMtools is a set of utilities for interacting with and post-processing
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short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
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These files are generated as output by short read aligners like BWA.
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homepage: http://www.htslib.org/
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documentation: hhttp://www.htslib.org/doc/samtools.html
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doi: 10.1093/bioinformatics/btp352
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input:
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-
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- input:
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type: file
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description: Input BAM or CRAM file
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pattern: "*.{bam,cram}"
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output:
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-
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- sorted_file:
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type: file
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description: Sorted BAM or CRAM file
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pattern: "*.{bam,cram}"
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authors:
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- "@ewels"
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@ -1,13 +0,0 @@
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#!/usr/bin/env nextflow
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echo true
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cheers = Channel.from 'Bonjour', 'Ciao', 'Hello', 'Hola'
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process sayHello {
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input:
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val x from cheers
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script:
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"""
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echo '$x world!'
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"""
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}
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docker.enabled = true
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params.outdir = './results'
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@ -1,10 +0,0 @@
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FROM nfcore/base:1.7
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LABEL authors="phil.ewels@scilifelab.se" \
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description="Docker image for nf-core modules trimgalore"
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#### THIS IS A BUG
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# foobar
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COPY environment.yml /
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RUN conda env create -f /environment.yml && conda clean -a
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ENV PATH /opt/conda/envs/nf-core-modules-trimgalore/bin:$PATH
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@ -1,9 +0,0 @@
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# You can use this file to create a conda environment for this pipeline:
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# conda env create -f environment.yml
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name: nf-core-modules-trimgalore
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channels:
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- conda-forge
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- bioconda
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- defaults
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dependencies:
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- trim-galore=0.6.4
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@ -1,102 +0,0 @@
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nextflow.preview.dsl=2
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params.singlecell = ''
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params.rrbs = ''
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params.pbat = ''
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params.single_end = false
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params.trim_nextseq = 0
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params.clip_r1 = 0
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params.clip_r2 = 0
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params.three_prime_clip_r1 = 0
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params.three_prime_clip_r2 = 0
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process TRIM_GALORE {
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// container 'quay.io/biocontainers/trim-galore:0.6.5--0' // maybe later
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// tag "$sample_id"
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// Trimming reports are not generated for e.g. --hardtrim5, --clock etc
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// saveAs: {filename ->
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// else if (filename.indexOf("trimming_report.txt") > 0) "logs/$filename"
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// else filename
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// }
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publishDir "${outdir}/trim_galore",
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mode: "copy", overwrite: true
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input:
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tuple val(name), path(reads)
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val outdir
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val trim_galore_args
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val verbose
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output:
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tuple val(name), path ("*fq.gz"), emit: reads
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path "*trimming_report.txt", optional: true, emit: report
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script:
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if (verbose){
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println ("[MODULE] TRIM GALORE ARGS: " + trim_galore_args)
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}
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trim_galore_args += " --gzip " // we like small files
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pairedString = 0
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if (reads instanceof List) {
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pairedString = 1
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trim_galore_args += " --paired "
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}
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if (params.clip_r1 > 0){
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trim_galore_args += " --clip_r1 ${params.clip_r1} "
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}
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if (params.clip_r2 > 0){
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trim_galore_args += " --clip_r2 ${params.clip_r2} "
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}
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if (params.three_prime_clip_r1> 0){
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trim_galore_args += " --three_prime_clip_r1 ${params.three_prime_clip_r1} "
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}
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if (params.three_prime_clip_r2 > 0){
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trim_galore_args += " --three_prime_clip_r2 ${params.three_prime_clip_r2} "
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}
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if (params.trim_nextseq > 0){
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trim_galore_args += " --nextseq ${params.trim_nextseq} "
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}
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// Pre-set parameters for certain bisulfite-seq applications
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if (params.singlecell){
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trim_galore_args += " --clip_r1 6 "
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if (pairedString == 1){
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trim_galore_args += " --clip_r2 6 "
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}
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}
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if (params.rrbs){
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trim_galore_args += " --rrbs "
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}
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if (params.pbat){
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trim_galore_args += " --clip_r1 $params.pbat "
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if (pairedString == 1){
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trim_galore_args += " --clip_r2 $params.pbat "
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}
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}
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"""
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module load trim_galore
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trim_galore $trim_galore_args $reads
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"""
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}
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name: Trim Galore!
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description: Trim FastQ files using Trim Galore!
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keywords:
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- trimming
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- adapters
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- sequencing adapters
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tools:
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- fastqc:
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description: |
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A wrapper tool around Cutadapt and FastQC to consistently apply quality
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and adapter trimming to FastQ files, with some extra functionality for
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MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
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homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
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documentation: https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md
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input:
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-
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- sample_id:
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type: string
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description: Sample identifier
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- reads:
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type: file
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description: Input FastQ file, or pair of files
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output:
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-
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- sample_id:
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type: string
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description: Sample identifier
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- trimmed_fastq:
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type: file
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description: Trimmed FastQ files
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pattern: "*fq.gz"
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-
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- report:
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type: file
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description: Trim Galore! trimming report
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pattern: "*trimming_report.txt"
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authors:
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- "@ewels"
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- "@FelixKrueger"
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../../../../tests/data/fastq/rna/test_R1.fastq.gz
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@ -1 +0,0 @@
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../../../../tests/data/fastq/rna/test_R2.fastq.gz
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#!/usr/bin/env nextflow
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nextflow.preview.dsl=2
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params.outdir = "." // gets set in the nextflow.config files (to './results/trim_galore')
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params.verbose = false
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params.trim_galore_args = ''
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// trim_galore_args are best passed into the workflow in the following manner, e.g.:
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// --trim_galore_args="--clip_r1 10 --clip_r2 15 -j 2"
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if (params.verbose){
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println ("[WORKFLOW] TRIM GALORE ARGS: " + params.trim_galore_args)
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}
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// TODO: check the output files in some way
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// include '../../../tests/functions/check_process_outputs.nf'
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include '../main.nf' // params (clip_r1: 6, clip_r2: 10) // how to pass additional parameters
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ch_read_files = Channel
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.fromFilePairs('../../../test-datasets/test*{1,2}.fastq.gz',size:-1)
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// .view() // to check whether the input channel works
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workflow {
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main:
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TRIM_GALORE (ch_read_files, params.outdir, params.trim_galore_args, params.verbose)
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}
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// docker.enabled = true
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params.outdir = './results'
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@ -1,97 +0,0 @@
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SUMMARISING RUN PARAMETERS
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==========================
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Input filename: test_R1.fastq.gz
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Trimming mode: paired-end
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Trim Galore version: 0.6.5
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Cutadapt version: 2.3
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Number of cores used for trimming: 1
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Quality Phred score cutoff: 20
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Quality encoding type selected: ASCII+33
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Using Nextera adapter for trimming (count: 83). Second best hit was smallRNA (count: 0)
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Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
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Maximum trimming error rate: 0.1 (default)
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Minimum required adapter overlap (stringency): 1 bp
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Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
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Output file will be GZIP compressed
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This is cutadapt 2.3 with Python 3.7.3
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Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA test_R1.fastq.gz
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Processing reads on 1 core in single-end mode ...
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Finished in 0.19 s (19 us/read; 3.12 M reads/minute).
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=== Summary ===
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Total reads processed: 10,000
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Reads with adapters: 3,225 (32.2%)
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Reads written (passing filters): 10,000 (100.0%)
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Total basepairs processed: 760,000 bp
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Quality-trimmed: 4,492 bp (0.6%)
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Total written (filtered): 748,403 bp (98.5%)
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=== Adapter 1 ===
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Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 3225 times.
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No. of allowed errors:
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0-9 bp: 0; 10-12 bp: 1
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Bases preceding removed adapters:
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A: 23.8%
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C: 28.2%
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G: 22.7%
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T: 25.3%
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none/other: 0.0%
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Overview of removed sequences
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length count expect max.err error counts
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1 2170 2500.0 0 2170
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2 622 625.0 0 622
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3 223 156.2 0 223
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4 64 39.1 0 64
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5 14 9.8 0 14
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6 9 2.4 0 9
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7 8 0.6 0 8
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8 5 0.2 0 5
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9 4 0.0 0 4
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10 8 0.0 1 7 1
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11 3 0.0 1 3
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12 4 0.0 1 4
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13 6 0.0 1 6
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14 5 0.0 1 4 1
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15 5 0.0 1 5
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16 6 0.0 1 5 1
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17 3 0.0 1 3
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18 3 0.0 1 3
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19 1 0.0 1 1
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20 3 0.0 1 3
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21 7 0.0 1 7
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22 7 0.0 1 7
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23 3 0.0 1 3
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24 6 0.0 1 6
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25 4 0.0 1 4
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26 2 0.0 1 2
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27 4 0.0 1 4
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28 1 0.0 1 1
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29 3 0.0 1 3
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30 4 0.0 1 4
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32 3 0.0 1 3
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33 2 0.0 1 1 1
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34 1 0.0 1 1
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35 1 0.0 1 1
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40 1 0.0 1 1
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42 1 0.0 1 0 1
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45 1 0.0 1 0 1
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49 1 0.0 1 0 1
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52 1 0.0 1 0 1
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56 2 0.0 1 0 2
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59 1 0.0 1 0 1
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67 1 0.0 1 0 1
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70 2 0.0 1 0 2
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RUN STATISTICS FOR INPUT FILE: test_R1.fastq.gz
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=============================================
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10000 sequences processed in total
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../../../../tests/data/fastq/rna/test_R1_val_1.fq.gz
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@ -1,100 +0,0 @@
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SUMMARISING RUN PARAMETERS
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==========================
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Input filename: test_R2.fastq.gz
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Trimming mode: paired-end
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Trim Galore version: 0.6.5
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Cutadapt version: 2.3
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Number of cores used for trimming: 1
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Quality Phred score cutoff: 20
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Quality encoding type selected: ASCII+33
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Using Nextera adapter for trimming (count: 83). Second best hit was smallRNA (count: 0)
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Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
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Maximum trimming error rate: 0.1 (default)
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Minimum required adapter overlap (stringency): 1 bp
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Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
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Output file will be GZIP compressed
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This is cutadapt 2.3 with Python 3.7.3
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Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA test_R2.fastq.gz
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Processing reads on 1 core in single-end mode ...
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Finished in 0.22 s (22 us/read; 2.71 M reads/minute).
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=== Summary ===
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Total reads processed: 10,000
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Reads with adapters: 3,295 (33.0%)
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Reads written (passing filters): 10,000 (100.0%)
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Total basepairs processed: 760,000 bp
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Quality-trimmed: 7,096 bp (0.9%)
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Total written (filtered): 745,649 bp (98.1%)
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=== Adapter 1 ===
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Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 3295 times.
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No. of allowed errors:
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0-9 bp: 0; 10-12 bp: 1
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Bases preceding removed adapters:
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A: 22.6%
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C: 28.2%
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G: 23.6%
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T: 25.6%
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none/other: 0.0%
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Overview of removed sequences
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length count expect max.err error counts
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1 2213 2500.0 0 2213
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2 647 625.0 0 647
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3 239 156.2 0 239
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4 53 39.1 0 53
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5 10 9.8 0 10
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6 7 2.4 0 7
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7 8 0.6 0 8
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8 5 0.2 0 5
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9 5 0.0 0 5
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10 10 0.0 1 8 2
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11 2 0.0 1 2
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12 4 0.0 1 4
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13 7 0.0 1 7
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14 3 0.0 1 3
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15 4 0.0 1 4
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16 5 0.0 1 5
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17 3 0.0 1 3
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18 5 0.0 1 4 1
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19 2 0.0 1 1 1
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20 3 0.0 1 3
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21 7 0.0 1 7
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22 6 0.0 1 6
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23 3 0.0 1 3
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24 7 0.0 1 7
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25 4 0.0 1 4
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26 2 0.0 1 2
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27 4 0.0 1 4
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28 1 0.0 1 1
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29 3 0.0 1 3
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30 4 0.0 1 4
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32 3 0.0 1 3
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33 1 0.0 1 1
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34 1 0.0 1 1
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35 2 0.0 1 1 1
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40 1 0.0 1 0 1
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41 1 0.0 1 1
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46 1 0.0 1 0 1
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48 1 0.0 1 0 1
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49 2 0.0 1 0 2
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56 2 0.0 1 0 2
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59 1 0.0 1 0 1
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70 1 0.0 1 0 1
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73 2 0.0 1 0 2
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RUN STATISTICS FOR INPUT FILE: test_R2.fastq.gz
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=============================================
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10000 sequences processed in total
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Total number of sequences analysed for the sequence pair length validation: 10000
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Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 21 (0.21%)
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@ -1 +0,0 @@
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../../../../tests/data/fastq/rna/test_R2_val_2.fq.gz
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