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Merge pull request #32 from B-UMMI/dev
Add StrainXpress to short-read assembly workflow
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‎README.md‎

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@@ -173,6 +173,8 @@ To use LMAS the following options are available:
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(default auto)
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--skesa Boolean controling the execution of the SKESA assembler.
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(default true)
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--strainxpress Boolean controling the execution of the StrainXpress assembler.
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(default true)
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--unicycler Boolean controling the execution of the Unicycler assembler.
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(default true)
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--velvetoptimiser Boolean controling the execution of the VelvetOptimiser assembler.

‎conf/containers.config‎

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@@ -2,6 +2,9 @@ process {
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withName: REFORMAT {
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container = "pcerqueira/bbtools:38.44"
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}
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withName: REFORMAT_FASTQ {
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container = "pcerqueira/bbtools:38.44"
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}
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withName: ABYSS {
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container = "cimendes/abyss:2.3.1-1"
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}
@@ -29,6 +32,9 @@ process {
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withName: SPADES {
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container = "cimendes/spades:3.15.3-1"
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}
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withName: STRAINXPRESS {
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container = "cimendes/strainxpress:11.08.2022"
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}
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withName: UNICYCLER {
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container = "cimendes/unicycler:0.4.9-1"
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}

‎conf/params.config‎

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@@ -46,6 +46,9 @@ params {
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spades = true
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spadesKmerSize = 'auto'
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//StrainXpress
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strainxpress = false
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//SKESA
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skesa = true
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‎docker/strainXpress/Dockerfile‎

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FROM continuumio/miniconda:4.7.12
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LABEL software="StrainXpress" \
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software.version="11.08.2022" \
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about.home="https://github.com/kangxiongbin/StrainXpress" \
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about.summary="De novo assembler based on overlap-layout-consensus to assemble high complexity metagenome sequencing data at strain resolution." \
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about.documentation="https://github.com/kangxiongbin/StrainXpress#readme" \
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about.license="https://github.com/kangxiongbin/StrainXpress/blob/main/LICENSE" \
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author="Inês Mendes <[email protected]>"
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WORKDIR /NGStools
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RUN apt-get --allow-releaseinfo-change update \
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&& apt-get install procps git build-essential cmake wget libboost-all-dev -y
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RUN conda install -c bioconda python=3.6 scipy pandas minimap2
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RUN git clone https://github.com/kangxiongbin/StrainXpress.git \
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&& cd StrainXpress \
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&& sh install.sh
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ENV PATH="/NGStools/StrainXpress/scripts:$PATH"

‎lib/Helper.groovy‎

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@@ -103,6 +103,8 @@ class Help {
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println " (default $params.spadesKmerSize)"
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println " --skesa Boolean controling the execution of the SKESA assembler."
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println " (default $params.skesa)"
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println " --strainxpress Boolean controling the execution of the StrainXpress assembler."
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println " (default $params.strainxpress)"
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println " --unicycler Boolean controling the execution of the Unicycler assembler."
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println " (default $params.unicycler)"
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println " --velvetoptimiser Boolean controling the execution of the VelvetOptimiser assembler."

‎modules/assembly/assembly.nf‎

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@@ -19,6 +19,24 @@ process REFORMAT {
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"reformat.sh in=${fastq_pair[0]} in2=${fastq_pair[1]} out=${sample_id}_reads.fasta"
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}
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process REFORMAT_FASTQ {
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tag { sample_id }
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label 'process_assembly'
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when:
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params.strainxpress
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input:
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tuple val(sample_id), path(fastq_pair)
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output:
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tuple val(sample_id), file('*_reads.fq')
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script:
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"reformat.sh in=${fastq_pair[0]} in2=${fastq_pair[1]} out=${sample_id}_reads.fq"
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}
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process ABYSS {
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tag { sample_id }
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"""
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}
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process STRAINXPRESS {
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tag { sample_id }
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label 'process_assembly'
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publishDir "results/$sample_id/assembly/strainxpress"
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when:
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params.strainxpress
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input:
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tuple val(sample_id), path(fasta_reads_single)
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output:
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tuple val(sample_id), val('StrainXpress'), path('*_strainxpress.fasta'), emit: assembly
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path('.*version'), emit: version
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script:
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"""
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echo '' > .${sample_id}_strainxpress_version
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{
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python3 /NGStools/StrainXpress/scripts/strainxpress.py -fq $fasta_reads_single -t $task.cpus
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mv all.contigs_*.fasta ${sample_id}_strainxpress.fasta
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echo pass > .status
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} || {
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echo fail > .status
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:> ${sample_id}_strainxpress.fasta
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}
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"""
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}
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process UNICYCLER {
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tag { sample_id }
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main:
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REFORMAT(IN_fastq_raw)
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REFORMAT_FASTQ(IN_fastq_raw)
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ABYSS(IN_fastq_raw, abyssKmerSize, abyssBloomSize)
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GATBMINIAPIPELINE(IN_fastq_raw, gatbKmerSize, GATB_error_correction, gatb_besst_iter)
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IDBA(REFORMAT.out)
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MINIA(IN_fastq_raw, miniaKmerSize)
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SKESA(IN_fastq_raw)
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SPADES(IN_fastq_raw, spadesKmerSize)
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STRAINXPRESS(REFORMAT_FASTQ.out)
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UNICYCLER(IN_fastq_raw)
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VELVETOPTIMISER(IN_fastq_raw)
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MINIA.out.assembly,
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SKESA.out.assembly,
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SPADES.out.assembly,
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STRAINXPRESS.out.assembly,
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UNICYCLER.out.assembly,
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VELVETOPTIMISER.out.assembly)
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all_versions = ABYSS.out.version | mix(GATBMINIAPIPELINE.out.version,
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MINIA.out.version,
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SKESA.out.version,
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SPADES.out.version,
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STRAINXPRESS.out.version,
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UNICYCLER.out.version,
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VELVETOPTIMISER.out.version) | collect
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‎pull_images.sh‎

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@@ -25,6 +25,7 @@ eval $pull_command"cimendes/mhm2:v2.0.0-65-gaad446d-generic"
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eval $pull_command"cimendes/spades:3.15.3-1"
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eval $pull_command"cimendes/minia:3.2.6-1"
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eval $pull_command"cimendes/skesa:2.5.0-1"
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eval $pull_command"cimendes/strainxpress:11.08.2022"
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eval $pull_command"cimendes/unicycler:0.4.9-1"
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eval $pull_command"cimendes/velvetoptimiser:2.2.6-1"
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eval $pull_command"cimendes/minimap2:2.22-1"

‎templates/process_assembly_stats_global.py‎

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ASSEMBLER_SKIP = {"ABySS":json.loads("$params.abyss"), "GATBMiniaPipeline": json.loads("$params.gatb_minia"),
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"MetaHipMer2": json.loads("$params.metahipmer2"), "MINIA": json.loads("$params.minia"), "MEGAHIT": json.loads("$params.megahit"),
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"metaSPAdes": json.loads("$params.metaspades"), "Unicycler": json.loads("$params.unicycler"), "SPAdes": json.loads("$params.spades"),
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"SKESA": json.loads("$params.skesa"), "VelvetOptimiser": json.loads("$params.velvetoptimiser"), "IDBA-UD": json.loads("$params.idba")}
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"SKESA": json.loads("$params.skesa"), "StrainXpress": json.loads("$params.strainxpress"),"VelvetOptimiser": json.loads("$params.velvetoptimiser"),
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"IDBA-UD": json.loads("$params.idba")}
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logger.debug("Running {} with parameters:".format(
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os.path.basename(__file__)))
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logger.debug("ASSEMBLY_STATS_GLOBAL_FILE: {}".format(

‎templates/process_assembly_stats_mapping.py‎

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ASSEMBLER_SKIP = {"ABySS":json.loads("$params.abyss"), "GATBMiniaPipeline": json.loads("$params.gatb_minia"),
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"MetaHipMer2": json.loads("$params.metahipmer2"), "MINIA": json.loads("$params.minia"), "MEGAHIT": json.loads("$params.megahit"),
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"metaSPAdes": json.loads("$params.metaspades"), "Unicycler": json.loads("$params.unicycler"), "SPAdes": json.loads("$params.spades"),
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"SKESA": json.loads("$params.skesa"), "VelvetOptimiser": json.loads("$params.velvetoptimiser"), "IDBA-UD": json.loads("$params.idba")}
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"SKESA": json.loads("$params.skesa"), "StrainXpress": json.loads("$params.strainxpress"), "VelvetOptimiser": json.loads("$params.velvetoptimiser"),
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"IDBA-UD": json.loads("$params.idba")}
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logger.debug("Running {} with parameters:".format(
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os.path.basename(__file__)))
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logger.debug("ASSEMBLY_STATS_GLOBAL_FILE_JSON: {}".format(

‎templates/process_versions.py‎

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"Unicycler": "UNICYCLER",
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"SPAdes": "SPADES",
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"SKESA": "SKESA",
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"strainxpress": "StrainXpress",
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"VelvetOptimiser": "VELVETOPTIMISER",
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"IDBA": "IDBA"}
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