diff --git a/modules/bowtie2/align/main.nf b/modules/bowtie2/align/main.nf index 38242fcb..c74e376f 100644 --- a/modules/bowtie2/align/main.nf +++ b/modules/bowtie2/align/main.nf @@ -11,6 +11,7 @@ process BOWTIE2_ALIGN { tuple val(meta), path(reads) path index val save_unaligned + val sort_bam output: tuple val(meta), path("*.bam") , emit: bam @@ -36,8 +37,7 @@ process BOWTIE2_ALIGN { reads_args = "-1 ${reads[0]} -2 ${reads[1]}" } - def samtools_command = "samtools view -@ $task.cpus --bam --with-header ${args2} > ${prefix}.bam" - + def samtools_command = sort_bam ? 'sort' : 'view' """ INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/.rev.1.bt2//"` @@ -51,7 +51,7 @@ process BOWTIE2_ALIGN { $unaligned \\ $args \\ 2> ${prefix}.bowtie2.log \\ - | $samtools_command + | samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam - if [ -f ${prefix}.unmapped.fastq.1.gz ]; then mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz @@ -69,4 +69,3 @@ process BOWTIE2_ALIGN { END_VERSIONS """ } - diff --git a/modules/bowtie2/align/meta.yml b/modules/bowtie2/align/meta.yml index f80421ec..c99fa4e3 100644 --- a/modules/bowtie2/align/meta.yml +++ b/modules/bowtie2/align/meta.yml @@ -29,6 +29,15 @@ input: type: file description: Bowtie2 genome index files pattern: "*.ebwt" + - save_unaligned: + type: boolean + description: | + Save reads that do not map to the reference (true) or discard them (false) + (default: false) + - sort_bam: + type: boolean + description: use samtools sort (true) or samtools view (false) + pattern: "true or false" output: - bam: type: file diff --git a/modules/gatk4/splitintervals/main.nf b/modules/gatk4/splitintervals/main.nf new file mode 100644 index 00000000..9df66c21 --- /dev/null +++ b/modules/gatk4/splitintervals/main.nf @@ -0,0 +1,48 @@ +process GATK4_SPLITINTERVALS { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + + input: + tuple val(meta), path(intervals) + path(fasta) + path(fasta_fai) + path(dict) + + output: + tuple val(meta), path("**.interval_list"), emit: split_intervals + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def reference = fasta ? "--reference $fasta" : "" + + def avail_mem = 3 + if (!task.memory) { + log.info '[GATK SplitIntervals] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' + } else { + avail_mem = task.memory.giga + } + + """ + gatk --java-options "-Xmx${avail_mem}g" SplitIntervals \\ + --output ${prefix} \\ + --intervals $intervals \\ + $reference \\ + --tmp-dir . \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/gatk4/splitintervals/meta.yml b/modules/gatk4/splitintervals/meta.yml new file mode 100644 index 00000000..ba557544 --- /dev/null +++ b/modules/gatk4/splitintervals/meta.yml @@ -0,0 +1,53 @@ +name: gatk4_splitintervals +keywords: + - interval + - bed +tools: + - gatk4: + description: Genome Analysis Toolkit (GATK4) + homepage: https://gatk.broadinstitute.org/hc/en-us + documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s + tool_dev_url: https://github.com/broadinstitute/gatk + doi: "10.1158/1538-7445.AM2017-3590" + licence: ["BSD-3-clause"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - interval: + type: file + description: Interval list or BED + pattern: "*.{interval,interval_list,bed}" + - fasta: + type: file + description: Reference FASTA + pattern: "*.{fa,fasta}" + - fasta_fai: + type: file + description: Reference FASTA index + pattern: "*.fai" + - dict: + type: file + description: Reference sequence dictionary + pattern: "*.dict" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - bed: + type: file + description: A list of scattered interval lists + pattern: "*.interval_list" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@nvnieuwk" diff --git a/modules/genomescope2/main.nf b/modules/genomescope2/main.nf new file mode 100644 index 00000000..2ddf9e43 --- /dev/null +++ b/modules/genomescope2/main.nf @@ -0,0 +1,40 @@ +process GENOMESCOPE2 { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::genomescope2=2.0" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/genomescope2:2.0--py310r41hdfd78af_5': + 'quay.io/biocontainers/genomescope2:2.0--py310r41hdfd78af_5' }" + + input: + tuple val(meta), path(histogram) + + output: + tuple val(meta), path("*_linear_plot.png") , emit: linear_plot_png + tuple val(meta), path("*_transformed_linear_plot.png"), emit: transformed_linear_plot_png + tuple val(meta), path("*_log_plot.png") , emit: log_plot_png + tuple val(meta), path("*_transformed_log_plot.png") , emit: transformed_log_plot_png + tuple val(meta), path("*_model.txt") , emit: model + tuple val(meta), path("*_summary.txt") , emit: summary + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + """ + genomescope2 \\ + --input $histogram \\ + $args \\ + --output . \\ + --name_prefix $prefix + + cat <<-END_VERSIONS > versions.yml + '${task.process}': + genomescope2: \$( genomescope2 -v | sed 's/GenomeScope //' ) + END_VERSIONS + """ +} diff --git a/modules/genomescope2/meta.yml b/modules/genomescope2/meta.yml new file mode 100644 index 00000000..505daafe --- /dev/null +++ b/modules/genomescope2/meta.yml @@ -0,0 +1,67 @@ +name: "genomescope2" +description: Estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach +keywords: + - "genome size" + - "genome heterozygosity" + - "repeat content" +tools: + - "genomescope2": + description: "Reference-free profiling of polyploid genomes" + homepage: "http://qb.cshl.edu/genomescope/genomescope2.0/" + documentation: "https://github.com/tbenavi1/genomescope2.0/blob/master/README.md" + tool_dev_url: "https://github.com/tbenavi1/genomescope2.0" + doi: "https://doi.org/10.1038/s41467-020-14998-3" + licence: "['Apache License, Version 2.0 (Apache-2.0)']" + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - histogram: + type: file + description: A K-mer histogram file + pattern: "*.hist" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - linear_plot_png: + type: file + description: A genomescope2 linear plot in PNG format + pattern: "*_linear_plot.png" + - linear_plot_png: + type: file + description: A genomescope2 linear plot in PNG format + pattern: "*_linear_plot.png" + - transformed_linear_plot_png: + type: file + description: A genomescope2 transformed linear plot in PNG format + pattern: "*_transformed_linear_plot.png" + - log_plot_png: + type: file + description: A genomescope2 log plot in PNG format + pattern: "*_log_plot.png" + - transformed_log_plot_png: + type: file + description: A genomescope2 transformed log plot in PNG format + pattern: "*_transformed_log_plot.png" + - model: + type: file + description: Genomescope2 model fit summary + pattern: "*_model.txt" + - summary: + type: file + description: Genomescope2 histogram summary + pattern: "*_summary.txt" + +authors: + - "@mahesh-panchal" diff --git a/modules/rtgtools/vcfeval/main.nf b/modules/rtgtools/vcfeval/main.nf index 1bad4231..27a488f7 100644 --- a/modules/rtgtools/vcfeval/main.nf +++ b/modules/rtgtools/vcfeval/main.nf @@ -35,12 +35,13 @@ process RTGTOOLS_VCFEVAL { def eval_regions = evaluation_regions ? "--evaluation-regions=$evaluation_regions" : "" def truth_index = truth_vcf_tbi ? "" : "rtg index $truth_vcf" def query_index = query_vcf_tbi ? "" : "rtg index $query_vcf" + def avail_mem = task.memory.toGiga() + "G" """ $truth_index $query_index - rtg vcfeval \\ + rtg RTG_MEM=$avail_mem vcfeval \\ $args \\ --baseline=$truth_vcf \\ $bed_regions \\ diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 428c3652..bc0aa79a 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -819,6 +819,10 @@ gatk4/selectvariants: - modules/gatk4/selectvariants/** - tests/modules/gatk4/selectvariants/** +gatk4/splitintervals: + - modules/gatk4/splitintervals/** + - tests/modules/gatk4/splitintervals/** + gatk4/splitncigarreads: - modules/gatk4/splitncigarreads/** - tests/modules/gatk4/splitncigarreads/** @@ -839,6 +843,10 @@ genmap/mappability: - modules/genmap/mappability/** - tests/modules/genmap/mappability/** +genomescope2: + - modules/genomescope2/** + - tests/modules/genomescope2/** + genrich: - modules/genrich/** - tests/modules/genrich/** @@ -1647,14 +1655,14 @@ samtools/bam2fq: - modules/samtools/bam2fq/** - tests/modules/samtools/bam2fq/** -samtools/convert: - - modules/samtools/convert/** - - tests/modules/samtools/convert/** - samtools/collatefastq: - modules/samtools/collatefastq/** - tests/modules/samtools/collatefastq/** +samtools/convert: + - modules/samtools/convert/** + - tests/modules/samtools/convert/** + samtools/depth: - modules/samtools/depth/** - tests/modules/samtools/depth/** diff --git a/tests/modules/bowtie2/align/main.nf b/tests/modules/bowtie2/align/main.nf index f91394ff..4f08b533 100644 --- a/tests/modules/bowtie2/align/main.nf +++ b/tests/modules/bowtie2/align/main.nf @@ -14,9 +14,25 @@ workflow test_bowtie2_align_single_end { ] fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) save_unaligned = false + sort = false BOWTIE2_BUILD ( fasta ) - BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned ) + BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort ) +} + +workflow test_bowtie2_align_single_end_sorted { + input = [ + [ id:'test', single_end:true ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + ] + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + save_unaligned = false + sort = true + + BOWTIE2_BUILD ( fasta ) + BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort ) } workflow test_bowtie2_align_paired_end { @@ -29,7 +45,55 @@ workflow test_bowtie2_align_paired_end { ] fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) save_unaligned = false + sort = false BOWTIE2_BUILD ( fasta ) - BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned ) -} \ No newline at end of file + BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort ) +} + +workflow test_bowtie2_align_paired_end_sorted { + input = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + ] + ] + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + save_unaligned = false + sort = true + + BOWTIE2_BUILD ( fasta ) + BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort ) +} + +workflow test_bowtie2_align_single_end_large_index { + input = [ + [ id:'test', single_end:true ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + ] + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + save_unaligned = false + sort = false + + BOWTIE2_BUILD ( fasta ) + BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort ) +} + +workflow test_bowtie2_align_paired_end_large_index { + input = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + ] + ] + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + save_unaligned = false + sort = false + + BOWTIE2_BUILD ( fasta ) + BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort ) +} diff --git a/tests/modules/bowtie2/align/nextflow.config b/tests/modules/bowtie2/align/nextflow.config index b4640de7..08f7bed0 100644 --- a/tests/modules/bowtie2/align/nextflow.config +++ b/tests/modules/bowtie2/align/nextflow.config @@ -5,6 +5,7 @@ params { process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + } if (params.force_large_index) { diff --git a/tests/modules/bowtie2/align/test.yml b/tests/modules/bowtie2/align/test.yml index ef05d70d..9c9ff7a1 100644 --- a/tests/modules/bowtie2/align/test.yml +++ b/tests/modules/bowtie2/align/test.yml @@ -1,21 +1,49 @@ - name: bowtie2 align test_bowtie2_align_single_end command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config tags: - - bowtie2/align - bowtie2 + - bowtie2/align files: - - path: output/bowtie2/test.bam - - path: output/bowtie2/test.bowtie2.log - md5sum: 7b8a9e61b7646da1089b041333c41a87 - - path: output/bowtie2/versions.yml + - path: ./output/bowtie2/test.bam + - path: ./output/bowtie2/test.bowtie2.log + - path: ./output/bowtie2/versions.yml + +- name: bowtie2 align test_bowtie2_align_single_end_sorted + command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end_sorted -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config + tags: + - bowtie2 + - bowtie2/align + files: + - path: ./output/bowtie2/test.bam + - path: ./output/bowtie2/test.bowtie2.log + - path: ./output/bowtie2/versions.yml - name: bowtie2 align test_bowtie2_align_paired_end - command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config + command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config tags: - - bowtie2/align - bowtie2 + - bowtie2/align files: - - path: output/bowtie2/test.bam - - path: output/bowtie2/test.bowtie2.log - md5sum: bd89ce1b28c93bf822bae391ffcedd19 - - path: output/bowtie2/versions.yml + - path: ./output/bowtie2/test.bam + - path: ./output/bowtie2/test.bowtie2.log + - path: ./output/bowtie2/versions.yml + +- name: bowtie2 align test_bowtie2_align_single_end_large_index + command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_single_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index + tags: + - bowtie2 + - bowtie2/align + files: + - path: ./output/bowtie2/test.bam + - path: ./output/bowtie2/test.bowtie2.log + - path: ./output/bowtie2/versions.yml + +- name: bowtie2 align test_bowtie2_align_paired_end_large_index + command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index + tags: + - bowtie2 + - bowtie2/align + files: + - path: ./output/bowtie2/test.bam + - path: ./output/bowtie2/test.bowtie2.log + - path: ./output/bowtie2/versions.yml diff --git a/tests/modules/gatk4/splitintervals/main.nf b/tests/modules/gatk4/splitintervals/main.nf new file mode 100644 index 00000000..f507ece5 --- /dev/null +++ b/tests/modules/gatk4/splitintervals/main.nf @@ -0,0 +1,33 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { GATK4_SPLITINTERVALS } from '../../../../modules/gatk4/splitintervals/main.nf' + +workflow test_gatk4_splitintervals_bed { + + input = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true) + ] + + fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + fasta_dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + + GATK4_SPLITINTERVALS ( input, fasta, fasta_fai, fasta_dict) +} + +workflow test_gatk4_splitintervals_intervals { + + input = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['genome']['genome_interval_list'], checkIfExists: true) + ] + + fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + fasta_dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + + GATK4_SPLITINTERVALS ( input, fasta, fasta_fai, fasta_dict) +} \ No newline at end of file diff --git a/tests/modules/gatk4/splitintervals/nextflow.config b/tests/modules/gatk4/splitintervals/nextflow.config new file mode 100644 index 00000000..10fda96c --- /dev/null +++ b/tests/modules/gatk4/splitintervals/nextflow.config @@ -0,0 +1,9 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + + + withName: GATK4_SPLITINTERVALS { + ext.args = "--scatter-count 2" + } +} \ No newline at end of file diff --git a/tests/modules/gatk4/splitintervals/test.yml b/tests/modules/gatk4/splitintervals/test.yml new file mode 100644 index 00000000..741c6bec --- /dev/null +++ b/tests/modules/gatk4/splitintervals/test.yml @@ -0,0 +1,23 @@ +- name: gatk4 splitintervals test_gatk4_splitintervals_bed + command: nextflow run tests/modules/gatk4/splitintervals -entry test_gatk4_splitintervals_bed -c tests/config/nextflow.config + tags: + - gatk4/splitintervals + - gatk4 + files: + - path: output/gatk4/test/0000-scattered.interval_list + md5sum: c8d6b19e7a92535b6ce9608eae558faa + - path: output/gatk4/test/0001-scattered.interval_list + md5sum: b1877ad96aec308906594c50ebbe3ded + - path: output/gatk4/versions.yml + +- name: gatk4 splitintervals test_gatk4_splitintervals_intervals + command: nextflow run tests/modules/gatk4/splitintervals -entry test_gatk4_splitintervals_intervals -c tests/config/nextflow.config + tags: + - gatk4/splitintervals + - gatk4 + files: + - path: output/gatk4/test/0000-scattered.interval_list + md5sum: ebd6b34a335efc6732ff541936c6d2d5 + - path: output/gatk4/test/0001-scattered.interval_list + md5sum: 9459b0e124fa84ec1e64ac4615bc9af7 + - path: output/gatk4/versions.yml diff --git a/tests/modules/genomescope2/main.nf b/tests/modules/genomescope2/main.nf new file mode 100644 index 00000000..5ceebfd6 --- /dev/null +++ b/tests/modules/genomescope2/main.nf @@ -0,0 +1,19 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { MERYL_COUNT } from '../../../modules/meryl/count/main.nf' +include { MERYL_HISTOGRAM } from '../../../modules/meryl/histogram/main.nf' +include { GENOMESCOPE2 } from '../../../modules/genomescope2/main.nf' + +workflow test_genomescope2 { + + input = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true) + ] + + MERYL_COUNT ( input ) + MERYL_HISTOGRAM ( MERYL_COUNT.out.meryl_db ) + GENOMESCOPE2 ( MERYL_HISTOGRAM.out.hist ) +} diff --git a/tests/modules/genomescope2/nextflow.config b/tests/modules/genomescope2/nextflow.config new file mode 100644 index 00000000..29a0be3a --- /dev/null +++ b/tests/modules/genomescope2/nextflow.config @@ -0,0 +1,13 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + + withName: 'MERYL.*' { + ext.args = 'k=21' + } + + withName: 'GENOMESCOPE2' { + ext.args = '-k 21 -p 1' + } + +} diff --git a/tests/modules/genomescope2/test.yml b/tests/modules/genomescope2/test.yml new file mode 100644 index 00000000..5b03f545 --- /dev/null +++ b/tests/modules/genomescope2/test.yml @@ -0,0 +1,22 @@ +- name: genomescope2 test_genomescope2 + command: nextflow run tests/modules/genomescope2 -entry test_genomescope2 -c tests/config/nextflow.config + tags: + - genomescope2 + files: + - path: output/genomescope2/test_linear_plot.png + md5sum: 94c165c5028156299a1d4d05766cac51 + - path: output/genomescope2/test_log_plot.png + md5sum: 9d25ca463d92a0c73a893da7fd3979ba + - path: output/genomescope2/test_model.txt + md5sum: 3caf62f715f64a2f2b8fdff5d079cb84 + - path: output/genomescope2/test_summary.txt + md5sum: 7452860e2cea99b85f3ff60daeac77f5 + - path: output/genomescope2/test_transformed_linear_plot.png + md5sum: 99a64c1c18d8670f64cb863d4334abbb + - path: output/genomescope2/test_transformed_log_plot.png + md5sum: b4e029c9fb9987ca33b17392a691c1b4 + - path: output/genomescope2/versions.yml + md5sum: 18afeb26f62a47f680b2bb3e27da9cbc + - path: output/meryl/test.hist + md5sum: f75362ab9cd70d96621b3690e952085f + - path: output/meryl/versions.yml