From e5f3dadf64a8b69bfa1816bde6a07e2183a23e7b Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Tue, 21 Mar 2023 10:57:03 +0000 Subject: [PATCH 1/4] Add credits to CHANGELOG --- CHANGELOG.md | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c3b5e034..5fe54284 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,20 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [[2.6](https://github.com/nf-core/viralrecon/releases/tag/2.6)] - 2023-03-17 +## [[2.6.0](https://github.com/nf-core/viralrecon/releases/tag/2.6.0)] - 2023-03-23 + +### Credits + +Special thanks to the following for their code contributions to the release: + +- [Friederike Hanssen](https://github.com/FriederikeHanssen) +- [Hugo Tavares](https://github.com/tavareshugo) +- [Matthew Wells](https://github.com/mattheww95) +- [Maxime Garcia](https://github.com/maxulysse) +- [Phil Ewels](https://github.com/ewels) +- [Sara Monzón](https://github.com/saramonzon) + +Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. ### Enhancements & fixes From 5bfaf6e1445c24695ee8d89b257e3064134ccdff Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Tue, 21 Mar 2023 10:57:12 +0000 Subject: [PATCH 2/4] Use semantic versioning --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 350dcd23..8641580f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -255,7 +255,7 @@ manifest { description = """Assembly and intrahost/low-frequency variant calling for viral samples""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '2.6' + version = '2.6.0' doi = 'https://doi.org/10.5281/zenodo.3901628' } From 0260f9ed0bfd684ca9f3e419696d4b39433e9945 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Tue, 21 Mar 2023 10:59:46 +0000 Subject: [PATCH 3/4] Update all nf-core/modules and subworkflows --- modules.json | 14 ++-- modules/nf-core/bcftools/norm/main.nf | 22 +++++-- modules/nf-core/bcftools/norm/meta.yml | 4 +- modules/nf-core/kraken2/kraken2/main.nf | 2 +- .../picard/collectmultiplemetrics/main.nf | 6 +- modules/nf-core/picard/markduplicates/main.nf | 6 +- .../nf-core/bam_markduplicates_picard/main.nf | 25 ++++--- .../bam_markduplicates_picard/meta.yml | 65 +++++++++---------- .../nf-core/bam_stats_samtools/main.nf | 18 ++--- .../nf-core/bam_stats_samtools/meta.yml | 52 ++++++--------- 10 files changed, 105 insertions(+), 109 deletions(-) diff --git a/modules.json b/modules.json index 7117a7a3..4e7dec6f 100644 --- a/modules.json +++ b/modules.json @@ -42,7 +42,7 @@ }, "bcftools/norm": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "bcad95fb35e567ad25840d3297c3e17eff211a3a", "installed_by": ["modules"] }, "bcftools/query": { @@ -142,7 +142,7 @@ }, "kraken2/kraken2": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "7c695e0147df1157413e06246d9b0094617d3e6b", "installed_by": ["modules"] }, "minia": { @@ -177,13 +177,13 @@ }, "picard/collectmultiplemetrics": { "branch": "master", - "git_sha": "2f88b26e9804b99e98f7cd08e74c3f88288a3358", + "git_sha": "75027bf77472b1f4fd2cdd7e46f83119dfb0f2c6", "installed_by": ["modules"] }, "picard/markduplicates": { "branch": "master", - "git_sha": "2f88b26e9804b99e98f7cd08e74c3f88288a3358", - "installed_by": ["bam_markduplicates_picard", "modules"] + "git_sha": "75027bf77472b1f4fd2cdd7e46f83119dfb0f2c6", + "installed_by": ["modules", "bam_markduplicates_picard"] }, "plasmidid": { "branch": "master", @@ -266,7 +266,7 @@ "nf-core": { "bam_markduplicates_picard": { "branch": "master", - "git_sha": "6daac2bc63f4847e0c7cc661f4f5b043ac13faaf", + "git_sha": "6f1697c121719dedde9e0537b6ed6a9cb8c13583", "installed_by": ["subworkflows"] }, "bam_sort_stats_samtools": { @@ -276,7 +276,7 @@ }, "bam_stats_samtools": { "branch": "master", - "git_sha": "92eb5091ae5368a60cda58b3a0ced8b36d715b0f", + "git_sha": "b4b7f89e7fd6d2293f0c176213f710e0bcdaf19e", "installed_by": ["bam_sort_stats_samtools", "bam_markduplicates_picard"] }, "fastq_align_bowtie2": { diff --git a/modules/nf-core/bcftools/norm/main.nf b/modules/nf-core/bcftools/norm/main.nf index ef95bee4..90387d6c 100644 --- a/modules/nf-core/bcftools/norm/main.nf +++ b/modules/nf-core/bcftools/norm/main.nf @@ -12,19 +12,25 @@ process BCFTOOLS_NORM { path(fasta) output: - tuple val(meta), path("*.gz") , emit: vcf - path "versions.yml" , emit: versions + tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}") , emit: vcf + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' + def args = task.ext.args ?: '--output-type z' def prefix = task.ext.prefix ?: "${meta.id}" + def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : + args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : + args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : + args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : + "vcf.gz" + """ bcftools norm \\ --fasta-ref ${fasta} \\ - --output ${prefix}.vcf.gz \\ + --output ${prefix}.${extension}\\ $args \\ --threads $task.cpus \\ ${vcf} @@ -36,9 +42,15 @@ process BCFTOOLS_NORM { """ stub: + def args = task.ext.args ?: '--output-type z' def prefix = task.ext.prefix ?: "${meta.id}" + def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : + args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : + args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : + args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : + "vcf.gz" """ - touch ${prefix}.vcf.gz + touch ${prefix}.${extension} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bcftools/norm/meta.yml b/modules/nf-core/bcftools/norm/meta.yml index 2b3c8eae..c3ea2c03 100644 --- a/modules/nf-core/bcftools/norm/meta.yml +++ b/modules/nf-core/bcftools/norm/meta.yml @@ -42,8 +42,8 @@ output: e.g. [ id:'test', single_end:false ] - vcf: type: file - description: VCF normalized output file - pattern: "*.vcf.gz" + description: One of uncompressed VCF (.vcf), compressed VCF (.vcf.gz), compressed BCF (.bcf.gz) or uncompressed BCF (.bcf) normalized output file + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - versions: type: file description: File containing software versions diff --git a/modules/nf-core/kraken2/kraken2/main.nf b/modules/nf-core/kraken2/kraken2/main.nf index 1b9e760d..5901064e 100644 --- a/modules/nf-core/kraken2/kraken2/main.nf +++ b/modules/nf-core/kraken2/kraken2/main.nf @@ -31,7 +31,7 @@ process KRAKEN2_KRAKEN2 { def unclassified = meta.single_end ? "${prefix}.unclassified.fastq" : "${prefix}.unclassified#.fastq" def classified_option = save_output_fastqs ? "--classified-out ${classified}" : "" def unclassified_option = save_output_fastqs ? "--unclassified-out ${unclassified}" : "" - def readclassification_option = save_reads_assignment ? "--output ${prefix}.kraken2.classifiedreads.txt" : "" + def readclassification_option = save_reads_assignment ? "--output ${prefix}.kraken2.classifiedreads.txt" : "--output /dev/null" def compress_reads_command = save_output_fastqs ? "pigz -p $task.cpus *.fastq" : "" """ diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf index 8861458e..ed88dbe7 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/main.nf +++ b/modules/nf-core/picard/collectmultiplemetrics/main.nf @@ -24,15 +24,15 @@ process PICARD_COLLECTMULTIPLEMETRICS { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" - def avail_mem = 3 + def avail_mem = 3072 if (!task.memory) { log.info '[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { - avail_mem = task.memory.giga + avail_mem = (task.memory.mega*0.8).intValue() } """ picard \\ - -Xmx${avail_mem}g \\ + -Xmx${avail_mem}M \\ CollectMultipleMetrics \\ $args \\ --INPUT $bam \\ diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index be243a95..1fe6ee2d 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -24,15 +24,15 @@ process PICARD_MARKDUPLICATES { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def avail_mem = 3 + def avail_mem = 3072 if (!task.memory) { log.info '[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { - avail_mem = task.memory.giga + avail_mem = (task.memory.mega*0.8).intValue() } """ picard \\ - -Xmx${avail_mem}g \\ + -Xmx${avail_mem}M \\ MarkDuplicates \\ $args \\ --INPUT $bam \\ diff --git a/subworkflows/nf-core/bam_markduplicates_picard/main.nf b/subworkflows/nf-core/bam_markduplicates_picard/main.nf index 9cb24cdc..6e3df332 100644 --- a/subworkflows/nf-core/bam_markduplicates_picard/main.nf +++ b/subworkflows/nf-core/bam_markduplicates_picard/main.nf @@ -9,9 +9,9 @@ include { BAM_STATS_SAMTOOLS } from '../bam_stats_samtools/main' workflow BAM_MARKDUPLICATES_PICARD { take: - ch_bam // channel: [ val(meta), [ bam ] ] - ch_fasta // channel: [ fasta ] - ch_fai // channel: [ fai ] + ch_bam // channel: [ val(meta), path(bam) ] + ch_fasta // channel: [ path(fasta) ] + ch_fai // channel: [ path(fai) ] main: @@ -23,7 +23,7 @@ workflow BAM_MARKDUPLICATES_PICARD { SAMTOOLS_INDEX ( PICARD_MARKDUPLICATES.out.bam ) ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) - PICARD_MARKDUPLICATES.out.bam + ch_bam_bai = PICARD_MARKDUPLICATES.out.bam .join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true) .join(SAMTOOLS_INDEX.out.csi, by: [0], remainder: true) .map { @@ -34,20 +34,19 @@ workflow BAM_MARKDUPLICATES_PICARD { [ meta, bam, csi ] } } - .set { ch_bam_bai } BAM_STATS_SAMTOOLS ( ch_bam_bai, ch_fasta ) ch_versions = ch_versions.mix(BAM_STATS_SAMTOOLS.out.versions) emit: - bam = PICARD_MARKDUPLICATES.out.bam // channel: [ val(meta), [ bam ] ] - metrics = PICARD_MARKDUPLICATES.out.metrics // channel: [ val(meta), [ bam ] ] - bai = SAMTOOLS_INDEX.out.bai // channel: [ val(meta), [ bai ] ] - csi = SAMTOOLS_INDEX.out.csi // channel: [ val(meta), [ csi ] ] - - stats = BAM_STATS_SAMTOOLS.out.stats // channel: [ val(meta), [ stats ] ] - flagstat = BAM_STATS_SAMTOOLS.out.flagstat // channel: [ val(meta), [ flagstat ] ] - idxstats = BAM_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), [ idxstats ] ] + bam = PICARD_MARKDUPLICATES.out.bam // channel: [ val(meta), path(bam) ] + metrics = PICARD_MARKDUPLICATES.out.metrics // channel: [ val(meta), path(bam) ] + bai = SAMTOOLS_INDEX.out.bai // channel: [ val(meta), path(bai) ] + csi = SAMTOOLS_INDEX.out.csi // channel: [ val(meta), path(csi) ] + + stats = BAM_STATS_SAMTOOLS.out.stats // channel: [ val(meta), path(stats) ] + flagstat = BAM_STATS_SAMTOOLS.out.flagstat // channel: [ val(meta), path(flagstat) ] + idxstats = BAM_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), path(idxstats) ] versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/nf-core/bam_markduplicates_picard/meta.yml b/subworkflows/nf-core/bam_markduplicates_picard/meta.yml index fdd9f8d1..822c6132 100644 --- a/subworkflows/nf-core/bam_markduplicates_picard/meta.yml +++ b/subworkflows/nf-core/bam_markduplicates_picard/meta.yml @@ -14,48 +14,47 @@ modules: - samtools/flagstat input: - - meta: - type: map + - ch_bam: description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - fasta: - type: file - description: Reference genome fasta file - pattern: "*.{fasta,fa}" - + BAM/CRAM/SAM file + Structure: [ val(meta), path(bam) ] + - ch_fasta: + description: | + Reference genome fasta file + Structure: [ path(fasta) ] + - ch_fasta: + description: | + Index of the reference genome fasta file + Structure: [ path(fai) ] output: - - meta: - type: map + - bam: description: | - Groovy Map containing sample information - e.g. [ id:'test' ] + processed BAM/CRAM/SAM file + Structure: [ val(meta), path(bam) ] - bai: - type: file - description: BAM/CRAM/SAM samtools index - pattern: "*.{bai,crai,sai}" + description: | + BAM/CRAM/SAM samtools index + Structure: [ val(meta), path(bai) ] - csi: - type: file - description: CSI samtools index - pattern: "*.csi" + description: | + CSI samtools index + Structure: [ val(meta), path(csi) ] - stats: - type: file - description: File containing samtools stats output + description: | + File containing samtools stats output + Structure: [ val(meta), path(stats) ] - flagstat: - type: file - description: File containing samtools flagstat output + description: | + File containing samtools flagstat output + Structure: [ val(meta), path(flagstat) ] - idxstats: - type: file - description: File containing samtools idxstats output - pattern: "*.{idxstats}" + description: | + File containing samtools idxstats output + Structure: [ val(meta), path(idxstats) ] - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + description: | + Files containing software versions + Structure: [ path(versions.yml) ] authors: - "@dmarron" - "@drpatelh" diff --git a/subworkflows/nf-core/bam_stats_samtools/main.nf b/subworkflows/nf-core/bam_stats_samtools/main.nf index cfcc48dd..c9d7c8b7 100644 --- a/subworkflows/nf-core/bam_stats_samtools/main.nf +++ b/subworkflows/nf-core/bam_stats_samtools/main.nf @@ -8,25 +8,25 @@ include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/m workflow BAM_STATS_SAMTOOLS { take: - bam_bai // channel: [ val(meta), [ bam/cram ], [bai/csi] ] - fasta // channel: [ fasta ] + ch_bam_bai // channel: [ val(meta), path(bam), path(bai) ] + ch_fasta // channel: [ path(fasta) ] main: ch_versions = Channel.empty() - SAMTOOLS_STATS ( bam_bai, fasta ) + SAMTOOLS_STATS ( ch_bam_bai, ch_fasta ) ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions) - SAMTOOLS_FLAGSTAT ( bam_bai ) + SAMTOOLS_FLAGSTAT ( ch_bam_bai ) ch_versions = ch_versions.mix(SAMTOOLS_FLAGSTAT.out.versions) - SAMTOOLS_IDXSTATS ( bam_bai ) + SAMTOOLS_IDXSTATS ( ch_bam_bai ) ch_versions = ch_versions.mix(SAMTOOLS_IDXSTATS.out.versions) emit: - stats = SAMTOOLS_STATS.out.stats // channel: [ val(meta), [ stats ] ] - flagstat = SAMTOOLS_FLAGSTAT.out.flagstat // channel: [ val(meta), [ flagstat ] ] - idxstats = SAMTOOLS_IDXSTATS.out.idxstats // channel: [ val(meta), [ idxstats ] ] + stats = SAMTOOLS_STATS.out.stats // channel: [ val(meta), path(stats) ] + flagstat = SAMTOOLS_FLAGSTAT.out.flagstat // channel: [ val(meta), path(flagstat) ] + idxstats = SAMTOOLS_IDXSTATS.out.idxstats // channel: [ val(meta), path(idxstats) ] - versions = ch_versions // channel: [ versions.yml ] + versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/nf-core/bam_stats_samtools/meta.yml b/subworkflows/nf-core/bam_stats_samtools/meta.yml index 5252b0e4..b6072686 100644 --- a/subworkflows/nf-core/bam_stats_samtools/meta.yml +++ b/subworkflows/nf-core/bam_stats_samtools/meta.yml @@ -11,44 +11,30 @@ modules: - samtools/idxstats - samtools/flagstat input: - - meta: - type: map + - ch_bam_bai: description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: Index for BAM/CRAM/SAM file - pattern: "*.{bai,crai,sai}" - - fasta: - type: file - description: Reference genome fasta file - pattern: "*.{fasta,fa}" -output: - - meta: - type: map + The input channel containing the BAM/CRAM and it's index + Structure: [ val(meta), path(bam), path(bai) ] + - ch_fasta: description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + Reference genome fasta file + Structure: [ path(fasta) ] +output: - stats: - type: file - description: File containing samtools stats output - pattern: "*.{stats}" + description: | + File containing samtools stats output + Structure: [ val(meta), path(stats) ] - flagstat: - type: file - description: File containing samtools flagstat output - pattern: "*.{flagstat}" + description: | + File containing samtools flagstat output + Structure: [ val(meta), path(flagstat) ] - idxstats: - type: file - description: File containing samtools idxstats output - pattern: "*.{idxstats}" + description: | + File containing samtools idxstats output + Structure: [ val(meta), path(idxstats)] - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + description: | + Files containing software versions + Structure: [ path(versions.yml) ] authors: - "@drpatelh" From 1faf8b13ff49927df4d2e87871f6aee3175a2413 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Tue, 21 Mar 2023 11:16:12 +0000 Subject: [PATCH 4/4] Fix paths in subworkflows --- .../bam_trim_primers_ivar.nf | 2 +- .../fastq_trim_fastp_fastqc.nf | 0 .../{nf-core => local}/filter_bam_samtools.nf | 2 +- subworkflows/local/snpeff_snpsift.nf | 2 +- subworkflows/local/variants_bcftools.nf | 2 +- subworkflows/local/variants_ivar.nf | 2 +- .../vcf_bgzip_tabix_stats.nf | 0 .../{nf-core => local}/vcf_tabix_stats.nf | 0 workflows/illumina.nf | 24 +++++++++---------- workflows/nanopore.nf | 6 +---- 10 files changed, 18 insertions(+), 22 deletions(-) rename subworkflows/{nf-core => local}/bam_trim_primers_ivar.nf (94%) rename subworkflows/{nf-core => local}/fastq_trim_fastp_fastqc.nf (100%) rename subworkflows/{nf-core => local}/filter_bam_samtools.nf (95%) rename subworkflows/{nf-core => local}/vcf_bgzip_tabix_stats.nf (100%) rename subworkflows/{nf-core => local}/vcf_tabix_stats.nf (100%) diff --git a/subworkflows/nf-core/bam_trim_primers_ivar.nf b/subworkflows/local/bam_trim_primers_ivar.nf similarity index 94% rename from subworkflows/nf-core/bam_trim_primers_ivar.nf rename to subworkflows/local/bam_trim_primers_ivar.nf index f67ff306..7a82ce30 100644 --- a/subworkflows/nf-core/bam_trim_primers_ivar.nf +++ b/subworkflows/local/bam_trim_primers_ivar.nf @@ -3,7 +3,7 @@ // include { IVAR_TRIM } from '../../modules/nf-core/ivar/trim/main' -include { BAM_SORT_STATS_SAMTOOLS } from './bam_sort_stats_samtools/main' +include { BAM_SORT_STATS_SAMTOOLS } from '../nf-core/bam_sort_stats_samtools/main' workflow BAM_TRIM_PRIMERS_IVAR { take: diff --git a/subworkflows/nf-core/fastq_trim_fastp_fastqc.nf b/subworkflows/local/fastq_trim_fastp_fastqc.nf similarity index 100% rename from subworkflows/nf-core/fastq_trim_fastp_fastqc.nf rename to subworkflows/local/fastq_trim_fastp_fastqc.nf diff --git a/subworkflows/nf-core/filter_bam_samtools.nf b/subworkflows/local/filter_bam_samtools.nf similarity index 95% rename from subworkflows/nf-core/filter_bam_samtools.nf rename to subworkflows/local/filter_bam_samtools.nf index 838f5ccc..2d47a29a 100644 --- a/subworkflows/nf-core/filter_bam_samtools.nf +++ b/subworkflows/local/filter_bam_samtools.nf @@ -4,7 +4,7 @@ include { SAMTOOLS_VIEW } from '../../modules/nf-core/samtools/view/main' include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main' -include { BAM_STATS_SAMTOOLS } from './bam_stats_samtools' +include { BAM_STATS_SAMTOOLS } from '../nf-core/bam_stats_samtools/main' workflow FILTER_BAM_SAMTOOLS { take: diff --git a/subworkflows/local/snpeff_snpsift.nf b/subworkflows/local/snpeff_snpsift.nf index a487fc0f..92a6a669 100644 --- a/subworkflows/local/snpeff_snpsift.nf +++ b/subworkflows/local/snpeff_snpsift.nf @@ -5,7 +5,7 @@ include { SNPEFF_ANN } from '../../modules/local/snpeff_ann' include { SNPSIFT_EXTRACTFIELDS } from '../../modules/local/snpsift_extractfields' -include { VCF_BGZIP_TABIX_STATS } from '../nf-core/vcf_bgzip_tabix_stats' +include { VCF_BGZIP_TABIX_STATS } from './vcf_bgzip_tabix_stats' workflow SNPEFF_SNPSIFT { take: diff --git a/subworkflows/local/variants_bcftools.nf b/subworkflows/local/variants_bcftools.nf index 37c53c50..103ba725 100644 --- a/subworkflows/local/variants_bcftools.nf +++ b/subworkflows/local/variants_bcftools.nf @@ -4,7 +4,7 @@ include { BCFTOOLS_MPILEUP } from '../../modules/nf-core/bcftools/mpileup/main' include { BCFTOOLS_NORM } from '../../modules/nf-core/bcftools/norm/main' -include { VCF_TABIX_STATS } from '../nf-core/vcf_tabix_stats' +include { VCF_TABIX_STATS } from './vcf_tabix_stats' include { VARIANTS_QC } from './variants_qc' workflow VARIANTS_BCFTOOLS { diff --git a/subworkflows/local/variants_ivar.nf b/subworkflows/local/variants_ivar.nf index eaae92d8..26e460aa 100644 --- a/subworkflows/local/variants_ivar.nf +++ b/subworkflows/local/variants_ivar.nf @@ -5,7 +5,7 @@ include { IVAR_VARIANTS } from '../../modules/nf-core/ivar/variants/main' include { IVAR_VARIANTS_TO_VCF } from '../../modules/local/ivar_variants_to_vcf' include { BCFTOOLS_SORT } from '../../modules/nf-core/bcftools/sort/main' -include { VCF_TABIX_STATS } from '../nf-core/vcf_tabix_stats' +include { VCF_TABIX_STATS } from './vcf_tabix_stats' include { VARIANTS_QC } from './variants_qc' workflow VARIANTS_IVAR { diff --git a/subworkflows/nf-core/vcf_bgzip_tabix_stats.nf b/subworkflows/local/vcf_bgzip_tabix_stats.nf similarity index 100% rename from subworkflows/nf-core/vcf_bgzip_tabix_stats.nf rename to subworkflows/local/vcf_bgzip_tabix_stats.nf diff --git a/subworkflows/nf-core/vcf_tabix_stats.nf b/subworkflows/local/vcf_tabix_stats.nf similarity index 100% rename from subworkflows/nf-core/vcf_tabix_stats.nf rename to subworkflows/local/vcf_tabix_stats.nf diff --git a/workflows/illumina.nf b/workflows/illumina.nf index 0233a176..6ff119a9 100644 --- a/workflows/illumina.nf +++ b/workflows/illumina.nf @@ -63,16 +63,18 @@ include { PLOT_MOSDEPTH_REGIONS as PLOT_MOSDEPTH_REGIONS_AMPLICON } from '../mod // // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules // -include { INPUT_CHECK } from '../subworkflows/local/input_check' -include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome_illumina' -include { VARIANTS_IVAR } from '../subworkflows/local/variants_ivar' -include { VARIANTS_BCFTOOLS } from '../subworkflows/local/variants_bcftools' -include { CONSENSUS_IVAR } from '../subworkflows/local/consensus_ivar' -include { CONSENSUS_BCFTOOLS } from '../subworkflows/local/consensus_bcftools' -include { VARIANTS_LONG_TABLE } from '../subworkflows/local/variants_long_table' -include { ASSEMBLY_SPADES } from '../subworkflows/local/assembly_spades' -include { ASSEMBLY_UNICYCLER } from '../subworkflows/local/assembly_unicycler' -include { ASSEMBLY_MINIA } from '../subworkflows/local/assembly_minia' +include { INPUT_CHECK } from '../subworkflows/local/input_check' +include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome_illumina' +include { VARIANTS_IVAR } from '../subworkflows/local/variants_ivar' +include { VARIANTS_BCFTOOLS } from '../subworkflows/local/variants_bcftools' +include { CONSENSUS_IVAR } from '../subworkflows/local/consensus_ivar' +include { CONSENSUS_BCFTOOLS } from '../subworkflows/local/consensus_bcftools' +include { VARIANTS_LONG_TABLE } from '../subworkflows/local/variants_long_table' +include { ASSEMBLY_SPADES } from '../subworkflows/local/assembly_spades' +include { ASSEMBLY_UNICYCLER } from '../subworkflows/local/assembly_unicycler' +include { ASSEMBLY_MINIA } from '../subworkflows/local/assembly_minia' +include { BAM_TRIM_PRIMERS_IVAR } from '../subworkflows/local/bam_trim_primers_ivar' +include { FASTQ_TRIM_FASTP_FASTQC } from '../subworkflows/local/fastq_trim_fastp_fastqc' /* ======================================================================================== @@ -94,9 +96,7 @@ include { MOSDEPTH as MOSDEPTH_AMPLICON } from '../modules/nf-core/mosdepth/main // // SUBWORKFLOW: Consisting entirely of nf-core/modules // -include { FASTQ_TRIM_FASTP_FASTQC } from '../subworkflows/nf-core/fastq_trim_fastp_fastqc' include { FASTQ_ALIGN_BOWTIE2 } from '../subworkflows/nf-core/fastq_align_bowtie2/main' -include { BAM_TRIM_PRIMERS_IVAR } from '../subworkflows/nf-core/bam_trim_primers_ivar' include { BAM_MARKDUPLICATES_PICARD } from '../subworkflows/nf-core/bam_markduplicates_picard' /* diff --git a/workflows/nanopore.nf b/workflows/nanopore.nf index f2f11371..854335fd 100644 --- a/workflows/nanopore.nf +++ b/workflows/nanopore.nf @@ -62,6 +62,7 @@ include { INPUT_CHECK } from '../subworkflows/local/input_check' include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome_nanopore' include { SNPEFF_SNPSIFT } from '../subworkflows/local/snpeff_snpsift' include { VARIANTS_LONG_TABLE } from '../subworkflows/local/variants_long_table' +include { FILTER_BAM_SAMTOOLS } from '../subworkflows/local/filter_bam_samtools' /* ======================================================================================== @@ -86,11 +87,6 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpso include { MOSDEPTH as MOSDEPTH_GENOME } from '../modules/nf-core/mosdepth/main' include { MOSDEPTH as MOSDEPTH_AMPLICON } from '../modules/nf-core/mosdepth/main' -// -// SUBWORKFLOW: Consisting entirely of nf-core/modules -// -include { FILTER_BAM_SAMTOOLS } from '../subworkflows/nf-core/filter_bam_samtools' - /* ======================================================================================== RUN MAIN WORKFLOW